Ribonuclease P from plant nuclei and photosynthetic organelles

A single Arabidopsis organellar protein has RNase P activity

The ubiquitous endonuclease RNase P is responsible for the 5' maturation of tRNA precursors. Until the discovery of human mitochondrial RNase P, these enzymes had typically been found to be ribonucleoproteins, the catalytic activity of which is associated with the RNA component. Here we show that, in Arabidopsis thaliana mitochondria and plastids, a single protein called 'proteinaceous RNase P' (PRORP1) can perform the endonucleolytic maturation of tRNA precursors that defines RNase P activity. In addition, PRORP1 is able to cleave tRNA-like structures involved in the maturation of plant mitochondrial mRNAs. Finally, we show that Arabidopsis PRORP1 can replace the bacterial ribonucleoprotein RNase P in Escherichia coli cells. PRORP2 and PRORP3, two paralogs of PRORP1, are both localized in the nucleus.

In vitro and in vivo processing of cyanelle tmRNA by RNase P

Ribonuclease P, the ubiquitous endonuclease required for generating mature tRNA 5' ends, is a ribonucleoprotein in most organisms and organelles, with the exception of mitochondria and chloroplasts of multicellular organisms. The cyanelle of the primitive alga Cyanophora paradoxa is the only photosynthetic organelle where the ribonucleoprotein nature of this enzyme has been functionally proven. tmRNA is another highly structured RNA: it can be aminoacylated with alanine, which is then incorporated into a tag peptide encoded on the same RNA molecule. This dual-function RNA has been found in bacteria, and its gene is also present in mitochondria and plastids from primitive organisms. Since nothing is known about the expression of this RNA in organelles, we have performed processing studies and determined the promoter of cyanelle pre-tmRNA. This RNA is transcribed as a precursor molecule in vivo. Synthetic transcripts of cyanelle pre-tmRNA, including or lacking the mature 3' CCA-end, are efficiently and correctly processed in vitro by bacterial RNase P ribo- and holoenzymes and by the homologous cyanelle RNase P. In addition to these experimental data, we propose a novel secondary structure model for this organellar tmRNA, which renders it more similar to its bacterial counterpart.

Cyanelle RNase P: RNA structure analysis and holoenzyme properties of an organellar ribonucleoprotein enzyme

The cyanelle of the primitive alga Cyanophora paradoxa is the only photosynthetic organelle where the ribonucleoprotein nature of ribonuclease P has been functionally proven. To increase our knowledge about RNA structure and overall composition of this enzyme, we have now determined relevant physical parameters and performed RNA accessibility experiments. Buoyant density and relative molecular mass of cyanelle RNase P were more similar to the eukaryotic (nuclear or mitochondrial) than to the bacterial enzyme type, despite the close phylogenetic relationship between plastids and cyanobacteria. Enzymatic and chemical probing was used to establish the secondary structure of cyanelle RNase P RNA. The results obtained with the naked transcript support the previously proposed, phylogenetically derived structure. Probing of the RNA in the holoenzyme resulted in reduced sensitivity at a large number of positions, indicating that these regions might be located in the interior of the ribonucleoprotein. Protection of the RNA in cyanelle RNase P was more extensive than reported for the Escherichia coli holoenzyme, but similar to the pattern observed in yeast nuclear RNase P. Taken together, these results indicate that the protein contribution in cyanelle RNase P is much larger than in the bacterial enzymes, and that the overall composition of the holoenzyme resembles that found in eukaryotes.

RNase P RNA from Prochlorococcus marinus: contribution of substrate domains to recognition by a cyanobacterial ribozyme

The molecular organisation of the Prochlorococcus marinus rnpB gene and the catalytic activity of the encoded RNA were characterised. Kinetic parameters for several pre-tRNA substrates were comparable to those from other eubacterial RNase P RNAs, although unusually high cation concentrations were required. The CCA-end of pre-tRNAs is essential for efficient turnover despite the lack of the canonical binding motif in P. marinus RNase P RNA. A trnR gene is located only 38 nt upstream the rnpB 5' end on the complementary strand. This arrangement resembles those in the plastids of Cyanophora and Porphyra but not in any other bacterium.

Sequence and functional characterization of RNase P RNA from the chl alb containing cyanobacterium Prochlorothrix hollandica

Only a few complete sequences and very limited functional data are available for the catalytic RNA component of cyanobacterial RNase P. The RNase P RNA from the chl alb containing cyanobacterium Prochlorothrix hollandica belongs to a rarely found structural subtype with an extended P15/16 domain. We have established conditions for optimal in vitro ribozyme activity, and determined the kinetic parameters for cleavage of pre-tRNA(Tyr). Analysis of pre-tRNA mutants revealed that the T-stem sequence only plays a modulating role, whereas the CCA end is essential for efficient product formation.