Structural basis of non-canonical transcriptional regulation by the σA-bound iron-sulfur protein WhiB1 in M. tuberculosis
Abstract
Abstract WhiB1 is a monomeric iron–sulfur cluster-containing transcription factor in the WhiB-like family that is widely distributed in actinobacteria including the notoriously persistent pathogen Mycobacterium tuberculosis (M. tuberculosis). WhiB1 plays multiple roles in regulating cell growth and responding to nitric oxide stress in M. tuberculosis, but its underlying mechanism is unclear. Here we report a 1.85 Å-resolution crystal structure of the [4Fe–4S] cluster-bound (holo-) WhiB1 in complex with the C-terminal domain of the σ70-family primary sigma factor σA of M. tuberculosis containing the conserved region 4 (σA4). Region 4 of the σ70-family primary sigma factors is commonly used by transcription factors for gene activation, and holo-WhiB1 has been proposed to activate gene expression via binding to σA4. The complex structure, however, unexpectedly reveals that the interaction between WhiB1 and σA4 is dominated by hydrophobic residues in the [4Fe–4S] cluster binding pocket, distinct from previously characterized canonical σ704-bound transcription activators. Furthermore, we show that holo-WhiB1 represses transcription by interaction with σA4in vitro and that WhiB1 must interact with σA4 to perform its essential role in supporting cell growth in vivo. Together, these results demonstrate that holo-WhiB1 regulates gene expression by a non-canonical mechanism relative to well-characterized σA4-dependent transcription activators.
- Authors:
-
- Department of Biochemistry
- Department of Biochemistry, Redox Biology Center
- Department of Biochemistry, Redox Biology Center, Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1577377
- Grant/Contract Number:
- AC02–76SF00515
- Resource Type:
- Published Article
- Journal Name:
- Nucleic Acids Research
- Additional Journal Information:
- Journal Name: Nucleic Acids Research Journal Volume: 48 Journal Issue: 2; Journal ID: ISSN 0305-1048
- Publisher:
- Oxford University Press
- Country of Publication:
- United Kingdom
- Language:
- English
Citation Formats
Wan, Tao, Li, Shanren, Beltran, Daisy Guiza, Schacht, Andrew, Zhang, Lu, Becker, Donald F., and Zhang, LiMei. Structural basis of non-canonical transcriptional regulation by the σA-bound iron-sulfur protein WhiB1 in M. tuberculosis. United Kingdom: N. p., 2019.
Web. doi:10.1093/nar/gkz1133.
Wan, Tao, Li, Shanren, Beltran, Daisy Guiza, Schacht, Andrew, Zhang, Lu, Becker, Donald F., & Zhang, LiMei. Structural basis of non-canonical transcriptional regulation by the σA-bound iron-sulfur protein WhiB1 in M. tuberculosis. United Kingdom. doi:10.1093/nar/gkz1133.
Wan, Tao, Li, Shanren, Beltran, Daisy Guiza, Schacht, Andrew, Zhang, Lu, Becker, Donald F., and Zhang, LiMei. Fri .
"Structural basis of non-canonical transcriptional regulation by the σA-bound iron-sulfur protein WhiB1 in M. tuberculosis". United Kingdom. doi:10.1093/nar/gkz1133.
@article{osti_1577377,
title = {Structural basis of non-canonical transcriptional regulation by the σA-bound iron-sulfur protein WhiB1 in M. tuberculosis},
author = {Wan, Tao and Li, Shanren and Beltran, Daisy Guiza and Schacht, Andrew and Zhang, Lu and Becker, Donald F. and Zhang, LiMei},
abstractNote = {Abstract WhiB1 is a monomeric iron–sulfur cluster-containing transcription factor in the WhiB-like family that is widely distributed in actinobacteria including the notoriously persistent pathogen Mycobacterium tuberculosis (M. tuberculosis). WhiB1 plays multiple roles in regulating cell growth and responding to nitric oxide stress in M. tuberculosis, but its underlying mechanism is unclear. Here we report a 1.85 Å-resolution crystal structure of the [4Fe–4S] cluster-bound (holo-) WhiB1 in complex with the C-terminal domain of the σ70-family primary sigma factor σA of M. tuberculosis containing the conserved region 4 (σA4). Region 4 of the σ70-family primary sigma factors is commonly used by transcription factors for gene activation, and holo-WhiB1 has been proposed to activate gene expression via binding to σA4. The complex structure, however, unexpectedly reveals that the interaction between WhiB1 and σA4 is dominated by hydrophobic residues in the [4Fe–4S] cluster binding pocket, distinct from previously characterized canonical σ704-bound transcription activators. Furthermore, we show that holo-WhiB1 represses transcription by interaction with σA4in vitro and that WhiB1 must interact with σA4 to perform its essential role in supporting cell growth in vivo. Together, these results demonstrate that holo-WhiB1 regulates gene expression by a non-canonical mechanism relative to well-characterized σA4-dependent transcription activators.},
doi = {10.1093/nar/gkz1133},
journal = {Nucleic Acids Research},
number = 2,
volume = 48,
place = {United Kingdom},
year = {2019},
month = {12}
}
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DOI: 10.1093/nar/gkz1133
DOI: 10.1093/nar/gkz1133
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Works referenced in this record:
Clustal Omega for making accurate alignments of many protein sequences: Clustal Omega for Many Protein Sequences
journal, October 2017
- Sievers, Fabian; Higgins, Desmond G.
- Protein Science, Vol. 27, Issue 1
Factor Independent Activation of rrnB P1
journal, February 1994
- Rao, Lin; Ross, Wilma; Appleman, J. Alex
- Journal of Molecular Biology, Vol. 235, Issue 5
Mechanistic Insight into the Nitrosylation of the [4Fe−4S] Cluster of WhiB-like Proteins
journal, February 2011
- Crack, Jason C.; Smith, Laura J.; Stapleton, Melanie R.
- Journal of the American Chemical Society, Vol. 133, Issue 4
Efficient and simple generation of multiple unmarked gene deletions in Mycobacterium smegmatis
journal, March 2016
- Mao, Xu-Jian; Yan, Mei-Yi; Zhu, Hui
- Scientific Reports, Vol. 6, Issue 1
Structure-Function Relationships of the Mycobacterium tuberculosis Transcription Factor WhiB1
journal, July 2012
- Smith, Laura J.; Stapleton, Melanie R.; Buxton, Roger S.
- PLoS ONE, Vol. 7, Issue 7
A regulatory protein that interferes with activator-stimulated transcription in bacteria
journal, March 2003
- Nakano, S.; Nakano, M. M.; Zhang, Y.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 7
Gene Expression of Mycobacterium tuberculosis Putative Transcription Factors whiB1-7 in Redox Environments
journal, July 2012
- Larsson, Christer; Luna, Brian; Ammerman, Nicole C.
- PLoS ONE, Vol. 7, Issue 7
Mycobacterium tuberculosis WhiB1 is an essential DNA-binding protein with a nitric oxide-sensitive iron–sulfur cluster
journal, November 2010
- Smith, Laura J.; Stapleton, Melanie R.; Fullstone, Gavin J. M.
- Biochemical Journal, Vol. 432, Issue 3
Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures
journal, July 2017
- Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.
- Nature Communications, Vol. 8, Issue 1
The mycobacterial antibiotic resistance determinant WhiB7 acts as a transcriptional activator by binding the primary sigma factor SigA (RpoV)
journal, August 2013
- Burian, Ján; Yim, Grace; Hsing, Michael
- Nucleic Acids Research, Vol. 41, Issue 22
Solvent Tuning of Electrochemical Potentials in the Active Sites of HiPIP Versus Ferredoxin
journal, November 2007
- Dey, A.; Jenney, F. E.; Adams, M. W. W.
- Science, Vol. 318, Issue 5855
Activating Transcription in Bacteria
journal, October 2012
- Lee, David J.; Minchin, Stephen D.; Busby, Stephen J. W.
- Annual Review of Microbiology, Vol. 66, Issue 1
Crystal structure of the Bacillus subtilis anti-alpha, global transcriptional regulator, Spx, in complex with the C-terminal domain of RNA polymerase
journal, October 2005
- Newberry, K. J.; Nakano, S.; Zuber, P.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 44
Nitric Oxide and Macrophage Function
journal, April 1997
- MacMicking, John; Xie, Qiao-wen; Nathan, Carl
- Annual Review of Immunology, Vol. 15, Issue 1
Recombineering in Mycobacterium tuberculosis
journal, December 2006
- van Kessel, Julia C.; Hatfull, Graham F.
- Nature Methods, Vol. 4, Issue 2
Calculation of the Redox Potentials of Iron-Sulfur Proteins: The 2-/3- Couple of [Fe4S4Cys4] Clusters in Peptococcus aerogenes Ferredoxin, Azotobacter vinelandii Ferredoxin I, and Chromatium vinosum High-Potential Iron Protein
journal, September 1994
- Jensen, G. M.; Warshel, A.; Stephens, P. J.
- Biochemistry, Vol. 33, Issue 36
Crystal structures of the NO sensor NsrR reveal how its iron-sulfur cluster modulates DNA binding
journal, April 2017
- Volbeda, Anne; Dodd, Erin L.; Darnault, Claudine
- Nature Communications, Vol. 8, Issue 1
Three-dimensional EM structure of an intact activator-dependent transcription initiation complex
journal, November 2009
- Hudson, B. P.; Quispe, J.; Lara-Gonzalez, S.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 47
Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences
journal, May 2014
- Chandra, Govind; Chater, Keith F.
- FEMS Microbiology Reviews, Vol. 38, Issue 3
Mycobacterium tuberculosis WhiB3 interacts with RpoV to affect host survival but is dispensable for in vivo growth
journal, March 2002
- Steyn, A. J. C.; Collins, D. M.; Hondalus, M. K.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 5
Transcription Activation at Class II CAP-Dependent Promoters: Two Interactions between CAP and RNA Polymerase
journal, December 1996
- Niu, Wei; Kim, Younggyu; Tau, Gregory
- Cell, Vol. 87, Issue 6
Mycobacterium tuberculosis WhiB3: A Novel Iron–Sulfur Cluster Protein That Regulates Redox Homeostasis and Virulence
journal, April 2012
- Saini, Vikram; Farhana, Aisha; Steyn, Adrie J. C.
- Antioxidants & Redox Signaling, Vol. 16, Issue 7
sigA is an essential gene in Mycobacterium smegmatis
journal, July 1998
- Gomez, Manuel; Doukhan, Laurence; Nair, Gopalan
- Molecular Microbiology, Vol. 29, Issue 2
Structural basis of transcription activation
journal, June 2016
- Feng, Y.; Zhang, Y.; Ebright, R. H.
- Science, Vol. 352, Issue 6291
Improved mycobacterial tetracycline inducible vectors
journal, September 2010
- Williams, Kerstin J.; Joyce, Graham; Robertson, Brian D.
- Plasmid, Vol. 64, Issue 2
Structure of the Bacterial RNA Polymerase Promoter Specificity σ Subunit
journal, March 2002
- Campbell, Elizabeth A.; Muzzin, Oriana; Chlenov, Mark
- Molecular Cell, Vol. 9, Issue 3
Structure of a Wbl protein and implications for NO sensing by M. tuberculosis
journal, December 2017
- Kudhair, Bassam K.; Hounslow, Andrea M.; Rolfe, Matthew D.
- Nature Communications, Vol. 8, Issue 1
Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts
journal, February 2018
- Boyaci, Hande; Chen, James; Lilic, Mirjana
- eLife, Vol. 7
T4 AsiA blocks DNA recognition by remodeling σ70 region 4
journal, July 2004
- Lambert, Lester J.; Wei, Yufeng; Schirf, Virgil
- The EMBO Journal, Vol. 23, Issue 15
The Structure of MbtI from Mycobacterium tuberculosis, the First Enzyme in the Biosynthesis of the Siderophore Mycobactin, Reveals It To Be a Salicylate Synthase
journal, August 2006
- Harrison, A. J.; Yu, M.; Gardenborg, T.
- Journal of Bacteriology, Vol. 188, Issue 17
Mycobacterium tuberculosis WhiB1 represses transcription of the essential chaperonin GroEL2
journal, July 2012
- Stapleton, Melanie R.; Smith, Laura J.; Hunt, Debbie M.
- Tuberculosis, Vol. 92, Issue 4
UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition
journal, August 2000
- Gourse, Richard L.; Ross, Wilma; Gaal, Tamas
- Molecular Microbiology, Vol. 37, Issue 4
XDS
journal, January 2010
- Kabsch, Wolfgang
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
Role of aromatic residues in stabilization of the [Fe4S4] cluster in high-potential iron proteins (HiPIPs): physical characterization and stability studies of Tyr-19 mutants of Chromatium vinosum HiPIP.
journal, October 1995
- Agarwal, A.; Li, D.; Cowan, J. A.
- Proceedings of the National Academy of Sciences, Vol. 92, Issue 21
Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA
journal, January 2017
- Hubin, Elizabeth A.; Fay, Allison; Xu, Catherine
- eLife, Vol. 6
An intersubunit contact stimulating transcription initiation by E. coli RNA polymerase: interaction of the alpha C-terminal domain and sigma region 4
journal, May 2003
- Ross, W.
- Genes & Development, Vol. 17, Issue 10
A regulator that inhibits transcription by targeting an intersubunit interaction of the RNA polymerase holoenzyme
journal, March 2004
- Gregory, B. D.; Nickels, B. E.; Garrity, S. J.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 13
The crystal structure of the global anaerobic transcriptional regulator FNR explains its extremely fine-tuned monomer-dimer equilibrium
journal, December 2015
- Volbeda, Anne; Darnault, Claudine; Renoux, Oriane
- Science Advances, Vol. 1, Issue 11
Genome-wide characterization of monomeric transcriptional regulators in Mycobacterium tuberculosis
journal, May 2016
- Feng, Lipeng; Chen, Zhenkang; Wang, Zhongwei
- Microbiology, Vol. 162, Issue 5
Identification of Novel Spx Regulatory Pathways in Bacillus subtilis Uncovers a Close Relationship between the CtsR and Spx Regulons
journal, April 2019
- Rojas-Tapias, Daniel F.; Helmann, John D.
- Journal of Bacteriology, Vol. 201, Issue 13
Chemistry of Nitric Oxide with Protein-Bound Iron Sulfur Centers. Insights on Physiological Reactivity
journal, May 1999
- Foster, Matthew W.; Cowan, J. A.
- Journal of the American Chemical Society, Vol. 121, Issue 17
Reassessing the Structure and Function Relationship of the O 2 Sensing Transcription Factor FNR
journal, December 2018
- Mettert, Erin L.; Kiley, Patricia J.
- Antioxidants & Redox Signaling, Vol. 29, Issue 18
Transcription Activation by Escherichia coli Rob at Class II Promoters: Protein–Protein Interactions between Rob's N-Terminal Domain and the σ70 Subunit of RNA Polymerase
journal, June 2012
- Taliaferro, Lanyn P.; Keen, Edward F.; Sanchez-Alberola, Neus
- Journal of Molecular Biology, Vol. 419, Issue 3-4
Charge-density analysis of an iron–sulfur protein at an ultra-high resolution of 0.48 Å
journal, May 2016
- Hirano, Yu; Takeda, Kazuki; Miki, Kunio
- Nature, Vol. 534, Issue 7606
Deciphering key features in protein structures with the new ENDscript server
journal, April 2014
- Robert, Xavier; Gouet, Patrice
- Nucleic Acids Research, Vol. 42, Issue W1
Features and development of Coot
journal, March 2010
- Emsley, P.; Lohkamp, B.; Scott, W. G.
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
Iron–Sulfur Clusters as Biological Sensors: The Chemistry of Reactions with Molecular Oxygen and Nitric Oxide
journal, September 2014
- Crack, Jason C.; Green, Jeffrey; Thomson, Andrew J.
- Accounts of Chemical Research, Vol. 47, Issue 10
NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility
journal, August 2009
- Partridge, Jonathan D.; Bodenmiller, Diane M.; Humphrys, Michael S.
- Molecular Microbiology, Vol. 73, Issue 4
PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010
- Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
Structural, functional, and genetic analyses of the actinobacterial transcription factor RbpA
journal, May 2015
- Hubin, Elizabeth A.; Tabib-Salazar, Aline; Humphrey, Laurence J.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 23
Endogenous Nitric Oxide Protects Bacteria Against a Wide Spectrum of Antibiotics
journal, September 2009
- Gusarov, I.; Shatalin, K.; Starodubtseva, M.
- Science, Vol. 325, Issue 5946
Spx-dependent global transcriptional control is induced by thiol-specific oxidative stress in Bacillus subtilis
journal, November 2003
- Nakano, S.; Kuster-Schock, E.; Grossman, A. D.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 23
Spx-RNA Polymerase Interaction and Global Transcriptional Control during Oxidative Stress
journal, March 2004
- Zuber, P.
- Journal of Bacteriology, Vol. 186, Issue 7
The Streptomyces coelicolor whiB gene encodes a small transcription factor-like protein dispensable for growth but essential for sporulation
journal, April 1992
- Davis, N. K.; Chater, K. F.
- MGG Molecular & General Genetics, Vol. 232, Issue 3
Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding
journal, January 2019
- Boyaci, Hande; Chen, James; Jansen, Rolf
- Nature, Vol. 565, Issue 7739
Nitric oxide-sensing mechanisms in Escherichia coli
journal, January 2006
- Spiro, S.
- Biochemical Society Transactions, Vol. 34, Issue 1
Protein–Protein Interactions Between σ70 Region 4 of RNA Polymerase and Escherichia coli SoxS, a Transcription Activator That Functions by the Prerecruitment Mechanism: Evidence for “Off-DNA” and “On-DNA” Interactions
journal, August 2010
- Zafar, M. Ammar; Shah, Ishita M.; Wolf, Richard E.
- Journal of Molecular Biology, Vol. 401, Issue 1
The Mycobacterial Transcriptional Regulator whiB7 Gene Links Redox Homeostasis and Intrinsic Antibiotic Resistance
journal, November 2011
- Burian, Ján; Ramón-García, Santiago; Sweet, Gaye
- Journal of Biological Chemistry, Vol. 287, Issue 1
Post-Translational Regulation via Clp Protease Is Critical for Survival of Mycobacterium tuberculosis
journal, March 2014
- Raju, Ravikiran M.; Jedrychowski, Mark P.; Wei, Jun-Rong
- PLoS Pathogens, Vol. 10, Issue 3
Local and global regulation of transcription initiation in bacteria
journal, August 2016
- Browning, Douglas F.; Busby, Stephen J. W.
- Nature Reviews Microbiology, Vol. 14, Issue 10
CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
journal, October 2012
- Chovancova, Eva; Pavelka, Antonin; Benes, Petr
- PLoS Computational Biology, Vol. 8, Issue 10
Mechanism of [4Fe-4S](Cys) 4 Cluster Nitrosylation Is Conserved among NO-responsive Regulators
journal, March 2013
- Crack, Jason C.; Stapleton, Melanie R.; Green, Jeffrey
- Journal of Biological Chemistry, Vol. 288, Issue 16
Identification of a contact site for different transcription activators in region 4 of the Escherichia coli RNA polymerase σ 70 subunit 1 1Edited by R. Ebright
journal, December 1998
- Lonetto, Michael A.; Rhodius, Virgil; Lamberg, Karin
- Journal of Molecular Biology, Vol. 284, Issue 5
Oxygen sensing by the global regulator, FNR: the role of the iron-sulfur cluster
journal, December 1998
- Kiley, Patricia J.; Beinert, Helmut
- FEMS Microbiology Reviews, Vol. 22, Issue 5
The rRNA Operons of Mycobacterium Smegmatis and Mycobacterium Tuberculosis: Comparison of Promoter Elements and of Neighbouring Upstream Genes
journal, March 1996
- Gonzalez-y-Merchand, J. A.; Colston, M. J.; Cox, R. A.
- Microbiology, Vol. 142, Issue 3
Iron—sulfur proteins: new roles for old clusters
journal, April 1998
- Johnson, Michael K.
- Current Opinion in Chemical Biology, Vol. 2, Issue 2
Spx, a versatile regulator of the Bacillus subtilis stress response
journal, March 2019
- Schäfer, Heinrich; Turgay, Kürşad
- Current Genetics, Vol. 65, Issue 4
Loss-of-function mutations in yjbD result in ClpX- and ClpP-independent competence development of Bacillus subtilis
journal, October 2001
- Nakano, Michiko M.; Hajarizadeh, Farin; Zhu, Yi
- Molecular Microbiology, Vol. 42, Issue 2