CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex

ELife
Brian BaeElizabeth A Campbell

Abstract

A key point to regulate gene expression is at transcription initiation, and activators play a major role. CarD, an essential activator in Mycobacterium tuberculosis, is found in many bacteria, including Thermus species, but absent in Escherichia coli. To delineate the molecular mechanism of CarD, we determined crystal structures of Thermus transcription initiation complexes containing CarD. The structures show CarD interacts with the unique DNA topology presented by the upstream double-stranded/single-stranded DNA junction of the transcription bubble. We confirm that our structures correspond to functional activation complexes, and extend our understanding of the role of a conserved CarD Trp residue that serves as a minor groove wedge, preventing collapse of the transcription bubble to stabilize the transcription initiation complex. Unlike E. coli RNAP, many bacterial RNAPs form unstable promoter complexes, explaining the need for CarD.

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Citations

Apr 2, 2016·Proceedings of the National Academy of Sciences of the United States of America·Bin LiuThomas A Steitz
Jun 11, 2016·Science·Yu FengRichard H Ebright
Oct 19, 2016·Transcription·Yuhong Zuo, Thomas A Steitz
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Dec 28, 2019·Transcription·Hande BoyaciElizabeth A Campbell
Nov 25, 2016·Frontiers in Molecular Biosciences·Jookyung Lee, Sergei Borukhov
Sep 30, 2020·Nature Chemical Biology·Chengli FangYu Zhang
Sep 8, 2017·Frontiers in Microbiology·Lei PanGraciela L Lorca
Nov 11, 2020·Proceedings of the National Academy of Sciences of the United States of America·Kemardo K HenryRichard L Gourse
Dec 2, 2020·Nature Communications·Sung-Hoon JunKatsuhiko S Murakami
Oct 31, 2020·Nature Reviews. Microbiology·James ChenElizabeth A Campbell
Feb 20, 2021·Proceedings of the National Academy of Sciences of the United States of America·Marie DelabyPatrick H Viollier
Jun 22, 2021·Journal of Bacteriology·Kemardo K HenryRichard L Gourse

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Methods Mentioned

BETA
Synthetic oligonucleotides
electrophoresis
X-ray
gel filtration
column chromatography

Software Mentioned

Xtriage
HKL2000
DNASTAR
Blast
ClustalW
Autobuild
TriLINK
Eco
MegAlign
Structural Biology Grid portal

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