Oxygen-responsive bacterial gene switch
Abstract
The invention provided herein relates to sequence determinants that elicit certain levels of gene expression and methods for obtaining engineered ligand-responsive gene switches comprising these sequence determinants. More particularly, the invention provided herein relates to molecular building blocks (i.e., discrete nucleotide sequences), synthetic ligand-responsive gene switches comprising an assembly of these molecular building blocks, and methods of using synthetic ligand-responsive gene switches as customizable and controllable expression systems and sensors.
- Inventors:
- Issue Date:
- Research Org.:
- Univ. of Wisconsin, Madison, WI (United States)
- Sponsoring Org.:
- USDOE; National Institutes of Health (NIH)
- OSTI Identifier:
- 1860180
- Patent Number(s):
- 11203759
- Application Number:
- 15/698,302
- Assignee:
- WISCONSIN ALUMNI RESEARCH FOUNDATION (Madison, WI)
- Patent Classifications (CPCs):
-
C - CHEMISTRY C12 - BIOCHEMISTRY C12N - MICROORGANISMS OR ENZYMES
- DOE Contract Number:
- FC02-07ER64494; FG02-04ER25627; GM045844
- Resource Type:
- Patent
- Resource Relation:
- Patent File Date: 09/07/2017
- Country of Publication:
- United States
- Language:
- English
Citation Formats
Kiley, Patricia J., and Park, Dan Mcfarland. Oxygen-responsive bacterial gene switch. United States: N. p., 2021.
Web.
Kiley, Patricia J., & Park, Dan Mcfarland. Oxygen-responsive bacterial gene switch. United States.
Kiley, Patricia J., and Park, Dan Mcfarland. Tue .
"Oxygen-responsive bacterial gene switch". United States. https://www.osti.gov/servlets/purl/1860180.
@article{osti_1860180,
title = {Oxygen-responsive bacterial gene switch},
author = {Kiley, Patricia J. and Park, Dan Mcfarland},
abstractNote = {The invention provided herein relates to sequence determinants that elicit certain levels of gene expression and methods for obtaining engineered ligand-responsive gene switches comprising these sequence determinants. More particularly, the invention provided herein relates to molecular building blocks (i.e., discrete nucleotide sequences), synthetic ligand-responsive gene switches comprising an assembly of these molecular building blocks, and methods of using synthetic ligand-responsive gene switches as customizable and controllable expression systems and sensors.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2021},
month = {12}
}
Works referenced in this record:
DNA structural variations in the E. coli tyrT promoter
journal, June 1984
- Drew, Horace R.; Travers, Andrew A.
- Cell, Vol. 37, Issue 2
Bacterial response regulators: versatile regulatory strategies from common domains
journal, May 2007
- Gao, Rong; Mack, Timothy R.; Stock, Ann M.
- Trends in Biochemical Sciences, Vol. 32, Issue 5
The OmpR protein of Escherichia coli binds to sites in the ompF promoter region in a hierarchical manner determined by its degree of phosphorylation.
journal, April 1994
- Rampersaud, A.; Harlocker, S. L.; Inouye, M.
- Journal of Biological Chemistry, Vol. 269, Issue 17
DNA Binding of PhoB and its Interaction with RNA Polymerase
journal, May 1996
- Makino, Kozo; Amemura, Mitsuko; Kawamoto, Takeshi
- Journal of Molecular Biology, Vol. 259, Issue 1
Tandem DNA Recognition by PhoB, a Two-Component Signal Transduction Transcriptional Activator
journal, May 2002
- Blanco, Alexandre G.; Sola, Maria; Gomis-Rüth, F. Xavier
- Structure, Vol. 10, Issue 5
A Degenerate Tripartite DNA-Binding Site Required for Activation of ComA-Dependent Quorum Response Gene Expression in Bacillus subtilis
journal, August 2008
- Griffith, Kevin L.; Grossman, Alan D.
- Journal of Molecular Biology, Vol. 381, Issue 2
Synthetic biology: applications come of age
journal, May 2010
- Khalil, Ahmad S.; Collins, James J.
- Nature Reviews Genetics, Vol. 11, Issue 5
Programming gene expression with combinatorial promoters
journal, January 2007
- Cox, Robert Sidney; Surette, Michael G.; Elowitz, Michael B.
- Molecular Systems Biology, Vol. 3, Issue 1
Free energy coupling within macromolecules
journal, October 1983
- Ackers, Gary K.; Shea, Madeline A.; Smith, Francine R.
- Journal of Molecular Biology, Vol. 170, Issue 1
Information Content of Individual Genetic Sequences
journal, December 1997
- Schneider, T. D.
- Journal of Theoretical Biology, Vol. 189, Issue 4
Structural Analysis and Solution Studies of the Activated Regulatory Domain of the Response Regulator ArcA: A Symmetric Dimer Mediated by the α4-β5-α5 Face
journal, May 2005
- Toro-Roman, Alejandro; Mack, Timothy R.; Stock, Ann M.
- Journal of Molecular Biology, Vol. 349, Issue 1
[57] Sequencing end-labeled DNA with base-specific chemical cleavages
book, January 1980
- Maxam, Allan M.; Gilbert, Walter
- Nucleic Acids Part I
A mutational study of the ArcA-P binding sequences in the aldA promoter of Escherichia coli
journal, February 1999
- Pellicer, M. Teresa; Lynch, A. S.; De Wulf, P.
- Molecular and General Genetics MGG, Vol. 261, Issue 1
Probing the Roles of the Two Different Dimers Mediated by the Receiver Domain of the Response Regulator PhoB
journal, June 2009
- Mack, Timothy R.; Gao, Rong; Stock, Ann M.
- Journal of Molecular Biology, Vol. 389, Issue 2
Sequence walkers: A graphical method to display how binding proteins interact with DNA or RNA sequences
journal, November 1997
- Schneider, T. D.
- Nucleic Acids Research, Vol. 25, Issue 21
Dual regulation of the ugp operon by phosphate and carbon starvation at two interspaced promoters
journal, January 1991
- Kasahara, M.; Makino, K.; Amemura, M.
- Journal of Bacteriology, Vol. 173, Issue 2
Genome-Wide Expression Analysis Indicates that FNR of Escherichia coli K-12 Regulates a Large Number of Genes of Unknown Function
journal, January 2005
- Kang, Y.; Weber, K. D.; Qiu, Y.
- Journal of Bacteriology, Vol. 187, Issue 3
Position and density effects on repression by stationary and mobile DNA-binding proteins.
journal, February 1989
- Elledge, S. J.; Davis, R. W.
- Genes & Development, Vol. 3, Issue 2
Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promoters.
journal, January 1996
- Lynch, A. S.; Lin, E. C.
- Journal of bacteriology, Vol. 178, Issue 21
Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR
journal, March 2002
- Schumacher, M. A.
- The EMBO Journal, Vol. 21, Issue 5
A search for amino acid substitutions that universally activate response regulators: Activating substitutions in response regulators
journal, December 2003
- Smith, Jenny G.; Latiolais, Jamie A.; Guanga, Gerald P.
- Molecular Microbiology, Vol. 51, Issue 3
Comprehensive Analysis of OmpR Phosphorylation, Dimerization, and DNA Binding Supports a Canonical Model for Activation
journal, May 2013
- Barbieri, Christopher M.; Wu, Ti; Stock, Ann M.
- Journal of Molecular Biology, Vol. 425, Issue 10
Cooperative Binding of PhoB DBD to Its Cognate DNA Sequence—A Combined Application of Single-Molecule and Ensemble Methods
journal, November 2013
- Ritzefeld, Markus; Walhorn, Volker; Kleineberg, Christin
- Biochemistry, Vol. 52, Issue 46
Aerobic regulation of isocitrate dehydrogenase gene (icd) expression in Escherichia coli by the arcA and fnr gene products.
journal, January 1997
- Chao, G.; Shen, J.; Tseng, C. P.
- Journal of bacteriology, Vol. 179, Issue 13
Promoters largely determine the efficiency of repressor action.
journal, December 1988
- Lanzer, M.; Bujard, H.
- Proceedings of the National Academy of Sciences, Vol. 85, Issue 23
Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis: Genome sequencing of Oryza glaberrima
journal, March 2011
- Sakai, Hiroaki; Ikawa, Hiroshi; Tanaka, Tsuyoshi
- The Plant Journal, Vol. 66, Issue 5
Discovery of Fur binding site clusters in Escherichia coli by information theory models
journal, October 2007
- Chen, Zehua; Lewis, Karen A.; Shultzaberger, Ryan K.
- Nucleic Acids Research, Vol. 35, Issue 20
Purification of ArcA and analysis of is specific interaction with the pfl promoter-regulatory region
journal, May 1995
- Drapal, Nikola; Sawers, Gary
- Molecular Microbiology, Vol. 16, Issue 3
Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA
journal, August 2006
- Cho, Byung-Kwan; Knight, Eric M.; Palsson, Bernhard Ø.
- Microbiology, Vol. 152, Issue 8
AppaDB: an AcedB database for the nematode satellite organism Pristionchus pacificus
journal, January 2004
- Srinivasan, J.
- Nucleic Acids Research, Vol. 32, Issue 90001
Global Gene Expression Profiling in Escherichia coli K12: EFFECTS OF OXYGEN AVAILABILITY AND ArcA
journal, February 2005
- Salmon, Kirsty A.; Hung, She-pin; Steffen, Nicholas R.
- Journal of Biological Chemistry, Vol. 280, Issue 15
ArcA and AppY Antagonize IscR Repression of Hydrogenase-1 Expression under Anaerobic Conditions, Revealing a Novel Mode of O 2 Regulation of Gene Expression in Escherichia coli
journal, December 2012
- Nesbit, A. D.; Fleischhacker, A. S.; Teter, S. J.
- Journal of Bacteriology, Vol. 194, Issue 24
Transcription Regulation of ompF and ompC by a Single Transcription Factor, OmpR
journal, April 2006
- Yoshida, Takeshi; Qin, Ling; Egger, Linda A.
- Journal of Biological Chemistry, Vol. 281, Issue 25
Inhibition of Transcription Initiation buIacRepressor
journal, January 1995
- Schlax, Paula J.; Capp, Michael W.; Record Jr, Thomas M.
- Journal of Molecular Biology, Vol. 245, Issue 4
Co-regulation of lipoamide dehydrogenase and 2-oxoglutarate dehydrogenase synthesis in Escherichia coli : characterisation of an ArcA binding site in the lpd promoter
journal, December 1998
- Cunningham, Louise; Georgellis, Dimitris; Green, Jeffrey
- FEMS Microbiology Letters, Vol. 169, Issue 2
Nucleotide sequence of the phoB gene, the positive regulatory gene for the phosphate regulon of Escherichia coli K-12
journal, July 1986
- Makino, Kozo; Shinagawa, Hideo; Amemura, Mitsuko
- Journal of Molecular Biology, Vol. 190, Issue 1
The Bacterial Response Regulator ArcA Uses a Diverse Binding Site Architecture to Regulate Carbon Oxidation Globally
journal, October 2013
- Park, Dan M.; Akhtar, Md. Sohail; Ansari, Aseem Z.
- PLoS Genetics, Vol. 9, Issue 10
Signaling by the Arc Two-Component System Provides a Link Between the Redox State of the Quinone Pool and Gene Expression
journal, May 2006
- Malpica, Roxana; Sandoval, Gabriela R. Peña; Rodríguez, Claudia
- Antioxidants & Redox Signaling, Vol. 8, Issue 5-6
A high-throughput percentage-of-binding strategy to measure binding energies in DNA–protein interactions: application to genome-scale site discovery
journal, July 2008
- Wang, Xiaohu; Gao, Haichun; Shen, Yufeng
- Nucleic Acids Research, Vol. 36, Issue 15
Notes on the use of propagation of error formulas
journal, October 1966
- Ku, H. H.
- Journal of Research of the National Bureau of Standards, Section C: Engineering and Instrumentation, Vol. 70C, Issue 4
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
journal, May 2000
- Datsenko, K. A.; Wanner, B. L.
- Proceedings of the National Academy of Sciences, Vol. 97, Issue 12, p. 6640-6645
A weight matrix for binding recognition by the redox-response regulator ArcA-P of Escherichia coli
journal, April 1999
- McGuire, Abigail M.; De Wulf, Peter; Church, George M.
- Molecular Microbiology, Vol. 32, Issue 1
Advances in bacterial promoter recognition and its control by factors that do not bind DNA
journal, June 2008
- Haugen, Shanil P.; Ross, Wilma; Gourse, Richard L.
- Nature Reviews Microbiology, Vol. 6, Issue 7
An asymmetric heterodomain interface stabilizes a response regulator–DNA complex
journal, February 2014
- Narayanan, Anoop; Kumar, Shivesh; Evrard, Amanda N.
- Nature Communications, Vol. 5, Issue 1
The bacterial LexA transcriptional repressor
journal, August 2008
- Butala, M.; Žgur-Bertok, D.; Busby, S. J. W.
- Cellular and Molecular Life Sciences, Vol. 66, Issue 1
Cross-induction of glc and ace Operons of Escherichia coli Attributable to Pathway Intersection : CHARACTERIZATION OF THE
journal, January 1999
- Pellicer, Maria Teresa; Fernandez, Carmen; Badı́a, Josefa
- Journal of Biological Chemistry, Vol. 274, Issue 3
Inactivation of isocitrate dehydrogenase by phosphorylation is mediated by the negative charge of the phosphate.
journal, August 1987
- Thorsness, P. E.; Koshland, D. E.
- Journal of Biological Chemistry, Vol. 262, Issue 22
EcoCyc: a comprehensive database of Escherichia coli biology
journal, November 2010
- Keseler, I. M.; Collado-Vides, J.; Santos-Zavaleta, A.
- Nucleic Acids Research, Vol. 39, Issue Database
Heat Shock Transcription Factors: Structure and Regulation
journal, November 1995
- Wu, Carl
- Annual Review of Cell and Developmental Biology, Vol. 11, Issue 1
Sequence-Specific Binding to a Subset of IscR-Regulated Promoters Does Not Require IscR Fe–S Cluster Ligation
journal, March 2009
- Nesbit, A. D.; Giel, J. L.; Rose, J. C.
- Journal of Molecular Biology, Vol. 387, Issue 1
Zymomonas pentose-sugar fermenting strains and uses thereof
patent-application, August 2003
- Zhang, Min; Chou, Yat-Chen; Howe, William
- US Patent Application 10/134655; 20030162271
Genome-Wide Detection of Fitness Genes in Uropathogenic Escherichia coli during Systemic Infection
journal, December 2013
- Subashchandrabose, Sargurunathan; Smith, Sara N.; Spurbeck, Rachel R.
- PLoS Pathogens, Vol. 9, Issue 12
Identification of a quinone-sensitive redox switch in the ArcB sensor kinase
journal, August 2004
- Malpica, R.; Franco, B.; Rodriguez, C.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 36