The long term goal of this research project is to achieve quantitative understandings of system-level E. coli chemotaxis behaviors and their underlying molecular level mechanisms. We will develop mathematical models of protein interaction network and its dynamics based on structural and biochemical details of the chemotaxis signaling pathway. These models will be studied by using analytical analysis and numerical simulation methods. The results from these models will be used to explain experimental data and make testable predictions. The iterative comparison between models and experimental data will be used to improve/refine the models. In this proposal, we will focus on studying two essential aspects of the E. coli chemotaxis pathway: 1) The signaling dynamics and function of the chemorecetor array. We will investigate how the mixed receptor array can distinguish different stimuli (signals) and how the cell makes decision based on the information. We want to study the effect of ATP hydrolysis in sensor kinase signaling and how it modulates the kinase response sensitivity to receptor ligand binding. 2) The switching mechanism for flagellar motor and its dependence on mechanical signals. We want to understand how the flagellar motor can be controlled by changes in its mechanical environment (force, load) in addition to the intracelur chemical signals. In summary, we plan to investigate and understand how an E. coli cell senses different (chemical and physical) signals, how it processes this information, and how it makes decisions in complex environments with multiple, time varying cues.

Public Health Relevance

The concepts and tools developed in the quantitative, system-level modeling of a complete sensory signal transduction pathway will be useful in understanding signaling pathways and sensory systems in higher organisms, including human. The molecular level understanding of the bacterial chemotaxis pathway is important to study the role of bacterial pathogens in human health.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM081747-05
Application #
8336875
Study Section
Special Emphasis Panel (ZRG1-BST-F (02))
Program Officer
Deatherage, James F
Project Start
2007-09-24
Project End
2015-08-31
Budget Start
2012-09-01
Budget End
2013-08-31
Support Year
5
Fiscal Year
2012
Total Cost
$259,481
Indirect Cost
$84,481
Name
Ibm Thomas J. Watson Research Center
Department
Type
DUNS #
084006741
City
Yorktown Heights
State
NY
Country
United States
Zip Code
10598
Cao, Li-Hui; Jing, Bi-Yang; Yang, Dong et al. (2016) Distinct signaling of Drosophila chemoreceptors in olfactory sensory neurons. Proc Natl Acad Sci U S A 113:E902-11
Lan, Ganhui; Tu, Yuhai (2016) Information processing in bacteria: memory, computation, and statistical physics: a key issues review. Rep Prog Phys 79:052601
Cao, Yuansheng; Wang, Hongli; Ouyang, Qi et al. (2015) The free energy cost of accurate biochemical oscillations. Nat Phys 11:772-778
Yu, Daqi; Ma, Xiaomin; Tu, Yuhai et al. (2015) Both piston-like and rotational motions are present in bacterial chemoreceptor signaling. Sci Rep 5:8640
Sartori, Pablo; Tu, Yuhai (2015) Free energy cost of reducing noise while maintaining a high sensitivity. Phys Rev Lett 115:118102
Hu, Bo; Tu, Yuhai (2014) Behaviors and strategies of bacterial navigation in chemical and nonchemical gradients. PLoS Comput Biol 10:e1003672
Zhu, Xuejun; Ge, Xin; Li, Ning et al. (2014) Angle sensing in magnetotaxis of Magnetospirillum magneticum AMB-1. Integr Biol (Camb) 6:706-13
Bi, Shuangyu; Yu, Daqi; Si, Guangwei et al. (2013) Discovery of novel chemoeffectors and rational design of Escherichia coli chemoreceptor specificity. Proc Natl Acad Sci U S A 110:16814-9
Hu, Bo; Tu, Yuhai (2013) Coordinated switching of bacterial flagellar motors: evidence for direct motor-motor coupling? Phys Rev Lett 110:158703
Vladimirov, Nikita; Tu, Yuhai; Traub, Roger D (2013) Synaptic gating at axonal branches, and sharp-wave ripples with replay: a simulation study. Eur J Neurosci 38:3435-47

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