PAP8/pTAC6 Is Part of a Nuclear Protein Complex and Displays RNA Recognition Motifs of Viral Origin.

Louise Chambon,Maha Chieb,David Cobessi,Robert Blanvillain,Thomas Pfannschmidt,François-Xavier Gillet

doi:10.3390/ijms23063059

Abstract

Chloroplast biogenesis depends on a complex transcriptional program involving coordinated expression of plastid and nuclear genes. In particular, photosynthesis-associated plastid genes are expressed by the plastid-encoded polymerase (PEP) that undergoes a structural rearrangement during chloroplast formation. The prokaryotic-type core enzyme is rebuilt into a larger complex by the addition of nuclear-encoded PEP-associated proteins (PAP1 to PAP12). Among the PAPs, some have been detected in the nucleus (PAP5 and PAP8), where they could serve a nuclear function required for efficient chloroplast biogenesis. Here, we detected PAP8 in a large nuclear subcomplex that may include other subunits of the plastid-encoded RNA polymerase. We have made use of PAP8 recombinant proteins in Arabidopsis thaliana to decouple its nucleus- and chloroplast-associated functions and found hypomorphic mutants pointing at essential amino acids. While the origin of the PAP8 gene remained elusive, we have found in its sequence a micro-homologous domain located within a large structural homology with a rhinoviral RNA-dependent RNA polymerase, highlighting potential RNA recognition motifs in PAP8. PAP8 in vitro RNA binding activity suggests that this domain is functional. Hence, we propose that the acquisition of PAPs may have occurred during evolution by different routes, including lateral gene transfer.

Highlights

Chloroplasts are of endosymbiotic origin, and as a remnant of their cyanobacterial ancestry, they have retained a small but highly conserved genome
We reported that PAP8 is a protein dually localized in the nucleus and plastids with a nuclear pool that is potentially involved in the proper timing of chloroplast biogenesis
PAP8 is detected in the heparin Sepharose chloroplastic plastid-encoded polymerase (PEP) purified samples as shown in previous studies [7], and in two discrete complexes from the nuclear protein fraction at a lower molecular weight from that of the known 1-MDa PEP complex

Summary

Introduction

Chloroplasts are of endosymbiotic origin, and as a remnant of their cyanobacterial ancestry, they have retained a small but highly conserved genome. Plastid genomes are composed of nearly 120 genes encoding housekeeping and photosynthesis genes found in multiple copies of circular DNA [1]. Transcription of plastid genes is due to the activity of a nuclear-encoded phage-type RNA polymerase (NEP) and the prokaryotic-type multi-subunit PEP complex. The latter transcribes the vast majority of all genes with prokaryotic-type promoters containing −35 and −10 elements, supporting the metabolic functions of plastids [3]. Only a few plastid-encoded subunits are present in the major functional protein complexes (such as the photosystems), while most chloroplast proteins are encoded by nuclear genes and imported through the plastid envelope (reviewed in the work of [4])

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Conclusion