Identification of a 67 kDa protein that binds specifically to the pre-rRNA primary processing site in a higher plant

Mutation of the pentatricopeptide repeat-SMR protein SVR7 impairs accumulation and translation of chloroplast ATP synthase subunits in Arabidopsis thaliana

RNA processing, RNA editing, RNA splicing and translational activation of RNAs are essential post-transcriptional steps in chloroplast gene expression. Typically, the factors mediating those processes are nuclear encoded and post-translationally imported into the chloroplasts. In land plants, members of the large pentatricopeptide repeat (PPR) protein family are required for individual steps in chloroplast RNA processing. Interestingly, a subgroup of PPR proteins carries a C-terminal small MutS related (SMR) domain. Here we analyzed the consequences of mutations in the SVR7 gene, which encodes a PPR-SMR protein, in Arabidopsis thaliana. We demonstrate that SVR7 mutations lead to a specific reduction in chloroplast ATP synthase levels. Furthermore, we found aberrant transcript patterns for ATP synthase coding mRNAs in svr7 mutants. Finally, a reduced ribosome association of atpB/E and rbcL mRNAs in svr7 mutants suggests the involvement of the PPR-SMR protein SVR7 in translational activation of these mRNAs. We describe that the function of SVR7 in translation has expanded relative to its maize ortholog ATP4. The results provide evidence for a relaxed functional conservation of this PPR-SMR protein in eudicotyledonous and monocotyledonous plants, thus adding to the knowledge about the function and evolution of PPR-SMR proteins.

An Arabidopsis pentatricopeptide repeat protein, SUPPRESSOR OF VARIEGATION7, is required for FtsH-mediated chloroplast biogenesis

The Arabidopsis (Arabidopsis thaliana) yellow variegated2 (var2) mutant has green- and white-sectored leaves due to loss of VAR2, a subunit of the chloroplast FtsH protease/chaperone complex. Suppressor screens are a valuable tool to gain insight into VAR2 function and the mechanism of var2 variegation. Here, we report the molecular characterization of 004-003, a line in which var2 variegation is suppressed. We found that the suppression phenotype in this line is caused by lack of a chloroplast pentatricopeptide repeat (PPR) protein that we named SUPPRESSOR OF VARIEGATION7 (SVR7). PPR proteins contain tandemly repeated PPR motifs that bind specific RNAs, and they are thought to be central regulators of chloroplast and mitochondrial nucleic acid metabolism in plants. The svr7 mutant has defects in chloroplast ribosomal RNA (rRNA) processing that are different from those in other svr mutants, and these defects are correlated with reductions in the accumulation of some chloroplast proteins, directly or indirectly. We also found that whereas var2 displays a leaf variegation phenotype at 22°C, it has a pronounced chlorosis phenotype at 8°C that is correlated with defects in chloroplast rRNA processing and a drastic reduction in chloroplast protein accumulation. Surprisingly, the cold-induced phenotype of var2 cannot be suppressed by svr7. Our results strengthen the previously established linkage between var2 variegation and chloroplast rRNA processing/chloroplast translation, and they also point toward the possibility that VAR2 mediates different activities in chloroplast biogenesis at normal and chilling temperatures.

A chloroplastic RNA-binding protein is a new member of the PPR family

P67, a new protein binding to a specific RNA probe, was purified from radish seedlings [Echeverria, M. and Lahmy, S. (1995) Nucleic Acids Res. 23, 4963-4970]. Amino acid sequence information obtained from P67 microsequencing allowed the isolation of genes encoding P67 in radish and Airabidopsis thaliana. Immunolocalisation experiments in transfected protoplasts demonstrated that this protein is addressed to the chloroplast. The RNA-binding activity of recombinant P67 was found to be similar to that of the native protein. A significant similarity with the maize protein CRP1 [Fisk, D.G., Walker, M.B. and Barkan, A. (1999) EMBO J. 18, 2621-2630] suggests that P67 belongs to the PPR family and could be involved in chloroplast RNA processing.

Two ribosomal DNA-binding factors interact with a cluster of motifs on the 5' external transcribed spacer, upstream from the primary pre-rRNA processing site in a higher plant

In radish the primary processing site in pre-rRNA has been mapped to a TTTTCGCGC sequence (motif P) in the 5' external transcribed spacer (5' ETS) of the ribosomal DNA (rDNA) [Delcasso-Tremousaygue, D., Grellet, F., Panabières, F., Ananiev, E. & Delseny, M. (1988) Eur. J. Biochem. 172, 767-776]. The processing site is just downstream of four similar motifs named A1, A2, A3 and B. The five motifs constitute cluster A123BP. We have described previously that in radish extracts a nuclear protein, nuclear factor B (NF B) specifically binds to motif B [Echeverría, M., Penon, P. & Delseny, M. (1994) Mol. Gen. Genet. 243, 442-452]. Here, by means of electrophoretic-mobility-shift assays, we describe an rDNA-binding activity, nuclear factor D (NF D), that interacts with the A123BP cluster. Using various rDNA probes and competitors we show that NF D binds specifically to the A123 clustered motifs but not to similar B or P motifs. We used sequence-specific DNA-affinity chromatography to separate NF D from NF B. DNase I footprinting was used to map the binding site of NF D on the A123BP cluster and we compared it with that of NF B on the same probe. The footprint of NF D extends from the A1 motif to the 5' end of the NF B-binding site and includes motifs A2 and A3 on each strand. The footprinting of NF B is restricted to motif B and adjacent nucleotides. Thus the NF D-binding and NF B-binding sites are distinct but overlap. These two factors bind with a high specificity to the A123BP cluster in the radish 5' ETS. The possibility that these factors regulate rDNA transcription elongation at the level of the primary pre-rRNA processing site in crucifers is discussed.