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Distinct modes of mature and precursor tRNA binding to Escherichia coli RNase P RNA revealed by NAIM analyses

Published online by Cambridge University Press:  09 April 2001

CORINNA HEIDE ,
SILKE BUSCH ,
RALPH FELTENS  and
ROLAND K. HARTMANN
CORINNA HEIDE
Affiliation:
Medizinische Universität zu Lübeck, Institut für Biochemie, D-23538 Lübeck, Germany
SILKE BUSCH
Affiliation:
Medizinische Universität zu Lübeck, Institut für Biochemie, D-23538 Lübeck, Germany Present address: Universitätsklinikum Tübingen, Institut für Pathologie, Abteilung Molekulare Pathologie, Liebermeisterstr. 8, 72076 Tübingen, Germany.
RALPH FELTENS
Affiliation:
Medizinische Universität zu Lübeck, Institut für Biochemie, D-23538 Lübeck, Germany
ROLAND K. HARTMANN
Affiliation:
Medizinische Universität zu Lübeck, Institut für Biochemie, D-23538 Lübeck, Germany
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Abstract

We have analyzed by nucleotide analog interference mapping (NAIM) pools of precursor or mature tRNA molecules, carrying a low level of Rp-RMPαS (R = A, G, I) or Rp-c7-deaza-RMPαS (R = A, G) modifications, to identify functional groups that contribute to the specific interaction with and processing efficiency by Escherichia coli RNase P RNA. The majority of interferences were found in the acceptor stem, T arm, and D arm, including the strongest effects observed at positions G19, G53, A58, and G71. In some cases (interferences at G5, G18, and G71), the affected functional groups are candidates for direct contacts with RNase P RNA. Several modifications disrupt intramolecular tertiary contacts known to stabilize the authentic tRNA fold. Such indirect interference effects were informative as well, because they allowed us to compare the structural constraints required for ptRNA processing versus product binding. Our ptRNA processing and mature tRNA binding NAIM analyses revealed overlapping but nonidentical patterns of interference effects, suggesting that substrate binding and cleavage involves binding modes or conformational states distinct from the binding mode of mature tRNA, the product of the reaction.

Keywords

c7-deaza-modificationsinosine modificationsnucleotide analog interference mapping (NAIM)ptRNA processing by E. coli RNase P RNAtRNA binding to E. coli RNase P RNA
Type
Research Article
Information
RNA , Volume 7 , Issue 4 , April 2001 , pp. 553 - 564
Copyright
© 2001 RNA Society

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