Mohammed Farshad Abdollah Nia, Ph.D. Quantitation of Bacterial Proteome Composition under Oxygen-limiting and Slow Growth Conditions Project Summary: In their natural habitat and in infectious diseases, bacterial cells continually face limitations in nutrient supply and oxygen availability and are subject to a variety of other challenges such as pH, osmotic, and antibiotic stress. These conditions limit how fast the bacteria can grow, and the cells must undergo substantial physiological changes in order to adapt and maintain competitive growth. It is a central aim of systems biology to understand how cell physiology is modulated in response to such environmental stimuli. Quantitative measurements of the proteome can yield comprehensive estimates of the physiological state of the cell under the conditions of interest. We use mass spectrometry for whole-proteome measurements in Escherichia coli to learn how bacterial cells can maintain optimal growth under limiting conditions. Previous work from our lab examined carbon, nitrogen, and antibiotic-induced ribosome limitations under fully aerobic conditions. It was demonstrated that the E. coli proteome partitions into coarse-grained sectors, with each sector’s total mass abundance exhibiting positive or negative linear relations with the growth rate. This led to a coarse-grained model that revealed basic principles of resource allocation in proteome economy of the cell. However, the current coarse-grained proteome sector model was not characterized under microaerobic conditions and at slow growth rates (> 2 h doubling time) which are the disease-relevant conditions in the gut and within bacterial biofilms. We have recently developed technical capabilities to culture E. coli under controlled anaerobic and microaerobic conditions in chemostat with access to slower growth rates. We hypothesize that the use of fermentation metabolism instead of aerobic respiration will require extensive remodeling of the E. coli proteome, resulting in a different characterization of the known proteome sectors and the emergence of new oxygen-dependent sectors with unstudied types of response to oxygen supply. The first aim of this proposal is to characterize the known proteome sectors under microaerobic and anerobic conditions and to compare the model parameters with aerobic results. The second aim is to identify new oxygen-dependent sectors and characterize their response to oxygen with an extended modelling approach. Our preliminary data suggest that the new oxygen-dependent sectors exhibit highly nonlinear response to oxygen, thus a kinetic version of the coarse-grained model needs to be developed. Through these studies, we will expand the predictive and applicable scope of coarse-grained proteome models to better understand bacterial physiology in a disease- relevant setting. This training will take place in the Williamson lab at Scripps Research in collaboration with the Hwa lab at UC San Diego. The training will enha...