# Quantitation of Bacterial Proteome Composition under Oxygen-limiting and Slow Growth Conditions

> **NIH NIH F32** · SCRIPPS RESEARCH INSTITUTE, THE · 2022 · $69,802

## Abstract

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...

## Key facts

- **NIH application ID:** 10426100
- **Project number:** 5F32GM142272-02
- **Recipient organization:** SCRIPPS RESEARCH INSTITUTE, THE
- **Principal Investigator:** Mohammad Farshad Abdollah Nia
- **Activity code:** F32 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $69,802
- **Award type:** 5
- **Project period:** 2021-06-15 → 2023-06-14

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10426100

## Citation

> US National Institutes of Health, RePORTER application 10426100, Quantitation of Bacterial Proteome Composition under Oxygen-limiting and Slow Growth Conditions (5F32GM142272-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10426100. Licensed CC0.

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