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Nucleic Acids Research Advance Access published online on January 9, 2009
Nucleic Acids Research, doi:10.1093/nar/gkn1078
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

Insights into the architecture and stoichiometry of Escherichia coli PepA•DNA complexes involved in transcriptional control and site-specific DNA recombination by atomic force microscopy

Phu Nguyen Le Minh1, Neel Devroede1, Jan Massant1, Dominique Maes2 and Daniel Charlier1,*

1Erfelijkheidsleer en Microbiologie and 2Laboratorium voor Ultrastructuur, Vrije Universiteit Brussel (VUB) and Vlaams Interuniversitair Instituut voor Biotechnologie (VIB), Pleinlaan 2, B-1050 Brussel, Belgium

*To whom correspondence should be addressed. Tel: + 32 2 629 1342; Fax: + 32 2 629 1345; Email: dcharlie{at}vub.ac.be

Received August 4, 2008. Revised December 23, 2008. Accepted December 23, 2008.

Multifunctional Aminopeptidase A (PepA) from Escherichia coli is involved in the control of two distinct DNA transaction processes: transcriptional repression of the carAB operon, encoding carbamoyl phosphate synthase and site-specific resolution of ColE1-type plasmid multimers. Both processes require communication at a distance along a DNA molecule and PepA is the major structural component of the nucleoprotein complexes that underlie this communication. Atomic Force Microscopy was used to analyze the architecture of PepA·carAB and PepA·cer site complexes. Contour length measurements, bending angle analyses and volume determinations demonstrate that the carP1 operator is foreshortened by ~235 bp through wrapping around one PepA hexamer. The highly deformed part of the operator extends from slightly upstream of the –35 hexamer of the carP1 promoter to just downstream of the IHF-binding site, and comprises the binding sites for the PurR and RutR transcriptional regulators. This extreme remodeling of the carP1 control region provides a straightforward explanation for the strict requirement of PepA in the establishment of pyrimidine and purine-specific repression of carAB transcription. We further provide a direct physical proof that PepA is able to synapse two cer sites in direct repeat in a large interwrapped nucleoprotein complex, likely comprising two PepA hexamers.


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