| Literature DB >> 27446814 |
Ugo Cenci1, Mathieu Ducatez1, Derifa Kadouche1, Christophe Colleoni1, Steven G Ball1.
Abstract
Chlamydiales were recently proposed to have sheltered the future cyanobacterial ancestor of plastids in a common inclusion. The intracellular pathogens are thought to have donated those critical transporters that triggered the efflux of photosynthetic carbon and the consequent onset of symbiosis. Chlamydiales are also suspected to have encoded glycogen metabolism TTS (Type Three Secretion) effectors responsible for photosynthetic carbon assimilation in the eukaryotic cytosol. We now review the reasons underlying other chlamydial lateral gene transfers evidenced in the descendants of plastid endosymbiosis. In particular we show that half of the genes encoding enzymes of tryptophan synthesis in Archaeplastida are of chlamydial origin. Tryptophan concentration is an essential cue triggering two alternative modes of replication in Chlamydiales. In addition, sophisticated tryptophan starvation mechanisms are known to act as antibacterial defenses in animal hosts. We propose that Chlamydiales have donated their tryptophan operon to the emerging plastid to ensure increased synthesis of tryptophan by the plastid ancestor. This would have allowed massive expression of the tryptophan rich chlamydial transporters responsible for symbiosis. It would also have allowed possible export of this valuable amino-acid in the inclusion of the tryptophan hungry pathogens. Free-living single cell cyanobacteria are devoid of proteins able to transport this amino-acid. We therefore investigated the phylogeny of the Tyr/Trp transporters homologous to E. coli TyrP/Mre and found yet another LGT from Chlamydiales to Archaeplastida thereby considerably strengthening our proposal.Entities:
Keywords: Chlamydiales; Photosynthesis; endosymbiosis; plastid; tryptophan metabolism
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Year: 2016 PMID: 27446814 PMCID: PMC4916741 DOI: 10.3389/fcimb.2016.00067
Source DB: PubMed Journal: Front Cell Infect Microbiol ISSN: 2235-2988 Impact factor: 5.293
Figure 1Consensus tree obtained with Phylobayes 4.1 with Bayesian posterior probabilities mapped onto the nodes of (A) phosphoribosylanthranilate isomerase (TrpF) and (B) anthranilate phosphoribosyltransferase (TrpD). Groups of interest are highlighted in purple (Chlamydiales), green (green algae and plants), red (red algae), cyan (Glaucophyta), and blue (Cyanobacteria). Lineages putatively derived from secondary endosymbiosis of Archaeplastida are displayed in brown. Bayesian posterior probabilities values (PP) higher than 0.7 are indicated onto the branches. The scale bars indicate the inferred number of amino acid substitutions per site. The trees were manually rooted for convenience of display. The nodes uniting Archaeplastida and their derived lineages to Chlamydiales by LGT are highlighted in bold. The Phosphoribosylanthranilate isomerase tree (A) shows a group with robust support (PP = 0.99) composed of Chlamydiales, all Archaeplastida, Alveolata, and the two intracellular γ-proteobacteria pathogens Coxiella and Piscirickettsia. Bonner et al. (2014) have proposed that Coxiella received its Tryptophan operon through LGT from Simkaniaceae (Chlamydiales) in a common intracellular environment (see text). (B) shows that the three Archaeplastida lineages are united through LGT together with a complex pattern of secondary endosymbiosis lineages (PP = 0.98). Here again intracellular γ-proteobacteria are recovered for the same reasons. Sequences used in the trees were retrieved by homology searches with BLAST against sequences of interest in a database composed of nr, MMETSP (Keeling et al., 2014), and genomes of interest. Sequences with an E < 1e-10 were selected and aligned using MAFFT (Katoh and Standley, 2013). We used BMGE (Criscuolo and Gribaldo, 2010) with a block size of four and the BLOSUM30 similarity matrix for block selection. We generated preliminary trees using Fasttree (Price et al., 2010). “Dereplication,” using TreeTrimmer (Maruyama et al., 2013), was applied to supported monophyletic clades in order to reduce sequence redundancy. The final set of sequences were selected manually. Finally, the sequences were re-aligned with MUSCLE (Edgar, 2004), block selection was carried out using BMGE with the same setting, and trees were generated using Phylobayes 4.1 (Lartillot et al., 2009) under the CAT+GTR model (Lartillot and Philippe, 2004). The two chains were stopped when convergence was reached (maxdiff < 0.1) after at least 300 cycles and a burn-in different for each alignment when equilibrium was reached between two chains.
Figure 2Consensus tree obtained with Phylobayes 4.1 with Bayesian posterior probabilities mapped onto the nodes of (A) indole-3-glycero phosphate synthase (TrpC) and (B) tyrosine/tryptophan permease (TyrP/Mtr). Bayesian posterior probabilities values (PP) higher than 0.7 are indicated onto the branches. The scale bars indicate the inferred number of amino acid substitutions per site. The trees were manually rooted for convenience of display. Groups of interest are highlighted in purple (Chlamydiales), green (green algae and plants), red (red algae), cyan (Glaucophyta), and blue (Cyanobacteria). Lineages putatively derived from secondary endosymbiosis of Archaeplastida are displayed in brown. The nodes uniting Archaeplastida and their derived lineages to Chlamydiales by LGT are highlighted in bold. Methods have been detailed in the legend of Figure 1. (A) The red algae and Chlamydiales are shown to be united through LGT (highlighted in bold, PP = 0.98), however the Green algae and plants and the Glaucophyta have acquired the gene from Cyanobacteria (PP = 1). Coxiella has been previously proposed to have received their genes from Simkaniaceae (Bonner et al., 2014). (B) The putative tyrosine/tryptophan transporter phylogeny displayed has been rooted within γ-proteobacteria for reasons discussed in the text. The node uniting Archaeplastida, secondary endosymbiosis lineages derived from them, Cyanobacteria and a few δ-proteobacteria is highlighted in bold (PP = 0.99). The transporter has experienced repeated exchanges in its gene history. Such multiple exchanges between intracellular bacteria are displayed. The root proposed supports a scenario where the gene originated from deeply rooted γ-proteobacteria which diversified in free living, facultative intracellular and obligatory intracellular lineages. In a common intracellular environment the gene was transferred by LGT to Chlamydiales and further exchanged on multiple occasions with intracellular γ-proteobacteria. The Chlamydiales have donated TyrP to Archaeplastida which have donated this to a restricted number of δ-proteobacteria and Nostocales. Only 2 Cyanobacterial lineages not related to Nostocales have been detected and are displayed. For convenience of display the total numbers of representatives of both cyanobacteria and γ-proteobacteria, respectively, of 29 and 692 sequences with at least a different genus have been reduced (see Methods in Figure 1). No TyrP/Mtr transporter have ever been studied in plants. The distantly related PheP E. coli translocator was only very recently identified in Petunia and shown to indeed define the major phenylalanine transporter of plant plastids (Widhalm et al., 2015). Neither PheP nor TyrP/Mtr could be recovered from documented plastid proteomes. Nevertheless, TyrP/Mtr green alga and plant sequences closest to the E. coli sequence do carry candidate transit peptide sequences. TyrP/Mtr is the only transporter known qualifying as a candidate Trp/Phe transporter in Chlamydiaceae.