# Determining the mechanism of heritable inactivation of bacterial immunity

> **NIH NIH F31** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2020 · $40,474

## Abstract

Abstract
Bacterial immune systems represent a potent barrier to genetic parasites including viruses (bacteriophages, or
phages). Harboring immunity against these often-lethal invaders represents a clear fitness benefit.
Unexpectedly, during growth at elevated temperatures (i.e. 42 °C), many Pseudomonas aeruginosa strains
inactivate a potent anti-bacteriophage immune system, type I restriction-modification (R-M). Remarkably, the
inactivation of restriction endonuclease (iREN) phenotype is heritable and persists for at least 60 generations
after return to a low temperature (i.e. 37 or 30 °C), well after the environmental stress has ended. This
phenomenon is an uncharacterized example of epigenetic regulation and cellular memory in bacteria.
Understanding iREN's mechanism could reveal novel bacterial biology, drug targets, and approaches to
potentiate bacteriophage therapeutics. This proposal's objective is to understand the molecular basis of iREN
and identify the genes involved in R-M inactivation and memory. This will be accomplished through 1) the use of
fluorescently tagged R-M proteins to determine their fate during iREN, and 2) the use of RNA sequencing and a
CRISPRi transcriptional repression screen coupled with a phage selection, to collectively observe and perturb
operons involved in iREN. These aims are essential to understanding how bacteria mount this regulatory
response and how this response persists for 60 generations. Our findings may detail a novel cellular strategy for
regulation and epigenetic inheritance, as well as explain how inactivation of immunity could be evolutionarily
beneficial to bacteria.
 This project will be conducted in the Bondy-Denomy lab in the Department of Microbiology and
Immunology at UCSF's School of Medicine. The Bondy-Denomy lab is a multicultural and intellectually diverse
laboratory where undergraduates, graduate students, and postdoctoral fellows work in approximately a 1:1:1
ratio. This distribution of training levels ensures that graduate students enjoy the opportunity to both find
mentorship from various perspectives, as well as develop the leadership skills needed to become a PI by
mentoring others. I have been a member of the Bondy-Denomy lab for 2.5 years, during which I have
spearheaded a collaborative project under Dr. Bondy-Denomy's supervision, culminating in a first author
publication. With two senior graduate students graduating shortly, I am rising to a position of leadership in the
lab. The culture of UCSF is guided by our PRIDE values: professionalism, respect, integrity, diversity, and
excellence. These values serve as both an ideal and the reality of our nurturing community encouraging an
environment of collaboration, mentorship, and rigorous standards for science. By training in this environment,
my scientific and leadership skills will be cultivated to become an excellent and responsible scientist at the head
of an academic research group.

## Key facts

- **NIH application ID:** 10067821
- **Project number:** 1F31GM136153-01A1
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** Senen Dario Mendoza
- **Activity code:** F31 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $40,474
- **Award type:** 1
- **Project period:** 2020-07-01 → 2021-06-13

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10067821

## Citation

> US National Institutes of Health, RePORTER application 10067821, Determining the mechanism of heritable inactivation of bacterial immunity (1F31GM136153-01A1). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10067821. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*