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Sequence-specific interaction between HIV-1 matrix protein and viral genomic RNA revealed by in vitro genetic selection

Published online by Cambridge University Press:  09 April 2001

PRAKASH PUROHIT ,
STEFAN DUPONT ,
MARIO STEVENSON  and
MICHAEL R. GREEN
PRAKASH PUROHIT
Affiliation:
Program in Gene Function and Expression, Howard Hughes Medical Institute, University of Massachusetts Medical Center, Worcester, Massachusetts 01605, USA Program in Molecular Medicine, University of Massachusetts Medical Center, Worcester, Massachusetts 01605, USA Present address: BioMerieux, Inc., 1022 Hingham Street, Rockland, Massachusetts 02370, USA.
STEFAN DUPONT
Affiliation:
Program in Gene Function and Expression, Howard Hughes Medical Institute, University of Massachusetts Medical Center, Worcester, Massachusetts 01605, USA Program in Molecular Medicine, University of Massachusetts Medical Center, Worcester, Massachusetts 01605, USA
MARIO STEVENSON
Affiliation:
Program in Molecular Medicine, University of Massachusetts Medical Center, Worcester, Massachusetts 01605, USA
MICHAEL R. GREEN
Affiliation:
Program in Gene Function and Expression, Howard Hughes Medical Institute, University of Massachusetts Medical Center, Worcester, Massachusetts 01605, USA Program in Molecular Medicine, University of Massachusetts Medical Center, Worcester, Massachusetts 01605, USA
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Abstract

The human immunodeficiency virus type-1 matrix protein (HIV-1 MA) is a multifunctional structural protein synthesized as part of the Pr55 gag polyprotein. We have used in vitro genetic selection to identify an RNA consensus sequence that specifically interacts with MA (Kd = 5 × 10−7 M). This 13-nt MA binding consensus sequence bears a high degree of homology (77%) to a region (nt 1433–1446) within the POL open reading frame of the HIV-1 genome (consensus sequence from 38 HIV-1 strains). Chemical interference experiments identified the nucleotides within the MA binding consensus sequence involved in direct contact with MA. We further demonstrate that this RNA–protein interaction is mediated through a stretch of basic amino acids within MA. Mutations that disrupt the interaction between MA and its RNA binding site within the HIV-1 genome resulted in a measurable decrease in viral replication.

Keywords

HIVin vitro selectionmatrix proteinRNA-protein interaction
Type
Research Article
Information
RNA , Volume 7 , Issue 4 , April 2001 , pp. 576 - 584
Copyright
© 2001 RNA Society

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