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RNA processing and decay in plastids

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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. WIREs RNA 2013, 4:295–316. doi: 10.1002/wrna.1161 The authors have declared no conflicts of interest for this article. This article is categorized under: RNA Processing > Capping and 5' End Modifications RNA Processing > 3' End Processing RNA Turnover and Surveillance > Regulation of RNA Stability RNA in Disease and Development > RNA in Development

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Model for the spatial coordination of transcription, RNA maturation, and RNA decay. The nucleoid, shown as a cloud, is home to transcription (1), RNA maturation (2), ribosome assembly (3), and RNA surveillance (4). Mature RNAs and assembled ribosomes exit the nucleoid, where protein synthesis (5) occurs prior to RNA decay (6). RNA decay might be initiated once the protective actions of ribosomes and RNA‐binding proteins (RBPs) discontinue because of dissociation from transcripts. The legend at the bottom denotes the identities of proteins and structures shown in the diagrams.

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Ribosomal RNA maturation. Top, the rRNA operon is transcribed as a single precursor. In this model, endonucleolytic cleavage by RNase P and RNase Z initiates maturation by releasing the tRNAs. Additional cleavages by other endoribonucleases could also occur at multiple sites, and must occur between the 4.5S and 5S rRNA coding regions. The pool of precursor rRNAs is processed at their 3′ ends by RNase II and at their 5′ ends by RNase J. The 23S and 4.5S rRNAs are initially released as a dicistronic moiety, which is subject to trimming and hidden break processing during or after ribosome assembly. A partial list of factors that directly or indirectly impact rRNA processing is listed in Table 2. While the figure shows the major enzymes for each step, in their absence other nucleases can also create WT‐like ends.

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Maturation of plastid mRNAs. A polycistronic mRNA precursor is bound by proteins at specific intergenic sites, and its 5′ and 3′ ends are matured exonucleolytically. This transcript is also subject to intercistronic cleavage by several RNases whose respective roles remain to be clarified. Specificity could derive from the fact that RNase E prefers AU‐rich regions and CSP41a/b preferentially cuts at stem–loops. Intercistronic cleavage produces new 5′ and 3′ ends, which are again subject to exoribonuclease activity, with RNase II generally following PNPase. Ribosomes may initiate translation on both monocistronic and polycistronic RNA forms.

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Relaxed transcription initiation and inefficient polymerase termination in plastids. Transcription initiation by nucleus‐encoded polymerase (NEP, blue ovals) and plastid‐encoded polymerase (PEP, brown ovals) occurs at widespread promoters found upstream of known open reading frames (ORF), within operons, and in noncoding regions. Many genes have both NEP and PEP promoters. Inefficient transcription termination creates multiple and poorly defined 3′ ends. The combination of multisite transcript initiation and imprecise termination creates a diverse pool of plastid RNA precursors, which will vary depending on polymerase concentrations.

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Nucleus‐encoded proteins that promote the splicing of group II introns in angiosperm chloroplasts. The intron set shown is characteristic of most land plants, with minor modifications. Introns found in Arabidopsis but not maize are marked with an asterisk. The genetically defined intron targets of each protein (i.e., those whose splicing is disrupted in corresponding mutant backgrounds) are circled. OTP51 has several minor targets that are not diagrammed.47,52 With the exception of OTP70, all of these proteins have been shown to coimmunoprecipitate with their cognate introns from chloroplast extract. This information is summarized from Refs 16, 44–58, 61, and 62. In addition, the plastid‐encoded protein MatK associates with most of the subgroup IIA introns and is likely to be required for their splicing.37 Abbreviations for RNA‐binding domains include CRM (CRS1‐YhbY or chloroplast RNA splicing and ribosome maturation), PPR (pentatricopeptide repeat), PORR (plant organellar RNA recognition or DUF860), RRM (RNA recognition motif), and DUF (domain of unknown function).

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Models for plastid RNA editing. A specific pentatricopeptide repeat (PPR) protein, with an RNA‐binding domain, a conserved E, and DYW domain (green shapes), is directed to an RNA editing site by the cis recognition sequence. The RIP/MORF protein (blue shape) interacts with the PPR protein RNA‐binding domain and is required for the deamination reaction. In one model (top), this complex recruits an unidentified deaminase (red shape) to catalyze C‐to‐U editing. A second hypothesis (bottom) is that the RIP/MORF protein binding causes a shift in the PPR DYW domain that positions it over the target nucleotide. In this case, the DYW domain performs the deamination reaction.

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Browse by Topic

RNA Processing > 3′ End Processing
RNA Turnover and Surveillance > Regulation of RNA Stability
RNA Processing > Capping and 5′ End Modifications
RNA in Disease and Development > RNA in Development

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