title: Systematic analysis of plant mitochondrial and chloroplast small RNAs suggests organelle-specific mRNA stabilization mechanisms.
abstract: Land plant organellar genomes encode a small number of genes, many of which are essential for respiration and photosynthesis. Organellar gene expression is characterized by a multitude of RNA processing events that lead to stable, translatable transcripts. RNA binding proteins (RBPs), have been shown to generate and protect transcript termini and eventually induce the accumulation of short RNA footprints. We applied knowledge of such RBP-derived footprints to develop software (sRNA miner) that enables identification of RBP footprints, or other clusters of small RNAs, in organelles. We used this tool to determine mitochondrial and chloroplast cosRNAs (clustered organellar sRNAs) in Arabidopsis. We found that in mitochondria, cosRNAs coincide with transcript 3'-ends, but are largely absent from 5'-ends. In chloroplasts this bias is absent, suggesting a different mode of 5' processing, possibly owing to different sets of RNases. Furthermore, we identified a large number of cosRNAs that represent silenced insertions of mitochondrial DNA in the nuclear genome of Arabidopsis. Steady-state RNA analyses demonstrate that cosRNAs display differential accumulation during development. Finally, we demonstrate that the chloroplast RBP PPR10 associates in vivo with its cognate cosRNA. A hypothetical role of cosRNAs as competitors of mRNAs for PPR proteins is discussed.
authors.affiliation: Molekulare Genetik, Institut für Biologie, Humboldt-Universität zu Berlin, Philippstr. 11-13, 10115 Berlin, Germany hannes.ruwe@hu-berlin.de.
authors.forename: Hannes
authors.initials: H
authors.lastname: Ruwe
authors.affiliation: Molekulare Genetik, Institut für Biologie, Humboldt-Universität zu Berlin, Philippstr. 11-13, 10115 Berlin, Germany.
authors.forename: Gongwei
authors.initials: G
authors.lastname: Wang
authors.affiliation: Molekulare Genetik, Institut für Biologie, Humboldt-Universität zu Berlin, Philippstr. 11-13, 10115 Berlin, Germany FU-Berlin, Fachbereich Biologie, Chemie, Pharmazie, Takustr. 3, 14195 Berlin, Germany.
authors.forename: Sandra
authors.initials: S
authors.lastname: Gusewski
authors.affiliation: Molekulare Genetik, Institut für Biologie, Humboldt-Universität zu Berlin, Philippstr. 11-13, 10115 Berlin, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Schmitz-Linneweber
mesh_terms: D017360:Arabidopsis / Q000166:cytology* / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000378:metabolism; D002736:Chloroplasts / Q000235:genetics* / Q000378:metabolism; D004272:DNA, Mitochondrial / Q000235:genetics / Q000378:metabolism; D066264:Datasets as Topic; D054629:Genome, Mitochondrial / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D008928:Mitochondria / Q000235:genetics* / Q000378:metabolism; D012313:RNA / Q000378:metabolism*; D020871:RNA Stability; D018747:RNA, Chloroplast / Q000378:metabolism*; D000077278:RNA, Mitochondrial; D016601:RNA-Binding Proteins / Q000378:metabolism; D012260:Ribonucleases / Q000378:metabolism; D012984:Software; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; D004272:DNA, Mitochondrial; C000620218:PPR10 protein, Arabidopsis; D018747:RNA, Chloroplast; D000077278:RNA, Mitochondrial; D016601:RNA-Binding Proteins; D012313:RNA; D012260:Ribonucleases