# Evolution and Regulation of Bacterial Proteome Composition

> **NIH NIH R35** · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · 2021 · $386,750

## Abstract

Project Summary/Abstract
 The proteome is a quantitative output of a genome and the ultimate effector of cellular functions. Yet
remarkably little is known about the logic behind proteome construction. The goal of my research program is to
understand the evolutionary driving forces that shape protein levels, as well as the precise regulation that is
employed to arrive at the exact set point. Our entry point is a powerful quantitative proteomics method based
on ribosome profiling. Using bacterial model systems, we have shown that many homologous proteins have
quantitatively conserved expression levels across divergent species, suggesting strong constraints on protein
abundance that we do not currently understand. To elucidate the mechanistic basis for the preferred protein
levels in relation to cell fitness, we are using theory-guided experimental design to investigate the
consequence of protein misregulation on global physiology in E. coli and B. subtilis. Furthermore, we are
establishing a comprehensive comparative proteomics approach to broadly identify key proteins whose levels
are invariant despite regulatory changes throughout evolution. This approach will open up new avenues for
uncovering the control points of biochemical systems, and provide a new way of thinking about proteome
imbalance in diseases.
 The second arm of my research program is to understand how cells produce their proteome with
quantitative precision. As indicated by our preliminary results, such precise control is clearly important to many
proteins, but we have only a rudimentary understanding of how these rates are finely tuned. We are now
developing genome-wide techniques to interrogate the prevalence of feedback regulation in maintaining
proteome homeostasis in bacteria. We are also investigating how co-regulated genes in operons are
differentially expressed to achieve exact protein levels. Our approach in this area focuses on the development
of quantitative assays that allow us to accurately characterize the molecular processes perfected by natural
selection. We anticipate that our mechanistic dissection, coupled with systems-level inquiry into proteome
composition, will make bacterial model organisms the first system for which we have a quantitative
understanding from genome to proteome to fitness and back.

## Key facts

- **NIH application ID:** 10246335
- **Project number:** 5R35GM124732-05
- **Recipient organization:** MASSACHUSETTS INSTITUTE OF TECHNOLOGY
- **Principal Investigator:** Gene-Wei Li
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $386,750
- **Award type:** 5
- **Project period:** 2017-09-01 → 2023-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10246335

## Citation

> US National Institutes of Health, RePORTER application 10246335, Evolution and Regulation of Bacterial Proteome Composition (5R35GM124732-05). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10246335. Licensed CC0.

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