Abstract
Modifications in nucleic acids are present in all three domains of life. More than 170 distinct chemical modifications have been reported in cellular RNAs to date. Collectively termed as epitranscriptome, these RNA modifications are often dynamic and involve distinct regulatory proteins that install, remove, and interpret these marks in a site-specific manner. Covalent nucleotide modifications-such as methylations at diverse positions in the bases, polyuridylation, and pseudouridylation and many others impact various events in the lifecycle of an RNA such as folding, localization, processing, stability, ribosome assembly, and translational processes and are thus crucial regulators of the RNA metabolism. In plants, the nuclear/cytoplasmic epitranscriptome plays important roles in a wide range of biological processes, such as organ development, viral infection, and physiological means. Notably, recent transcriptome-wide analyses have also revealed novel dynamic modifications not only in plant nuclear/cytoplasmic RNAs related to photosynthesis but especially in chloroplast mRNAs, suggesting important and hitherto undefined regulatory steps in plastid functions and gene expression. Here we report on the latest findings of known plastid RNA modifications and highlight their relevance for the post-transcriptional regulation of chloroplast gene expression and their role in controlling plant development, stress reactions, and acclimation processes.
Highlights
The chloroplast is the result of an endosymbiotic event in which a cyanobacterium was ingested by a eukaryotic host cell
While the role of polyadenylation in RNA degradation and mostly C to U editing events in chloroplasts are well understood [23], little is known about the nature, dynamics, and functions of other modifications such as the diverse methylation steps methylation at the N6 position (m6 A), m1 A, m7 G, m5 C or hm5 C, adenosine dimethyltransfer (m6 Am) [9] as well as uridylation, pseudouridylation, removal of the noncanonical NAD+ cap, the biosynthesis of 5-methylaminomethyl2-thiouridine (mnm(5)s(2)U) of tRNAs, and many others (Figure 1)
Since antibodies are available for m1 A, m6 A, and m5 C and other base modifications, several studies of the cellular epitranscriptome in Arabidopsis focused on immunological approaches, such as the predominant N6 A-methylated RNA immunoprecipitation sequencing (MeRIP/m6 A-seq)
Summary
The chloroplast is the result of an endosymbiotic event in which a cyanobacterium was ingested by a eukaryotic host cell. While the role of polyadenylation in RNA degradation and mostly C to U editing events in chloroplasts are well understood [23], little is known about the nature, dynamics, and functions of other modifications such as the diverse methylation steps m6 A, m1 A, m7 G, m5 C or hm C, adenosine dimethyltransfer (m6 Am) [9] as well as uridylation, pseudouridylation, removal of the noncanonical NAD+ cap, the biosynthesis of 5-methylaminomethyl2-thiouridine (mnm(5)s(2)U) of tRNAs, and many others (Figure 1) All their functions are embedded in the transition from RNAs to proteins and are most likely important for the regulation of RNA localization, structure, stability, processing, ribosome assembly, and translational events. We discuss our present knowledge about novel methods for the identification of RNA modifications, bioinformatic tools, and the potential physiological roles of RNA modifiers and interpreters in plant nuclear/cytoplasmic gene expression related to photosynthesis and the post-transcriptional fate of chloroplast RNAs
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