Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes

Abstract

Background: Chlamydiae are obligate intracellular bacteria of protists, invertebrates and vertebrates, but have not been found to date in photosynthetic eukaryotes (algae and embryophytes). Genes of putative chlamydial origin, however, are present in significant numbers in sequenced genomes of photosynthetic eukaryotes. It has been suggested that such genes were acquired by an ancient horizontal gene transfer from Chlamydiae to the ancestor of photosynthetic eukaryotes. To further test this hypothesis, an extensive search for proteins of chlamydial origin was performed using several recently sequenced algal genomes and EST databases, and the proteins subjected to phylogenetic analyses.

Results: A total of 39 proteins of chlamydial origin were retrieved from the photosynthetic eukaryotes analyzed and their identity verified through phylogenetic analyses. The distribution of the chlamydial proteins among four groups of photosynthetic eukaryotes (Viridiplantae, Rhodoplantae, Glaucoplantae, Bacillariophyta) was complex suggesting multiple acquisitions and losses. Evidence is presented that all except one of the chlamydial genes originated from an ancient endosymbiosis of a chlamydial bacterium into the ancestor of the Plantae before their divergence into Viridiplantae, Rhodoplantae and Glaucoplantae, i.e. more than 1.1 BYA. The chlamydial proteins subsequently spread through secondary plastid endosymbioses to other eukaryotes. Of 20 chlamydial proteins recovered from the genomes of two Bacillariophyta, 10 were of rhodoplant, and 10 of viridiplant origin suggesting that they were acquired by two different secondary endosymbioses. Phylogenetic analyses of concatenated sequences demonstrated that the viridiplant secondary endosymbiosis likely occurred before the divergence of Chlorophyta and Streptophyta.

Conclusion: We identified 39 proteins of chlamydial origin in photosynthetic eukaryotes signaling an ancient invasion of the ancestor of the Plantae by a chlamydial bacterium accompanied by horizontal gene transfer. Subsequently, chlamydial proteins spread through secondary endosymbioses to other eukaryotes. We conclude that intracellular chlamydiae likely persisted throughout the early history of the Plantae donating genes to their hosts that replaced their cyanobacterial/plastid homologs thus shaping early algal/plant evolution before they eventually vanished.

Figure 1

Phylogenetic analysis of chlamydial genes in photoautotrophic eukaryotes. Unrooted maximum likelihood trees of single-gene data sets. Evolutionary models of all data sets: WAG+I+Γ, except for Fig. 1E: RtREV+I+Γ ([85]. Support values: maximum likelihood bootstrap/posterior probability; branches in bold: ML bootstrap > 95% and posterior probability of 1.0. Scale bars = substitutions per site. For enlarged trees with taxon names, see Additional File 4. (A) Glycerol-3-phosphate acyltransferase (EC 2.3.1.15; 21 taxa, 281 amino acid positions). (B) tRNA delta(2)-isopentenylpyrophosphate transferase (EC 2.5.2.8; 38 taxa, 240 positions). (C) 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (ispD; EC 2.7.7.60; 38 taxa, 198 positions). Rhodoplantae, Bacillariophyta and Viridiplantae group with the Chlamydiae. (D) Putative ribosome release/recycling factor (COG0233; 30 taxa, 171 positions). (E) Ribosomal large subunit pseudouridine synthase (EC 4.2.1.70; 38 taxa, 262 positions). (F) Folylpolyglutamate synthase (EC 6.3.2.17; 26 taxa, 208 positions).

Figure 2

Venn diagram showing the number of chlamydial proteins shared by different photoautotrophic eukaryotes.

Figure 3

Phylogenetic analyses of chlamydial proteins in the Bacillariophyta support the occurrence of two independent HGT/EGT events. Unrooted maximum likelihood trees of concatenated data sets. Support values: maximum likelihood bootstrap/posterior probability. Scale bars = substitutions per site. (A) Concatenated data set of seven proteins showing relationship of diatoms to rhodoplants (12 taxa; 2675 amino acid positions). (B) Concatenated data set of five proteins showing a relationship of viridiplant and diatom genes (same 12 taxa as in Fig. 3A; 1736 amino acid positions). For a complete list of genes used in the two concatenated analyses see Additional File 5.

Figure 4

Scenarios to explain the simultaneous presence of cyanobacterial and chlamydial protein homologues in photosynthetic eukaryotes. (A) Multiple HGTs of chlamydial genes from a single donor into different photosynthetic eukaryotes. (B) Single or multiple HGTs of chlamydial genes into the cyanobacterial ancestor of plastids and group-specific gene losses from different photosynthetic eukaryotes. (C) HGT or EGT from intracellular chlamydiae to the cyanobacterial endosymbiont of a photosynthetic eukaryote and group-specific chlamydial gene losses from different photosynthetic eukaryotes. In a variation of this scenario the intracellular chlamydiae donate genes by EGT or HGT to the eukaryotic host little before or at the time of cyanobacterial endosymbiosis and group-specific multiple gene losses of chlamydial genes. (D) Origin of chlamydial proteins in heterokont algae. Two secondary endosymbioses are shown involving sequentially a viridiplant and a rhodoplant symbiont. The endosymbiosis of a cyanobacterium has been omitted from Figure 4D for clarity.