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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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A model for the hypothetical function of RapA: the disruption of non-canonical DNA–RNA complexes in transcription. See text for a detailed discussion of this model.
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Figure 9: A model for the hypothetical function of RapA: the disruption of non-canonical DNA–RNA complexes in transcription. See text for a detailed discussion of this model.

Mentions: In summary, we propose that RapA remodels RNA–DNA and/or RNA–RNA polymerase complexes during transcription; this remodeling may ultimately contribute to transcript release. Our previously proposed, general model for RapA catalysis [(23); Figure 8 therein] thus remains correct; however, we have shifted emphasis from the possible destabilization of RNA polymerase–DNA complexes to remodeling of RNA–RNA polymerase and RNA–DNA complexes. We also propose that this hypothetical role of RapA in RNA remodeling may include the disruption of salt-stabilized non-canonical DNA–RNA complexes (putative DNA–RNA triplexes) (Figure 9); this activity likely accounts for pronounced slow-growth phenotype of the rapA deletion mutant (Figure 9, left panels; also, ref. 23), thus explaining the salt-selectivity of the in vitro and in vivo data.Figure 9.


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)

A model for the hypothetical function of RapA: the disruption of non-canonical DNA–RNA complexes in transcription. See text for a detailed discussion of this model.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 9: A model for the hypothetical function of RapA: the disruption of non-canonical DNA–RNA complexes in transcription. See text for a detailed discussion of this model.
Mentions: In summary, we propose that RapA remodels RNA–DNA and/or RNA–RNA polymerase complexes during transcription; this remodeling may ultimately contribute to transcript release. Our previously proposed, general model for RapA catalysis [(23); Figure 8 therein] thus remains correct; however, we have shifted emphasis from the possible destabilization of RNA polymerase–DNA complexes to remodeling of RNA–RNA polymerase and RNA–DNA complexes. We also propose that this hypothetical role of RapA in RNA remodeling may include the disruption of salt-stabilized non-canonical DNA–RNA complexes (putative DNA–RNA triplexes) (Figure 9); this activity likely accounts for pronounced slow-growth phenotype of the rapA deletion mutant (Figure 9, left panels; also, ref. 23), thus explaining the salt-selectivity of the in vitro and in vivo data.Figure 9.

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