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Nucleic Acids Research Advance Access published online on October 2, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm747
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© 2007 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.

Nucleic Acid Enzymes

Escherichia coli RNA polymerase-associated SWI/SNF protein RapA: evidence for RNA-directed binding and remodeling activity

Brian A. McKinley and Maxim V. Sukhodolets*

Laboratory of Biochemistry, Department of Chemistry, Lamar University, Beaumont, TX 77710, USA

*To whom correspondence should be addressed. Tel: +1 409 880 7905 (office) +1 409 880 7906 (laboratory); Fax: +1 409 880 8270; Email: msoukhodol{at}my.lamar.edu

Received May 21, 2007. Revised August 22, 2007. Accepted September 10, 2007.

Helicase-like SWI/SNF proteins are present in organisms belonging to distant kingdoms from bacteria to humans, indicating that they perform a very basic and ubiquitous form of nucleic acid management; current studies associate the activity of SWI/SNF proteins with remodeling of DNA and DNA–protein complexes. The bacterial SWI/SNF homolog RapA—an integral part of the Escherichia coli RNA polymerase complex—has been implicated in remodeling post-termination DNA–RNA polymerase–RNA ternary complexes (PTC), however its explicit nucleic acid substrates and mechanism remain elusive. Our work presents evidence indicating that RNA is a key substrate of RapA. Specifically, the formation of stable RapA–RNA intermediates in transcription and other, independent lines of evidence presented herein indicate that RapA binds and remodels RNA during transcription. Our results are consistent with RapA promoting RNA release from DNA–RNA polymerase–RNA ternary complexes; this process may be accompanied by the destabilization of non-canonical DNA–RNA complexes (putative DNA–RNA triplexes). Taken together, our data indicate a novel RNA remodeling activity for RapA, a representative of the SWI/SNF protein superfamily.


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