RNA processing and decay in plastids

Abstract

Plastids were derived through endosymbiosis from a cyanobacterial ancestor, whose uptake was followed by massive gene transfer to the nucleus, resulting in the compact size and modest coding capacity of the extant plastid genome. Plastid gene expression is essential for plant development, but depends on nucleus-encoded proteins recruited from cyanobacterial or host-cell origins. The plastid genome is heavily transcribed from numerous promoters, giving posttranscriptional events a critical role in determining the quantity and sizes of accumulating RNA species. The major events reviewed here are RNA editing, which restores protein conservation or creates correct open reading frames by converting C residues to U, RNA splicing, which occurs both in cis and trans, and RNA cleavage, which relies on a variety of exoribonucleases and endoribonucleases. Because the RNases have little sequence specificity, they are collectively able to remove extraneous RNAs whose ends are not protected by RNA secondary structures or sequence-specific RNA-binding proteins (RBPs). Other plastid RBPs, largely members of the helical-repeat superfamily, confer specificity to editing and splicing reactions. The enzymes that catalyze RNA processing are also the main actors in RNA decay, implying that these antagonistic roles are optimally balanced. We place the actions of RBPs and RNases in the context of a recent proteomic analysis that identifies components of the plastid nucleoid, a protein-DNA complex with multiple roles in gene expression. These results suggest that sublocalization and/or concentration gradients of plastid proteins could underpin the regulation of RNA maturation and degradation.

HIGH CHLOROPHYLL FLUORESCENCE145 Binds to and Stabilizes the psaA 5′ UTR via a Newly Defined Repeat Motif in Embryophyta

“…This is supported by several lines of evidence: (1) the psaA 59 UTRs are conserved, (2) high sequence identity and similarity among homologous HCF145 proteins in land plants, and (3) the comparable phenotypes in the hcf145 knockouts in Arabidopsis and moss. Most likely, a high evolutionary pressure during endosymbiosis caused a bias for the recruitment of plant-specific nucleus-encoded factors, like many PPR proteins, and other factors for stabilization and processing of organellar RNAs (Germain et al, 2013;Shikanai and Fujii, 2013).…”

“…Unlike in cyanobacteria, nearly, if not all, polycistronic precursor transcripts are processed by endo-and exonucleases, splicing activities, and editing events (Stern et al, 2010;Meurer, 2012, 2013;Germain et al, 2013). In several cases, processing within intergenic regions is required for subsequent translation of the 59 processed product (Germain et al, 2013) and regulation of stability of individual mRNAs at both ends (Barkan, 2011;Zhelyazkova et al, 2012).…”

“…In several cases, processing within intergenic regions is required for subsequent translation of the 59 processed product (Germain et al, 2013) and regulation of stability of individual mRNAs at both ends (Barkan, 2011;Zhelyazkova et al, 2012). The 39 processing has been hypothesized to be a prerequisite also for efficient translation of plastid transcripts (Stoppel et al, 2011).…”

“…The 39 processing has been hypothesized to be a prerequisite also for efficient translation of plastid transcripts (Stoppel et al, 2011). Degradation of plastid RNAs is often initiated by endonucleolytic processing and by the subsequent action of unspecific 59 → 39 and 39 → 59 exonucleases (Germain et al, 2013). The resulting processing products have obtained phylogenetically new 59 and 39 untranslated regions (UTRs) that have to be stabilized either by complex secondary stem loop structures and/or by the recruitment of factors that have gained sequence-specific RNA binding capabilities (Stern et al, 2010;Barkan, 2011;Germain et al, 2013).…”

“…Accordingly, many UTR binding proteins also evolved de novo. This is supported by the presence of only few RNases with little sequence specificity in chloroplasts and the action of nuclearencoded proteins in a gene-specific manner (Stern et al, 2010;Barkan, 2011;Germain et al, 2013).…”