Impact of light intensity and quality on chromatophore and nuclear gene expression in Paulinella chromatophora, an amoeba with nascent photosynthetic organelles

Abstract

SUMMARYPlastid evolution has been attributed to a single primary endosymbiotic event that occurred about 1.6 billion years ago (BYA) in which a cyanobacterium was engulfed and retained by a eukaryotic cell, although early steps in plastid integration are poorly understood. The photosynthetic amoeba Paulinella chromatophora represents a unique model for the study of plastid evolution because it contains cyanobacterium-derived photosynthetic organelles termed 'chromatophores' that originated relatively recently (0.09-0.14 BYA). The chromatophore genome is about a third the size of the genome of closely related cyanobacteria, but 10-fold larger than most plastid genomes. Several genes have been transferred from the chromatophore genome to the host nuclear genome through endosymbiotic gene transfer (EGT). Some EGT-derived proteins could be imported into chromatophores for function. Two photosynthesis-related genes (psaI and csos4A) are encoded by both the nuclear and chromatophore genomes, suggesting that EGT in Paulinella chromatophora is ongoing. Many EGT-derived genes encode proteins that function in photosynthesis and photoprotection, including an expanded family of high-light-inducible (ncHLI) proteins. Cyanobacterial hli genes are high-light induced and required for cell viability under excess light. We examined the impact of light on Paulinella chromatophora and found that this organism is light sensitive and lacks light-induced transcriptional regulation of chromatophore genes and most EGTderived nuclear genes. However, several ncHLI genes have reestablished light-dependent regulation, which appears analogous to what is observed in cyanobacteria. We postulate that expansion of the ncHLI gene family and its regulation may reflect the light/oxidative stress experienced by Paulinella chromatophora as a consequence of the as yet incomplete integration of host and chromatophore metabolisms.

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

“…Notably, among the short LC import candidates were the nuclear-encoded PSI subunits PsaE and PsaK, which have been demonstrated before to be part of PSI [13]. Other short import candidates were four EGT-derived high-light-inducible (HLI) photoprotective proteins [10,11] and two proteins annotated as cold-shock proteins. However, most of the short import candidates do not have homologs in other organisms (67 proteins) or are conserved proteins of unknown function (10 proteins).…”

“…The chromatophore is surrounded by two envelope membranes and a peptidoglycan layer [7]. Its genome (1 Mb) is reduced to approximately one-third of the ancestral cyanobacterial genome [8], and >70 genes of a-cyanobacterial origin, which most likely result from endosymbiotic gene transfers (EGTs) from the chromatophore, are now expressed from the nuclear genome [9][10][11]. Overall, nuclear-and chromatophore-encoded functions are highly complementary, with many genes for proteins involved in the same metabolic pathway or cellular process being distributed over both chromatophore and nuclear genome [9].…”

Horizontal and endosymbiotic gene transfer in early plastid evolution

“…The chromatophore genome is highly reduced, encoding 867 proteins that represent about one-third of proteins of its free-living counterparts (Nowack et al, 2008). Similar to the EGTs found in Archaeplastida, P. chromatophora has relocated > 70 chromatophore genes into the nuclear genome (mostly involved in photosynthesis-related functions) (Nowack et al, 2016;Zhang et al, 2017). By contrast, these genes represent < 1% of the Paulinella nuclear genome, while in A. thaliana some reports have suggested that the genes of cyanobacterial origin can account for up to 18% of the nuclear genes (Martin et al, 2002).…”

Paulinella micropora KR01 holobiont genome assembly for studying primary plastid evolution

“…A bacteria-reduced culture was used for HiSeq 2500 and Illumina Nova Seq 6000 sequencing. For transcriptome sequencing, control and high light stress conditions (control=10 µmol photons m -2 sec -1 ; stress=120 µmol photons m -2 sec -1 ; see Zhang, et al 2017) over a 12/ 12h light/ dark cycle and temperature stress conditions (control=24°C; stress=4°C, 38°C) were sequenced using the Illumina Truseq stranded mRNA library prep kit. All sequencing was done by DNA Link Inc. (Seoul, Korea).…”

“…In contrast to the highly reduced plastid genomes of algae and plants (i.e., 100-200 kbp in size in Archaeplastida), the cyanobacterium-derived plastid (referred to as the chromatophore) in phototrophic Paulinella is in a less derived stage of organelle evolution and is ca. 1 Mbp in size (Lhee, et al 2017;Nowack, et al 2008;Reyes-Prieto, et al 2010;Zhang, et al 2017).…”