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Pentatricopeptide repeat (PPR) proteins constitute a large family in land plants and are required for various post-transcriptional steps associated with RNA in plant organelles. The mossPhyscomitrella patensPPR protein, PpPPR_38, is a nuclear-encoded chloroplast protein and was previously shown to be involved in the maturation step of chloroplastclpPpre-mRNA. | A moss pentatricopeptide repeat protein binds to the 3 end of plastid clpP pre-mRNA and assists with mRNA maturation Mitsuru Hattori1 2 and Mamoru Sugita1 1 Center for Gene Research Nagoya University Japan 2 Department of Chemistry Schoolof Science The University of Tokyo Japan Keywords clpP Physcomitrella patens PPR protein RNA cleavage RNA stability Correspondence M. Sugita Center for Gene Research Nagoya University Nagoya 464-8602 Japan Fax 81 52 789 3080 Tel 81 52 789 3080 E-mail sugita@gene.nagoya-u.ac.jp Received 22 June 2009 revised 5 August 2009 accepted 7 August 2009 doi 10.1111 j.1742-4658.2009.07267.x Pentatricopeptide repeat PPR proteins constitute a large family in land plants and are required for various post-transcriptional steps associated with RNA in plant organelles. The moss Physcomitrella patens PPR protein PpPPR_38 is a nuclear-encoded chloroplast protein and was previously shown to be involved in the maturation step of chloroplast clpP pre-mRNA. To understand precisely the molecular function of PpPPR_38 we prepared recombinant PpPPR_38 protein and characterized it in maturation steps of clpP pre-mRNA. In vitro RNA-binding assays showed that the recombinant protein strongly bound to the clpP-5 -rps12 intergenic region which is highly AU-rich and includes an inverted repeat sequence potentially forming a stem-loop structure. Digestion of the bound RNA region by RNase V1 was significantly accelerated by the addition of the recombinant protein. This strongly suggests that the binding of PpPPR_38 facilitates the formation of a stable stem-loop structure. An in vitro degradation assay using chloroplast lysates gave rise to the possibility that the stable stem-loop structure formed by PpPPR_38 contributes the correct intergenic RNA cleavage and protection of mature clpP mRNA against 3 to 5 exoribonuclease. Because an RNA-binding assay also showed weak binding to the clpP first exon-intron region PpPPR_38 is likely to be related to the splicing of .
