Diversification of Ferredoxins across Living Organisms

Abstract

Ferredoxins, iron-sulfur (Fe-S) cluster proteins, play a key role in oxidoreduction reactions. To date, evolutionary analysis of these proteins across the domains of life have been confined to observing the abundance of Fe-S cluster types (2Fe-2S, 3Fe-4S, 4Fe-4S, 7Fe-8S (3Fe-4s and 4Fe-4S) and 2[4Fe-4S]) and the diversity of ferredoxins within these cluster types was not studied. To address this research gap, here we propose a subtype classification and nomenclature for ferredoxins based on the characteristic spacing between the cysteine amino acids of the Fe-S binding motif as a subtype signature to assess the diversity of ferredoxins across the living organisms. To test this hypothesis, comparative analysis of ferredoxins between bacterial groups, Alphaproteobacteria and Firmicutes and ferredoxins collected from species of different domains of life that are reported in the literature has been carried out. Ferredoxins were found to be highly diverse within their types. Large numbers of alphaproteobacterial species ferredoxin subtypes were found in Firmicutes species and the same ferredoxin subtypes across the species of Bacteria, Archaea, and Eukarya, suggesting shared common ancestral origin of ferredoxins between Archaea and Bacteria and lateral gene transfer of ferredoxins from prokaryotes (Archaea/Bacteria) to eukaryotes. This study opened new vistas for further analysis of diversity of ferredoxins in living organisms.

Keywords: Archaea; Bacteria; Eukarya; domains of life; evolution; ferredoxins; iron-sulfur proteins; lateral gene transfer.

Figure 1

Ferredoxin nomenclature based on the spacing between the cysteine amino acids of the Fe-S cluster binding motif. Ferredoxins start with their Fe-S cluster type, followed by their ST indicating subtype and then the numeral indicating its subtype number in that type. Proteins grouped into different subtypes have the same characteristic spacing between the cysteine amino acids of the Fe-S cluster binding motif.

Figure 2

Comparative analysis of ferredoxins iron-sulfur (Fe-S) cluster features between alphaproteobacterial species and Firmicutes species. The number next to the bar indicates the count for that category. Detailed information on species and their ferredoxins is presented in Table S1.

Figure 3

Phylogenetic analysis of ferredoxins. Ferredoxins belonging to different Fe-S cluster types were highlighted in different colors and indicated in the figure. Archaea and Eukaryota ferredoxin sequences were marked with pink and brown stripe, respectively. All other sequences originate from Bacteria. Ferredoxin protein sequences used to construct the phylogenetic tree are presented in Tables S2 and S3.

Figure 4

Heat map figure representing the presence (red) and absence (green) of ferredoxin subtypes in Archaea, Bacteria and Eukarya. Ferredoxin subtypes form the vertical axis and domains of life forms the horizontal axis.