Genetic analysis, structural modeling, and direct coupling analysis suggest a mechanism for phosphate signaling in Escherichia coli

Stewart G. Gardner; Justin B. Miller; Tanner Dean; Tanner Robinson; McCall Erickson; Perry G. Ridge; William R. McCleary

doi:10.1186/1471-2156-16-S2-S2

Genetic analysis, structural modeling, and direct coupling analysis suggest a mechanism for phosphate signaling in Escherichia coli

Stewart G. Gardner, Justin B. Miller, Tanner Dean, Tanner Robinson, McCall Erickson, Perry G. Ridge, William R. McCleary

Research output: Contribution to journal › Article › peer-review

21 Scopus citations

Abstract

Background: Proper phosphate signaling is essential for robust growth of Escherichia coli and many other bacteria. The phosphate signal is mediated by a classic two component signal system composed of PhoR and PhoB. The PhoR histidine kinase is responsible for phosphorylating/dephosphorylating the response regulator, PhoB, which controls the expression of genes that aid growth in low phosphate conditions. The mechanism by which PhoR receives a signal of environmental phosphate levels has remained elusive. A transporter complex composed of the PstS, PstC, PstA, and PstB proteins as well as a negative regulator, PhoU, have been implicated in signaling environmental phosphate to PhoR. Results: This work confirms that PhoU and the PstSCAB complex are necessary for proper signaling of high environmental phosphate. Also, we identify residues important in PhoU/PhoR interaction with genetic analysis. Using protein modeling and docking methods, we show an interaction model that points to a potential mechanism for PhoU mediated signaling to PhoR to modify its activity. This model is tested with direct coupling analysis. Conclusions: These bioinformatics tools, in combination with genetic and biochemical analysis, help to identify and test a model for phosphate signaling and may be applicable to several other systems.

Original language	English
Article number	S2
Journal	BMC Genetics
Volume	16
DOIs	https://doi.org/10.1186/1471-2156-16-S2-S2
State	Published - 2015

Bibliographical note

Funding Information:
Acknowledgements We thank Kathryn Hanks, Alex Cummock, Evan Christensen, Bethany Evans, Gregory Bowden, and Michael Barrus for help with sequence collection and mutant characterization. This work was supported by Public Health Service grant R15GM96222 from the National Institute of General Medical Sciences. Declarations The publication costs for this article were funded by the Department of Microbiology and Molecular Biology at Brigham Young University, the College of Life Sciences at Brigham Young University, and the Public Health Service grant R15GM96222 from the National Institute of General Medical Sciences.This article has been published as part of BMC Genetics Volume 16 Supplement 2, 2015: Selected articles from The 11th Annual Biotechnology and Bioinformatics Symposium (BIOT-2014): Genetics. The full contents of the supplement are available online at http://www.biomedcentral.com/ bmcgenet/supplements/16/S2.

Funding Information:
We thank Kathryn Hanks, Alex Cummock, Evan Christensen, Bethany Evans, Gregory Bowden, and Michael Barrus for help with sequence collection and mutant characterization. This work was supported by Public Health Service grant R15GM96222 from the National Institute of General Medical Sciences.

Funding Information:
The publication costs for this article were funded by the Department of Microbiology and Molecular Biology at Brigham Young University, the College of Life Sciences at Brigham Young University, and the Public Health Service grant R15GM96222 from the National Institute of General Medical Sciences.

Publisher Copyright:
© 2015 Gardner et al.; licensee BioMed Central Ltd.

ASJC Scopus subject areas

Genetics
Genetics(clinical)

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title = "Genetic analysis, structural modeling, and direct coupling analysis suggest a mechanism for phosphate signaling in Escherichia coli",

abstract = "Background: Proper phosphate signaling is essential for robust growth of Escherichia coli and many other bacteria. The phosphate signal is mediated by a classic two component signal system composed of PhoR and PhoB. The PhoR histidine kinase is responsible for phosphorylating/dephosphorylating the response regulator, PhoB, which controls the expression of genes that aid growth in low phosphate conditions. The mechanism by which PhoR receives a signal of environmental phosphate levels has remained elusive. A transporter complex composed of the PstS, PstC, PstA, and PstB proteins as well as a negative regulator, PhoU, have been implicated in signaling environmental phosphate to PhoR. Results: This work confirms that PhoU and the PstSCAB complex are necessary for proper signaling of high environmental phosphate. Also, we identify residues important in PhoU/PhoR interaction with genetic analysis. Using protein modeling and docking methods, we show an interaction model that points to a potential mechanism for PhoU mediated signaling to PhoR to modify its activity. This model is tested with direct coupling analysis. Conclusions: These bioinformatics tools, in combination with genetic and biochemical analysis, help to identify and test a model for phosphate signaling and may be applicable to several other systems.",

author = "Gardner, {Stewart G.} and Miller, {Justin B.} and Tanner Dean and Tanner Robinson and McCall Erickson and Ridge, {Perry G.} and McCleary, {William R.}",

note = "Funding Information: Acknowledgements We thank Kathryn Hanks, Alex Cummock, Evan Christensen, Bethany Evans, Gregory Bowden, and Michael Barrus for help with sequence collection and mutant characterization. This work was supported by Public Health Service grant R15GM96222 from the National Institute of General Medical Sciences. Declarations The publication costs for this article were funded by the Department of Microbiology and Molecular Biology at Brigham Young University, the College of Life Sciences at Brigham Young University, and the Public Health Service grant R15GM96222 from the National Institute of General Medical Sciences.This article has been published as part of BMC Genetics Volume 16 Supplement 2, 2015: Selected articles from The 11th Annual Biotechnology and Bioinformatics Symposium (BIOT-2014): Genetics. The full contents of the supplement are available online at http://www.biomedcentral.com/ bmcgenet/supplements/16/S2. Funding Information: We thank Kathryn Hanks, Alex Cummock, Evan Christensen, Bethany Evans, Gregory Bowden, and Michael Barrus for help with sequence collection and mutant characterization. This work was supported by Public Health Service grant R15GM96222 from the National Institute of General Medical Sciences. Funding Information: The publication costs for this article were funded by the Department of Microbiology and Molecular Biology at Brigham Young University, the College of Life Sciences at Brigham Young University, and the Public Health Service grant R15GM96222 from the National Institute of General Medical Sciences. Publisher Copyright: {\textcopyright} 2015 Gardner et al.; licensee BioMed Central Ltd.",

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T1 - Genetic analysis, structural modeling, and direct coupling analysis suggest a mechanism for phosphate signaling in Escherichia coli

AU - Gardner, Stewart G.

AU - Miller, Justin B.

AU - Dean, Tanner

AU - Robinson, Tanner

AU - Erickson, McCall

AU - Ridge, Perry G.

AU - McCleary, William R.

N1 - Funding Information: Acknowledgements We thank Kathryn Hanks, Alex Cummock, Evan Christensen, Bethany Evans, Gregory Bowden, and Michael Barrus for help with sequence collection and mutant characterization. This work was supported by Public Health Service grant R15GM96222 from the National Institute of General Medical Sciences. Declarations The publication costs for this article were funded by the Department of Microbiology and Molecular Biology at Brigham Young University, the College of Life Sciences at Brigham Young University, and the Public Health Service grant R15GM96222 from the National Institute of General Medical Sciences.This article has been published as part of BMC Genetics Volume 16 Supplement 2, 2015: Selected articles from The 11th Annual Biotechnology and Bioinformatics Symposium (BIOT-2014): Genetics. The full contents of the supplement are available online at http://www.biomedcentral.com/ bmcgenet/supplements/16/S2. Funding Information: We thank Kathryn Hanks, Alex Cummock, Evan Christensen, Bethany Evans, Gregory Bowden, and Michael Barrus for help with sequence collection and mutant characterization. This work was supported by Public Health Service grant R15GM96222 from the National Institute of General Medical Sciences. Funding Information: The publication costs for this article were funded by the Department of Microbiology and Molecular Biology at Brigham Young University, the College of Life Sciences at Brigham Young University, and the Public Health Service grant R15GM96222 from the National Institute of General Medical Sciences. Publisher Copyright: © 2015 Gardner et al.; licensee BioMed Central Ltd.

PY - 2015

Y1 - 2015

N2 - Background: Proper phosphate signaling is essential for robust growth of Escherichia coli and many other bacteria. The phosphate signal is mediated by a classic two component signal system composed of PhoR and PhoB. The PhoR histidine kinase is responsible for phosphorylating/dephosphorylating the response regulator, PhoB, which controls the expression of genes that aid growth in low phosphate conditions. The mechanism by which PhoR receives a signal of environmental phosphate levels has remained elusive. A transporter complex composed of the PstS, PstC, PstA, and PstB proteins as well as a negative regulator, PhoU, have been implicated in signaling environmental phosphate to PhoR. Results: This work confirms that PhoU and the PstSCAB complex are necessary for proper signaling of high environmental phosphate. Also, we identify residues important in PhoU/PhoR interaction with genetic analysis. Using protein modeling and docking methods, we show an interaction model that points to a potential mechanism for PhoU mediated signaling to PhoR to modify its activity. This model is tested with direct coupling analysis. Conclusions: These bioinformatics tools, in combination with genetic and biochemical analysis, help to identify and test a model for phosphate signaling and may be applicable to several other systems.

AB - Background: Proper phosphate signaling is essential for robust growth of Escherichia coli and many other bacteria. The phosphate signal is mediated by a classic two component signal system composed of PhoR and PhoB. The PhoR histidine kinase is responsible for phosphorylating/dephosphorylating the response regulator, PhoB, which controls the expression of genes that aid growth in low phosphate conditions. The mechanism by which PhoR receives a signal of environmental phosphate levels has remained elusive. A transporter complex composed of the PstS, PstC, PstA, and PstB proteins as well as a negative regulator, PhoU, have been implicated in signaling environmental phosphate to PhoR. Results: This work confirms that PhoU and the PstSCAB complex are necessary for proper signaling of high environmental phosphate. Also, we identify residues important in PhoU/PhoR interaction with genetic analysis. Using protein modeling and docking methods, we show an interaction model that points to a potential mechanism for PhoU mediated signaling to PhoR to modify its activity. This model is tested with direct coupling analysis. Conclusions: These bioinformatics tools, in combination with genetic and biochemical analysis, help to identify and test a model for phosphate signaling and may be applicable to several other systems.

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Genetic analysis, structural modeling, and direct coupling analysis suggest a mechanism for phosphate signaling in Escherichia coli

Abstract

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