Endosymbiotic Gene Transfer and Transcriptional Regulation of Transferred Genes in Paulinella chromatophora

Abstract

Paulinella chromatophora is a cercozoan amoeba that contains "chromatophores," which are photosynthetic inclusions of cyanobacterial origin. The recent discovery that chromatophores evolved independently of plastids, underwent major genome reduction, and transferred at least two genes to the host nucleus has highlighted P. chromatophora as a model to infer early steps in the evolution of photosynthetic organelles. However, owing to the paucity of nuclear genome sequence data, the extent of endosymbiotic gene transfer (EGT) and host symbiont regulation are currently unknown. A combination of 454 and Illumina next generation sequencing enabled us to generate a comprehensive reference transcriptome data set for P. chromatophora on which we mapped short Illumina cDNA reads generated from cultures from the dark and light phases of a diel cycle. Combined with extensive phylogenetic analyses of the deduced protein sequences, these data revealed that 1) about 0.3-0.8% of the nuclear genes were obtained by EGT compared with 11-14% in the Plantae, 2) transferred genes show a distinct bias in that many encode small proteins involved in photosynthesis and photoacclimation, 3) host cells established control over expression of transferred genes, and 4) not only EGT, but to a minor extent also horizontal gene transfer from organisms that presumably served as food sources, helped to shape the nuclear genome of P. chromatophora. The identification of a significant number of transferred genes involved in photosynthesis and photoacclimation of thylakoid membranes as well as the observed transcriptional regulation of these genes strongly implies import of the encoded gene products into chromatophores, a feature previously thought to be restricted to canonical organelles. Thus, a possible mechanism by which P. chromatophora exerts control over the performance of its newly acquired photosynthetic organelle may involve controlling the expression of nuclear-encoded chromatophore-targeted regulatory components of the thylakoid membranes.

Trafficking of protein into the recently established photosynthetic organelles of Paulinella chromatophora

“…Transcriptional/translational control of these solute transporters would allow the host to impact CR growth and performance. Both our recent data (13), and data presented in this study, have revealed that, in addition to host control of metabolite fluxes, the host may exert direct control over CR activity by regulating the abundance of nuclear-encoded proteins involved in physiological processes that occur within CRs.…”

“…As a number of proteins encoded by EGT genes of P. chromatophora likely function in thylakoid membranes, we speculated that a subset of proteins synthesized in the P. chromatophora cytoplasm would be imported into the CR (13). In this study, we show that the nuclear-encoded PsaE, PsaK1, and PsaK2 polypeptides are synthesized in the host cell cytoplasm, imported into the CR, and associate with CR-encoded PSI subunits in functional PSI complexes.…”

“…P. chromatophora harbors two photosynthetic compartments of cyanobacterial origin, termed chromatophores (CRs), that are delineated from the "host cell" cytoplasm by a double envelope membrane and peptidoglycan layer. Recent evidence suggests that CRs evolved independently of plastids (6-9) and experienced a major genome size reduction [∼3.0 to ∼1.0 Mb (10, 11)], and that more than 30 expressed nuclear genes are the result of EGT from the CR (11)(12)(13). Interestingly, most of the transferred genes encode small proteins predicted to have a function associated with photosynthesis and light-acclimation.…”

Protein translocons in photosynthetic organelles of Paulinella chromatophora

“…Since signal peptides are involved in protein import into the endoplasmic reticulum, such a presequence in the case of PsaE indicates the possibility of endomembranedependent targeting to the outer chromatophore membrane. Subsequent studies confirmed the presence of a signal peptide-like presequence in another four of nine investigated EGT-derived proteins that evolved by modification of their N-terminal mature parts, but not the missing Toc and Tic components in the nuclear genome [16,19].…”

“…The genome-size reduction involved loss of many genes, including those engaged in essential biosynthetic pathways and endosymbiotic gene transfer [11,14]. Transcriptome analyses have identified more than 30 EGT-derived genes in the Paulinella nuclear genome [14][15][16]; however, many more are expected; Nowack et al [16] estimated their number between 40 and 125. Because the lost genes are of the utmost importance for cell functioning, and at least some of the transferred ones are transcriptionally regulated by the host and involved in photosynthesis or photosynthesis-related processes, Paulinella chromatophores are expected to have evolved a protein import route, or routes.…”