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Nucleic Acids Research, 2000, Vol. 28, No. 22 4497-4505
© 2000 Oxford University Press

Conformational changes induced in the Saccharomyces cerevisiae GTPase-associated rRNA by ribosomal stalk components and a translocation inhibitor

Carlos Briones and Juan P. G. Ballesta*

Centro de Biología Molecular ‘Severo Ochoa’, Consejo Superior de Investigaciones Científicas y Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain

The yeast ribosomal GTPase associated center is made of parts of the 26S rRNA domains II and VI, and a number of proteins including P0, P1{alpha}, P1ß, P2{alpha}, P2ß and L12. Mapping of the rRNA neighborhood of the proteins was performed by footprinting in ribosomes from yeast strains lacking different GTPase components. The absence of protein P0 dramatically increases the sensitivity of the defective ribosome to degradation hampering the RNA footprinting. In ribosomes lacking the P1/P2 complex, protection of a number of nucleotides is detected around positions 840, 880, 1100, 1220–1280 and 1350 in domain II as well as in several positions in the domain VI {alpha}-sarcin region. The protection pattern resembles the one reported for the interaction of elongation factors in bacterial systems. The results exclude a direct interaction of these proteins with the rRNA and are compatible with an increase in the ribosome affinity for EF-2 in the absence of the acidic P proteins. Interestingly, a sordarin derivative inhibitor of EF-2 causes an opposite effect, increasing the reactivity in positions protected by the absence of P1/P2. Similarly, a deficiency in protein L12 exposes nucleotides G1235, G1242, A1262, A1269, A1270 and A1272 to chemical modification, thus situating the protein binding site in the most conserved part of the 26S rRNA, equivalent to the bacterial protein L11 binding site.

* To whom correspondence should be addressed. Tel: +34 91 397 5076; Fax: +34 91 397 4799; Email: jpgballesta{at}cbm.uam.es Present address: Carlos Briones, Centro de Astrobiología, INTA-CSIC, Carretera de Ajalvir km 4, 28850 Torrejón de Ardoz, Madrid, Spain


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