A number of new principles have emerged from the study of inorganic physiology, including the idea that intracellular metals such as zinc, copper and iron are not `trace elements' from a cellular point of view. Metallome analysis for many cell types reveals that essential metal ions are routinely maintained in most cells at much higher levels (i.e., 0.6 mM). These insights, as well as the emerging literature linking metal physiology to many disease states, underscore the importance of establishing the fundamental principles, general pathways and macromolecular mechanisms required to manage cellular regulation of millions of metal ions. Our approach to delineating these new principles involves mechanistic and structural characterization of metal receptors that switch on and off genes in a metal dependent manner. This proposal addresses several issues in the field of inorganic physiology. The first question is: how do regulatory metal receptors work within the larger macromolecular complexes that they control, including the multisubunit enzymes RNA polymerase and the ribosome? Our preliminary work indicates that copper and zinc homeostasis in E. coli is under the control of complex transcriptional and translational mechanisms that involve protein-induced distortions in DNA structure. The proposed studies also employ advanced sequencing and quantitative proteomic technology to understand how cells control the overall metal economy. This work is revealing many new metal responsive genes in E. coli, which in turn informs our knowledge of fundamental mechanisms used by pathogens when they are subjected to metal limitation by the host immune system.
The specific aims focus on resolving fundamental questions about the structures, functions and molecular mechanisms of these key metal sensing metalloregulatory proteins. The proposed experimental approach will employ x-ray crystallography, biophysical methods, single particle electron microscopy, and proteomic and bioinformatic methods to understand the pathways that E. coli uses to respond to changing metal ion levels in the growth media. The effects of these biophysical switching mechanisms on intracellular metal physiology will then be examined using novel single cell analytical and imaging methods with the overarching goal of establishing general principles and mechanisms that control metal ion homeostasis in normal and disease states.

Public Health Relevance

This proposal focuses on the fundamental ways in which living cells sense, regulate and manage the chemistry of essential nutrient metals such as copper, zinc and iron. For instance, when cells need more metal, some of these sensors turn on metal uptake machinery, and when cells need to get rid of excess metal, other sensors turn on machinery that ejects metals from the cell. This control is important because cellular metal imbalances may lead to diseases involving infectious agents, liver disorders, diabetes and brain functions.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM038784-30
Application #
9606486
Study Section
Macromolecular Structure and Function A Study Section (MSFA)
Program Officer
Anderson, Vernon
Project Start
1987-07-01
Project End
2020-11-30
Budget Start
2018-12-01
Budget End
2019-11-30
Support Year
30
Fiscal Year
2019
Total Cost
Indirect Cost
Name
Northwestern University at Chicago
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
160079455
City
Evanston
State
IL
Country
United States
Zip Code
60201
Que, Emily L; Duncan, Francesca E; Bayer, Amanda R et al. (2017) Zinc sparks induce physiochemical changes in the egg zona pellucida that prevent polyspermy. Integr Biol (Camb) 9:135-144
Mendoza, Adelita D; Woodruff, Teresa K; Wignall, Sarah M et al. (2017) Zinc availability during germline development impacts embryo viability in Caenorhabditis elegans. Comp Biochem Physiol C Toxicol Pharmacol 191:194-202
Deng, Junjing; Hong, Young Pyo; Chen, Si et al. (2017) Nanoscale x-ray imaging of circuit features without wafer etching. Phys Rev B 95:
Staehlin, Benjamin M; Gibbons, John G; Rokas, Antonis et al. (2016) Evolution of a Heavy Metal Homeostasis/Resistance Island Reflects Increasing Copper Stress in Enterobacteria. Genome Biol Evol 8:811-26
Que, Emily L; Bleher, Reiner; Duncan, Francesca E et al. (2015) Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks. Nat Chem 7:130-9
Philips, Steven J; Canalizo-Hernandez, Monica; Yildirim, Ilyas et al. (2015) TRANSCRIPTION. Allosteric transcriptional regulation via changes in the overall topology of the core promoter. Science 349:877-81
Yildirim, Ilyas; Chakraborty, Debayan; Disney, Matthew D et al. (2015) Computational investigation of RNA CUG repeats responsible for myotonic dystrophy 1. J Chem Theory Comput 11:4943-58
Kong, Betty Y; Duncan, Francesca E; Que, Emily L et al. (2015) The inorganic anatomy of the mammalian preimplantation embryo and the requirement of zinc during the first mitotic divisions. Dev Dyn 244:935-47
Hong, Young Pyo; Gleber, Sophie-Charlotte; O'Halloran, Thomas V et al. (2014) Alignment of low-dose X-ray fluorescence tomography images using differential phase contrast. J Synchrotron Radiat 21:229-34
Gilston, Benjamin A; Wang, Suning; Marcus, Mason D et al. (2014) Structural and mechanistic basis of zinc regulation across the E. coli Zur regulon. PLoS Biol 12:e1001987

Showing the most recent 10 out of 25 publications