Abstract
Proteins from the ferredoxin (Fd) and flavodoxin (Fld) families function as low potential electrical transfer hubs in cells, at times mediating electron transfer between overlapping sets of oxidoreductases. To better understand protein electron carrier (PEC) use across the domains of life, we evaluated the distribution of genes encoding [4Fe-4S] Fd, [2Fe-2S] Fd, and Fld electron carriers in over 7,000 organisms. Our analysis targeted genes encoding small PEC genes encoding proteins having ≤200 residues. We find that the average number of small PEC genes per Archaea (~13), Bacteria (~8), and Eukarya (~3) genome varies, with some organisms containing as many as 54 total PEC genes. Organisms fall into three groups, including those lacking genes encoding low potential PECs (3%), specialists with a single PEC gene type (20%), and generalists that utilize multiple PEC types (77%). Mapping PEC gene usage onto an evolutionary tree highlights the prevalence of [4Fe-4S] Fds in ancient organisms that are deeply rooted, the expansion of [2Fe-2S] Fds with the advent of photosynthesis and a concomitant decrease in [4Fe-4S] Fds, and the expansion of Flds in organisms that inhabit low-iron host environments. Surprisingly, [4Fe-4S] Fds present a similar abundance in aerobes as [2Fe-2S] Fds. This bioinformatic study highlights understudied PECs whose structure, stability, and partner specificity should be further characterized.
Highlights
Redox-active cofactors are essential components of metabolism, functioning as molecules that transfer electrons at various reduction potentials, according to metabolic need
To gain a better understanding of how evolution has selected extant protein electron carrier (PEC), we report on the genome mining of 7,079 organisms for sequence motifs that are characteristic of three different lowpotential PEC families, including the [4Fe-4S] Fds, [2Fe-2S] Fds, and Flds
By using a size cutoff that exceeds the length of PECs with single domain structures in the PDB, we sought to evaluate how the size of these three PEC families varies beyond the family members that have already been studied
Summary
Redox-active cofactors are essential components of metabolism, functioning as molecules that transfer electrons at various reduction potentials, according to metabolic need. These pools of small molecules (e.g., NADH, NADPH, FADH, FMN, riboflavin, and quinones) can couple their reducing power to a wide range of oxidoreductases in parallel. The quinone that functions in aerobic respiration within Escherichia coli interacts with two dozen oxidoreductases, while NADH/NADPH are used by over one hundred oxidoreductases in this microbe (Orth et al, 2011) What these small molecules lack, is the ability to evolve structures that discriminate partner binding and tune their midpoint potentials. This tunability is thought to enable the evolution of protein-controlled, energy-conserving electron transfer (ET) pathways
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