Evolution and diversity of glutaredoxins in photosynthetic organisms

Abstract

The genome sequencing of prokaryotic and eukaryotic photosynthetic organisms enables a comparative genomic study of the glutaredoxin (Grx) family. The analysis of 58 genomes, using a specific motif composed of the active site sequence and of amino acids involved in glutathione binding, led to an updated classification of Grxs into six classes. Only two classes (I and II) are common to all photosynthetic organisms. Eukaryotes and cyanobacteria have two specific Grx classes (classes III and IV and classes V and VI, respectively). The classes IV, V and VI have not yet been identified and contain multimodular Grx fusions. In addition, putative Grx partners were identified from the presence of fusion proteins, the conservation of gene order in bacterial operons, and the gene co-occurrence. The genes encoding class II Grxs and BolA/YrbA proteins are frequently adjacent, in the same transcriptional orientation in prokaryote genomes and present in the same organisms.

Fig. 1

Unrooted, neighbor-joining (NJ)-based tree of the Grx family in photosynthetic organisms. The analysis was performed using MEGA 4 with the setup described in “Material and methods”. Branch lengths are proportional to phylogenetic distances. For clarity, the protein names have been removed but they are available in Figs. 3, 4, 5, 6 and 7. The full names and the corresponding accession numbers of all Grx sequences are available in ESM file 1. Around 99% of the members are clustering into one of the six Grx classes defined

Fig. 2

Unrooted, NJ-based tree of class I glutaredoxins in photosynthetic organisms. The analysis was performed using MEGA 4. Branch lengths are proportional to phylogenetic distances. The name of the species is abbreviated with a two-letter code, except for close cyanobacterial species where the associated number has been indicated. The sequences from cyanobacteria and eukaryotes are forming two independent groups, except a few algal members, i.e., EhGrx2.1 and 2.2, MpGrx2.1 and 2.2, MsGrx2.1, 2.2 and 2.3, TpGrx2 and PhtGrx2.2, from the haptophyta E. huxleyi, from the green alga Micromonas and from the two diatoms, which are clustering on two separate branches. Cyanobacterial Grxs are branching into six major subgroups. Grxs from terrestrial plants are clustering in the previous Grx subgroups described for higher plants, i.e., Grx C1 to C4 and C5/S12, while algal sequences are forming separate clads with an unclear organisation which does not match their phylogenetic grouping

Fig. 3

Unrooted, NJ-based tree of class II glutaredoxins in photosynthetic organisms. The analysis was performed using MEGA 4. Branch lengths are proportional to phylogenetic distances. The name of the species is abbreviated with a two-letter code, except for the three Osterococcus species (Ost9901, OstRCC809 and Ostta). The cyanobacterial sequences form an independent group with two branches, whereas most eukaryote CGFS Grxs are clustering in the previous Grx subgroups described for higher plants, Grx S14 to S17. As for class I Grxs, a few algal members are isolated

Fig. 4

Schematic representation of the putative reconstituted evolution of GrxS17 orthologs in living organisms. Trx and Grx domains are represented by rectangles with the active site indicated on top. The putative major steps for the formation of higher plants GrxS17 isoforms from cyanobacterial members may consist in three consecutive events (shaded boxes): (1) Trx-Grx gene fusion; (2) addition of a Grx domain in a common ancestor of heterokonta and green algae; and (3) addition of a second Grx domain in lycophytes. As the whole fusion has not been duplicated entirely, we hypothesize that the addition of a Grx domain in the C-terminal part of the protein is arising from a partial duplication. We have also indicated the possible evolution of the active site in the thioredoxin domain by indicating the point mutations required (open boxes)

Fig. 5

Unrooted, NJ-based tree of class III glutaredoxins from land plants. The analysis was performed using MEGA 4. Branch lengths are proportional to phylogenetic distances. The name of the protein is composed of the two-letter code for the species followed by the number of the isoform, for example, 1–24 for Populus. The exception is for A. thaliana sequences which follow the nomenclature defined in [2], with a C or an S indicating the dithiol or monothiol nature of the active site. The proteins are distributed into four subgroups (see the text for their description). The sequences from cyanobacteria form an independent group with two branches, whereas most eukaryote CGFS Grxs are clustering in the previous Grx subgroups described for higher plants, Grx S14 to S17. As for class I Grxs, a few algal members are isolated

Fig. 6

Unrooted, NJ-based tree of class IV glutaredoxins in photosynthetic eukaryotes. The analysis was performed using MEGA 4. Branch lengths are proportional to phylogenetic distances. Proteins of this class are clustering into four subgroups, two for algal members and two for terrestrial plant members. The domain architecture of these Grxs is represented in the lower part of the figure

Fig. 7

Unrooted, NJ-based tree of class V glutaredoxins in cyanobacteria. The analysis was performed using MEGA4. Branch lengths are proportional to phylogenetic distances. Proteins of this class are clustering into two separate branches depending on the organisation of the C-terminal transmembrane part

Fig. 8

Unrooted, NJ-based tree of class VI glutaredoxins in cyanobacteria. The analysis was performed using MEGA4. Branch lengths are proportional to phylogenetic distances. The domain architecture of these Grxs is represented in the lower part of the figure. This protein is only present in most cyanobacteria of the order Synechococales but not all, and in a closely related Chroococcale, cyanobium sp. PCC7001

Fig. 9

Gene clustering and co-occurrence between CGFS Grxs and BolA. Analysis of gene co-occurence between CGFS Grx (COG0278) and BolA (COG0271) genes was performed using the “STRING” database (http://string.embl.de/) [15]. From 630 organisms analyzed, only two (Magnetococcus sp. and Giardia lamblia) possess only one of the two genes. Moreover, when CGFS Grx and BolA genes are clustering in all or only some prokaryote organisms of a given phylum, an asterisk has been added. The two genes are clustering in the large cyanobacteria and alpha-proteobacteria genus, whereas, except in a few cases, they do not cluster in beta- and gamma-proteobacteria. The analysis of the clustering of Grx genes was performed using “protein clusters” tool available at the NCBI webpage and the Microbial Genome Database (MGDB, http://mbgd.genome.ad.jp/)