Disease relevance of rnpB

• Mutant RNase P RNA alleles (rnpBC292 and rnpBC293) caused severe growth defects in the E. coli rnpB mutant strain DW2 and abolished growth in the newly constructed mutant strain BW, in which chromosomal rnpB expression strictly depended on the presence of arabinose [1].
• Modification of nucleotides 330-332 in the J15/16 loop of Synechocystis RNase P RNA from GGU to CCA has a modest effect on kcat for CCA-containing substrates and has no effect on cleavage-site selection [2].
• Phylogenetic comparative analyses of RNase P RNA-encoding gene sequences from Chlorobium limicola, Chlorobium tepidum, Bacteroides thetaiotaomicron, and Flavobacterium yabuuchiae refine the secondary structure model of the general (eu)bacterial RNase P RNA and show that a highly conserved feature of that RNA is not essential [3].
• To verify that the RNase P RNA gene was analyzed, a modified, putative gene was cloned adjacent to a bacteriophage T7 promoter and various transcripts were tested for RNase P activity [4].
• RNase P RNA from T. thermophilus cleaved a pre-tRNA(Tyr) from E. coli with highest efficiency between 55 degrees C and 65 degrees C. The T. thermophilus RNA, which has a G-C content of 86% in helical regions, displays several structural idiosyncrasies, although its secondary structure is similar to that of proteobacteria [5].

High impact information on rnpB

• This feature strongly constrains the three-dimensional structure of RNase P RNA near the active site [6].
• The bacterial RNase P protein is required to activate bacterial RNase P RNA in vivo, but previous studies have yielded contradictory conclusions regarding its specific functions [7].
• Manganese rescue at positions U69, C70, A130 and A132 identified, for the first time, sites of direct metal ion coordination in RNase P RNA [8].
• Base pairing between Escherichia coli RNase P RNA and its substrate [9].
• RNase P RNA was modified with dimethylsulfate or kethoxal in the presence or absence of tRNA, and sites of modification were detected by primer extension [10].

Chemical compound and disease context of rnpB

• Efficient cleavage of pre-tRNAs by E. coli RNAse P RNA requires the 2'-hydroxyl of the ribose at the cleavage site [11].
• Fidelity in tRNA processing by the RNase P RNA from Escherichia coli depends, in part, on interactions with the nucleobase and 2' hydroxyl group of N(-1), the nucleotide immediately upstream of the site of RNA strand cleavage [12].
• Here, we describe our studies on the folding of the M1 RNA sub-unit of Escherichia coli RNase P. We performed kinetic footprinting studies of M1 RNA folding with the chemical footprinting reagent peroxynitrous acid to provide a detailed description of the folding pathway of RNase P RNA [13].
• Purine N7 groups that are crucial to the interaction of Escherichia coli rnase P RNA with tRNA [14].
• Furthermore, addition of manganese enhances pre-tRNA cleavage catalyzed by B. subtilis RNase P RNA containing an Sp phosphorothioate modification at A49, as observed for Escherichia coli P RNA [Christian et al., RNA, 2000, 6:511-519], suggesting that an essential metal ion may be coordinated at this site [15].

Biological context of rnpB

• Cell growth could be rescued when expressing a second bacterial RNase P RNA with an unrelated sequence in the target region [16].
• The P4 metal binding site in RNase P RNA affects active site metal affinity through substrate positioning [17].
• Unlike 16S rRNA phylogeny that has placed the Aquificales as the deepest lineage of the bacterial phylogenetic tree, RNase P RNA-based phylogeny groups S. azorense and P. marina with the green sulfur, cyanobacterial, and delta/epsilon proteobacterial branches [18].
• Base pairing between the substrate and the ribozyme has previously been shown to be essential for catalytic activity of most ribozymes, but not for RNase P RNA [9].
• The nucleotide sequence of the gene and its surroundings was determined from the cloned DNA and by directly sequencing or reverse transcribing the RNase P RNA [4].

Anatomical context of rnpB

• The plastid (cyanelle) from the Glaucocystophyceae alga Cyanophora paradoxa contains an RNase P RNA subunit (P RNA) similar to the cyanobacterial P RNA [19].

Associations of rnpB with chemical compounds

• Studies of lead(II)-induced cleavage of RNase P RNA suggested that binding of neomycin B interfered with the binding of divalent metal ions to the RNA [20].
• The results suggest that G350 contributes to Mg(2+) binding at helix P4 of RNase P RNA [21].
• Lead-ion-induced cleavage of RNase P RNA [22].

Physical interactions of rnpB

• The photoagent (azidophenacyl) was coupled uniquely to the 5'-thiophosphate of the tRNA, the site of action by RNase P. The photoagent-containing tRNA binds to RNase P RNA and is cross-linked by UV irradiation to it at high efficiency (10-30%) [23].

Enzymatic interactions of rnpB

• Moreover, a deletion of the RNase P protein motif significantly reduces the ability of Hera to hydrolyze ATP in the presence of RNase P RNA [24].

Other interactions of rnpB

• The RNase P RNA (rnpB) and protein (rnpA) genes were identified in the two Aquificales Sulfurihydrogenibium azorense and Persephonella marina [18].
• Thus, the rnpB genes from these organisms are capable of functioning as the sole source of RNase P RNA in E. coli [25].
• The tRNA processing endonuclease ribonuclease P contains an essential and highly conserved RNA molecule (RNase P RNA) that is the catalytic subunit of the enzyme [26].

References