TY - JOUR
T1 - Escherichia coli RNA polymerase-associated SWI/SNF protein RapA
T2 - Evidence for RNA-directed binding and remodeling activity
AU - Mckinley, Brian A.
AU - Sukhodolets, Maxim V.
N1 - Funding Information:
During the final stage of this work, Prof. Vitaly V. Sukhodolets—whose work was a key inspiration for the senior author’s own research with E. coli—passed away. I (M.V.S.) therefore dedicate this work to the memory of my father. M.V.S. is indebted to Sankar Adhya for support and help in establishing an independent research laboratory at Lamar University; this transition was also greatly enhanced by a generous gift of equipment and materials from NIH. We thank Karen Sukhodolets and multiple anonymous reviewers for helpful comments and suggestions. This work was supported in part by Grant Number R15GM081803 from the National Institute of General Medical Sciences (to M. V. S.) (the content of this study is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute Of General Medical Sciences or the National Institutes of Health), a Welch Foundation grant (V-0004), and departmental funds. Funding to pay the Open Access publication charges for this article was provided by Grant Number R15GM081803 from the National Institute of General Medical Sciences.
PY - 2007/12
Y1 - 2007/12
N2 - 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.
AB - 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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U2 - 10.1093/nar/gkm747
DO - 10.1093/nar/gkm747
M3 - Article
C2 - 17913745
AN - SCOPUS:37549059934
SN - 0305-1048
VL - 35
SP - 7044
EP - 7060
JO - Nucleic acids research
JF - Nucleic acids research
IS - 21
ER -