Analysis of pentatricopeptide repeat proteins in vivo: target RNAs and functions
Final Report Abstract
This Emmy Noether project focused initially on the functional analysis of a set of PPR proteins essential for embryo development in Arabidopsis. By combining reverse genetic analyses in maize with the identification of RNA ligands of PPR proteins using RIP-Chip, we could demonstrate that these PPR proteins are required for chloroplast translation. From here, several novel projects have radiated. First, we investigated the evolution of RNA editing, a process mediated by PPR proteins. We developed tools to determine RNA editing on a transcriptome-wide scale quantitatively and looked at individual RNA editing sites across angiosperm evolution. These analyses demonstrated that RNA editing sites are not only frequently lost (as known from the literature), but also that RNA editing sites are gained. Our data suggest that promiscuous binding of PPR proteins to novel sites can lead to the emergence of new editing events. Second, we identified a large number (>130) of short RNAs (sRNAs) in chloroplast and mitochondrial transcriptomes and demonstrated that most if not all are caused by the protective action of PPR proteins. We are currently testing whether these sRNAs could be regulators of gene expression like so many short RNAs in bacterial and eukaryotic systems. Third, we became interested in the chloroplast splicing factor MatK, one of the chloroplast open reading frames essential for plant cell development. We demonstrated by combining chloroplast transplastomics with RIP-Chip that MatK associates specifically with seven group IIA introns. This project has led to the acquisition of funding independent of the Emmy Noether project. Fourth, since our data and other studies suggested that most PPR proteins are rather part of the basic RNA processing machinery but unlikely to be true regulators of plant organellar gene expression, we turned to a different family of chloroplast RNA binding proteins, the cpRNPs. We identified functions and RNA targets of these highly regulated proteins and recently demonstrated their importance for plant cold tolerance. The link between the chloroplast and cold tolerance holds the promise for projects with applications for agricultural sciences. This project has also led to the acquisition of funding independent of the Emmy Noether project.
Publications
- (2006). A pentatricopeptide repeat protein facilitates the trans-splicing of the maize chloroplast rps12 pre-mRNA. Plant Cell. 18:2650-2663
Schmitz-Linneweber C, Williams-Carrier R, Williams-Voelker PM, Kroeger, TS, Vichas, A, and Barkan A
- (2006). Conservation of Plastid RNA editing factors independently of their target sites. EMBO Rep. 7(3):308-13
Tillich M, Poltnigg P, Kushnir S, and Schmitz-Linneweber C
- (2007). RNA splicing and RNA editing in chloroplasts. In: Plastid Development. Topics in Current Genetics. (R. Bock, ed.) Springer, Berlin, Heidelberg. 19, 213-248
Schmitz-Linneweber C, and Barkan, A
- (2008) Pentatricopeptide repeat proteins – a socket set for organelle gene expression. Trends Plant Sci. 13:663-670
Schmitz-Linneweber C and Small I
- (2008). On the expansion of the pentatricopeptide repeat gene family in plants: Mol Biol Evol. 25:1120-1128
O’Toole N, Hattori M, Andres C, Iida K, Lurin C, Schmitz-Linneweber C, Sugita M, and Small I
- (2008). The pentatricopeptide repeat protein PPR5 stabilizes a specific tRNA precursor in maize chloroplasts. Mol Cell Biol; 28:5337-5347
Beick S, Schmitz-Linneweber C, Williams-Carrier R, Jensen B, and Barkan A
- (2009) Chloroplast ribonucleoprotein CP31A is required for editing and stability of specific chloroplast mRNAs. Proc Natl Acad Sci USA 106:6002-6007
Tillich M, Hardel S, Kupsch C, Armbruster U, Delannoy E, Gualberto J, Lehwark P, Leister D, Small I, and Schmitz-Linneweber C
- (2009) Frequent Losses and a Rare Gain of Chloroplast RNA Editing Sites in Seed Plants. BMC Evol Biol 9:201
Tillich M, Le Sy V, Schulerowitz K, von Haeseler A, Maier U, and Schmitz-Linneweber C
- (2010) Chloroplast RNA binding proteins: Repair and regulation of chloroplast transcripts. RNA Biology 7:172-8
Tillich M, Beick S, Schmitz-Linneweber C
- (2010) RNA Binding Proteins for Chloroplast RNA Processing. In: Plant Mitochondria (R. Kempken, ed.). Advances in Plant Biology; Springer, New York; 1, 177-206
Zoschke R, Kupsch C, and Schmitz-Linneweber C
- (2011) The RNA-recognition motif in chloroplasts. J Plant Physiol. 168:1361-71
Ruwe H, Kupsch C, Teubner M, Schmitz-Linneweber C
- (2012) Mutation of the pentatricopeptide repeat-SMR protein SVR7 impairs accumulation and translation of chloroplast ATP synthase subunits in Arabidopsis thaliana. J Plant Res. 2012 Oct 18
Zoschke R, Qu Y, Zubo YO, Börner T, Schmitz-Linneweber C
(See online at https://doi.org/10.1007/s10265-012-0527-1) - (2012) Short non-coding RNA fragments accumulating in chloroplasts: footprints of RNA binding proteins? Nucleic Acids Res. 40:3106-16
Ruwe H, Schmitz-Linneweber C
(See online at https://doi.org/10.1093/nar/gkr1138) - (2012) The Pentatricopeptide Repeat-SMR Protein ATP4 promotes translation of the chloroplast atpB/E mRNA. Plant J. 72:547–558
Zoschke R, Kroeger T, Belcher S, Schöttler MA, Barkan A, Schmitz-Linneweber C
(See online at https://doi.org/10.1111/j.1365-313X.2012.05081.x)
