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Important role of the tetraloop region of 4.5S RNA in SRP binding to its receptor FtsY

Published online by Cambridge University Press:  07 February 2001

JUNUTULA R. JAGATH
Affiliation:
Institute of Molecular Biology, University of Witten/Herdecke, D-58448 Witten, Germany Present address: Department of Molecular and Cellular Physiology, Beckman Center, B-137, Stanford University Medical Center, Stanford, California 94305-5345, USA.
NATALIA B. MATASSOVA
Affiliation:
Institute of Molecular Biology, University of Witten/Herdecke, D-58448 Witten, Germany Present address: RiboTargets Ltd., Granta Park, Abington, Cambridge CB1 6GB, United Kingdom.
ERIK DE LEEUW
Affiliation:
Department of Molecular Microbiology, Institute of Molecular Biological Sciences, Biocentrum, Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam
JENS M. WARNECKE
Affiliation:
Institute of Molecular Biology, University of Witten/Herdecke, D-58448 Witten, Germany
GEORG LENTZEN
Affiliation:
Institute of Molecular Biology, University of Witten/Herdecke, D-58448 Witten, Germany Present address: RiboTargets Ltd., Granta Park, Abington, Cambridge CB1 6GB, United Kingdom.
MARINA V. RODNINA
Affiliation:
Institute of Physical Biochemistry, University of Witten/Herdecke, D-58448 Witten, Germany
JOEN LUIRINK
Affiliation:
Department of Molecular Microbiology, Institute of Molecular Biological Sciences, Biocentrum, Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam
WOLFGANG WINTERMEYER
Affiliation:
Institute of Molecular Biology, University of Witten/Herdecke, D-58448 Witten, Germany
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Abstract

Binding of Escherichia coli signal recognition particle (SRP) to its receptor, FtsY, requires the presence of 4.5S RNA, although FtsY alone does not interact with 4.5S RNA. In this study, we report that the exchange of the GGAA tetraloop sequence in domain IV of 4.5S RNA for UUCG abolishes SRP-FtsY interaction, as determined by gel retardation and membrane targeting experiments, whereas replacements with other GNRA-type tetraloops have no effect. A number of other base exchanges in the tetraloop sequence have minor or intermediate inhibitory effects. Base pair disruptions in the stem adjacent to the tetraloop or replacement of the closing C-G base pair with G-C partially restored function of the otherwise inactive UUCG mutant. Chemical probing by hydroxyl radical cleavage of 4.5S RNA variants show that replacing GGAA with UUCG in the tetraloop sequence leads to structural changes both within the tetraloop and in the adjacent stem; the latter change is reversed upon reverting the C-G closing base pair to G-C. These results show that the SRP-FtsY interaction is strongly influenced by the structure of the tetraloop region of SRP RNA, in particular the tetraloop stem, and suggest that both SRP RNA and Ffh undergo mutual structural adaptation to form SRP that is functional in the interaction with the receptor, FtsY.

Type
Research Article
Copyright
2001 RNA Society

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