COMPARATIVE PHOTOCROSS-LINKING ANALYSIS OF THE TERTIARY STRUCTURES OFESCHERICHIA-COLI AND BACILLUS-SUBTILIS RNASE-P RNAS

Bacterial ribonuclease P contains a catalytic RNA subunit that cleaves precursor sequences from the 5' ends of pre-tRNAs, The RNase P RNAs f rom Bacillus subtilis and Escherichia coli each contain several unique secondary structural elements not present in the other, To understand better how these phylogenetically variable elements affect the global architecture of the ribozyme, photoaffinity cross-linking studies wer e carried out, Photolysis of photoagents attached at homologous sites in the two RNAs results in nearly identical cross-linking patterns, co nsistent with the homology of the RNAs and indicating that these RNAs contain a common, core tertiary structure, Distance constraints were u sed to derive tertiary structure models using a molecular mechanics-ba sed modeling protocol, The resulting superimposition of large sets of equivalent models provides a low resolution (5-10 Angstrom) structure for each RNA, Comparison of these structure models shows that the cons erved core helices occupy similar positions in space, Variably present helical elements that may play a role in global structural stability are found at the periphery of the core structure, The P5.1 and P15.1 h elical elements, unique to the B. subtilis RNase P RNA, and the P6/16/ 17 helices, unique to the E. coli RNA, occupy similar positions in the structure models and, therefore, may have analogous structural functi on.