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

McKinley BA, Sukhodolets MV - Nucleic Acids Res. (2007)

Bottom Line: 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.

View Article: PubMed Central - PubMed

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

ABSTRACT
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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Three plausible mechanisms explaining the RapA-mediated remodeling of non-productive post-termination complexes (23). See text for a detailed description of each of the indicated models.
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Figure 1: Three plausible mechanisms explaining the RapA-mediated remodeling of non-productive post-termination complexes (23). See text for a detailed description of each of the indicated models.

Mentions: Previously, it was demonstrated that excess RapA can promote transcriptional cycling via some undetermined means of remodeling post-termination, DNA–RNA polymerase–RNA ternary complexes (23). However, it is unclear which component(s) of the ternary, post-termination DNA–RNA polymerase–RNA complex (PTC) are targeted by RapA. In principle, RapA may (i) facilitate the release of nascent RNA from RNA polymerase (Model 1, Figure 1A), (ii) promote the release of RNA polymerase (with or without nascent RNA) from DNA (Model 2, Figure 1B), and/or (iii) stimulate transcriptional cycling by means of disrupting non-productive DNA–RNA complexes, irrespective of either the DNA-bound or free status of the polymerase (Model 3, Figure 1C). [Factors that may potentially hinder transcriptional cycling are summarized in our recent study (26).] (iv) Alternatively, RapA activity can be described as a combination of Models 1 through 3 (particularly 1 and 3). In this study, we carried out experiments to clarify the mechanistic aspects of RapA catalysis in terms of its general compatibility with one or more of the aforementioned models.Figure 1.


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

McKinley BA, Sukhodolets MV - Nucleic Acids Res. (2007)

Three plausible mechanisms explaining the RapA-mediated remodeling of non-productive post-termination complexes (23). See text for a detailed description of each of the indicated models.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2175355&req=5

Figure 1: Three plausible mechanisms explaining the RapA-mediated remodeling of non-productive post-termination complexes (23). See text for a detailed description of each of the indicated models.
Mentions: Previously, it was demonstrated that excess RapA can promote transcriptional cycling via some undetermined means of remodeling post-termination, DNA–RNA polymerase–RNA ternary complexes (23). However, it is unclear which component(s) of the ternary, post-termination DNA–RNA polymerase–RNA complex (PTC) are targeted by RapA. In principle, RapA may (i) facilitate the release of nascent RNA from RNA polymerase (Model 1, Figure 1A), (ii) promote the release of RNA polymerase (with or without nascent RNA) from DNA (Model 2, Figure 1B), and/or (iii) stimulate transcriptional cycling by means of disrupting non-productive DNA–RNA complexes, irrespective of either the DNA-bound or free status of the polymerase (Model 3, Figure 1C). [Factors that may potentially hinder transcriptional cycling are summarized in our recent study (26).] (iv) Alternatively, RapA activity can be described as a combination of Models 1 through 3 (particularly 1 and 3). In this study, we carried out experiments to clarify the mechanistic aspects of RapA catalysis in terms of its general compatibility with one or more of the aforementioned models.Figure 1.

Bottom Line: 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.

View Article: PubMed Central - PubMed

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

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus