Massive Protein Import into the Early-Evolutionary-Stage Photosynthetic Organelle of the Amoeba Paulinella chromatophora

Abstract

The endosymbiotic acquisition of mitochondria and plastids more than 1 Ga ago profoundly impacted eukaryote evolution. At the heart of understanding organelle evolution is the re-arrangement of the endosymbiont proteome into a host-controlled organellar proteome. However, early stages in this process as well as the timing of events that underlie organelle integration remain poorly understood. The amoeba Paulinella chromatophora contains cyanobacterium-derived photosynthetic organelles, termed "chromatophores," that were acquired more recently (around 100 Ma ago). To explore the re-arrangement of an organellar proteome during its integration into a eukaryotic host cell, here we characterized the chromatophore proteome by protein mass spectrometry. Apparently, genetic control over the chromatophore has shifted substantially to the nucleus. Two classes of nuclear-encoded proteins-which differ in protein length-are imported into the chromatophore, most likely through independent pathways. Long imported proteins carry a putative, conserved N-terminal targeting signal, and many specifically fill gaps in chromatophore-encoded metabolic pathways or processes. Surprisingly, upon heterologous expression in a plant cell, the putative chromatophore targeting signal conferred chloroplast localization. This finding suggests common features in the protein import pathways of chromatophores and plastids, two organelles that evolved independently and more than 1 Ga apart from each other. By combining experimental data with in silico predictions, we provide a comprehensive catalog of almost 450 nuclear-encoded, chromatophore-targeted proteins. Interestingly, most imported proteins seem to derive from ancestral host genes, suggesting that the re-targeting of nuclear-encoded proteins that resulted from endosymbiotic gene transfers plays only a minor role at the onset of chromatophore integration.

Evidence supporting an antimicrobial origin of targeting peptides to endosymbiotic organelles

“…P. chromatophora acquired a novel primary endosymbiotic organelle called "chromatophore" approximately 100 million years ago (Delaye et al 2016). Proteomic analysis of these chromatophores identified a large set of imported AMP-like peptides as well as chromatophore-imported proteins harboring common N-terminal sequences containing AMP-like motifs (Singer et al 2017). These findings thus provide an independent example of a third primary endosymbiosis that is accompanied by the evolution of an AMP-derived protein import process.…”

Horizontal and endosymbiotic gene transfer in early plastid evolution

“…However, based on the reduced number of chromatophore-derived genes in the nuclear genome, it seems that EGT may have been less important in the establishment of the chromatophore in P. chromatophora than HGT from other bacteria, as c.170 genes of bacterial origin encode proteins likely to be targeted to the chromatophore (Nowack et al, 2016). Interestingly, the largest contribution of identified chromatophore-targeted proteins derive from the ancestral host genetic repertoire (Singer et al, 2017), a similar pattern to the one observed in Archaeplastida proteomes (Qiu et al, 2013), suggesting that in both primary endosymbioses the host played a crucial role in mediating cyanobiont integration.…”

No genome is an island: toward a 21st century agenda for evolution

“…A second primary symbiogenesis, involving a distinct cyanobacterial strain from the Synechococcus ‐ Prochloron clade, generated a single species of photosynthetic amoeba called Paulinella chromatophora . Since P. chromatophora is unique among amoebae and has not diversified into multiple species, this second primary symbiogenetic event appears to have occurred very recently in amoeba evolution…”

“…31 A second primary symbiogenesis, involving a distinct cyanobacterial strain from the Synechococcus-Prochloron clade, generated a single species of photosynthetic amoeba called Paulinella chromatophora. 32 Since P. chromatophora is unique among amoebae and has not diversified into multiple species, this second primary symbiogenetic event appears to have occurred very recently in amoeba evolution. p Both red and green algae have participated in many secondary symbiogenesis events with unrelated eukaryotes that generated photosynthetic organisms with a more complex organelle structure, which also includes DNA from the algal nucleus.…”