Crystal structure of an Escherichia coli Hfq Core (residues 2-69)-DNA complex reveals multifunctional nucleic acid binding sites

Nucleic Acids Research
Jillian OransRichard G Brennan

Abstract

Hfq regulates bacterial gene expression post-transcriptionally by binding small RNAs and their target mRNAs, facilitating sRNA-mRNA annealing, typically resulting in translation inhibition and RNA turnover. Hfq is also found in the nucleoid and binds double-stranded (ds) DNA with a slight preference for A-tracts. Here, we present the crystal structure of the Escherichia coli Hfq Core bound to a 30 bp DNA, containing three 6 bp A-tracts. Although previously postulated to bind to the 'distal' face, three statistically disordered double stranded DNA molecules bind across the proximal face of the Hfq hexamer as parallel, straight rods with B-DNA like conformational properties. One DNA duplex spans the diameter of the hexamer and passes over the uridine-binding proximal-face pore, whereas the remaining DNA duplexes interact with the rims and serve as bridges between adjacent hexamers. Binding is sequence-independent with residues N13, R16, R17 and Q41 interacting exclusively with the DNA backbone. Atomic force microscopy data support the sequence-independent nature of the Hfq-DNA interaction and a role for Hfq in DNA compaction and nucleoid architecture. Our structure and nucleic acid-binding studies also provide insight into the me...Continue Reading

References

May 5, 1988·Journal of Molecular Biology·C R CalladineM J McCall
Feb 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·L UlanovskyM Choder
Jan 1, 1994·Journal of Bacteriology·M KajitaniA Ishihama
Jul 30, 1997·Biochemical and Biophysical Research Communications·A TakadaK Nagai
Oct 3, 1998·Acta Crystallographica. Section D, Biological Crystallography·A T BrüngerG L Warren
Aug 17, 1999·The EMBO Journal·C RivettiC Bustamante
Aug 18, 2000·Genes to Cells : Devoted to Molecular & Cellular Mechanisms·T A AzamA Ishihama
May 2, 2001·Proceedings of the National Academy of Sciences of the United States of America·C MuraD S Eisenberg
Jul 11, 2001·Genes & Development·K M WassarmanS Gottesman
Jan 24, 2002·Molecular Cell·Aixia ZhangGisela Storz
Jan 24, 2002·Molecular Cell·Thorleif MøllerPoul Valentin-Hansen
Aug 31, 2002·Nucleic Acids Research·Xueguang SunRoger M Wartell
Jul 11, 2003·The EMBO Journal·Kerren K SwingerPhoebe A Rice
Oct 3, 2003·Microbial Pathogenesis·Elisabeth SonnleitnerUdo Bläsi
Mar 11, 2004·Molecular Microbiology·Poul Valentin-HansenChristina Udesen
Apr 6, 2004·Current Opinion in Microbiology·Gisela StorzAixia Zhang
Jul 1, 2004·Molecular Microbiology·Yanpeng DingMatthew K Waldor
Oct 19, 2004·Annual Review of Microbiology·Susan Gottesman
Dec 2, 2004·Acta Crystallographica. Section D, Biological Crystallography·Paul Emsley, Kevin Cowtan
Dec 16, 2004·Proceedings of the National Academy of Sciences of the United States of America·Maria GaczynskaJerard Hurwitz
Jun 29, 2005·Acta Crystallographica. Section D, Biological Crystallography·Pavel V AfoninePaul D Adams
Jul 19, 2005·Nucleic Acids Research·Michael Y TolstorukovVictor B Zhurkin
Dec 14, 2006·Molecular Microbiology·Alexandra SittkaJörg Vogel
Feb 13, 2007·BMC Microbiology·Chantal BohnPhilippe Bouloc
Mar 31, 2007·Current Opinion in Microbiology·Richard G Brennan, Todd M Link
Nov 15, 2007·Nucleic Acids Research·Branislav VecerekUdo Bläsi
May 7, 2008·Infection and Immunity·Richard R KulesusMatthew A Mulvey
Aug 1, 2007·Journal of Applied Crystallography·Airlie J McCoyRandy J Read
Jun 11, 2009·Quarterly Reviews of Biophysics·Tali E Haran, Udayan Mohanty
Nov 6, 2009·Proceedings of the National Academy of Sciences of the United States of America·Todd M LinkRichard G Brennan
Feb 9, 2010·Nature Reviews. Microbiology·Shane C Dillon, Charles J Dorman
Feb 20, 2010·BMC Molecular Biology·Jacques Le DeroutEliane Hajnsdorf

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Citations

Oct 22, 2020·Microorganisms·Virali J ParekhRichard R Sinden
Aug 14, 2020·Biomacromolecules·Omar El HamouiVéronique Arluison
Apr 4, 2021·Antibiotics·Florian TurbantVéronique Arluison
Jun 3, 2021·International Journal of Molecular Sciences·Juan A Subirana, Xavier Messeguer

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Methods Mentioned

BETA
atomic
isothermal titration calorimetry
X-ray
Fluorescence
NMR
AFM
SANS
ChIP-seq

Software Mentioned

CNS
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Coot
Gwyddion
Phenix
Phaser
ImageJ
KaleidaGraph

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