# Molecular Basis for mRNA Decay in Bacteria

> **NIH NIH R01** · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · 2020 · $355,950

## Abstract

Summary
mRNA degradation affects virtually all cellular activities by limiting the number of times each mRNA can be
translated into protein molecules. By affecting protein synthesis, mRNA degradation allows organisms to adapt
to changing environmental conditions and is therefore particularly important in enabling pathogenic bacteria to
invade and survive in host cells. mRNA degradation in E. coli and many other bacteria involves a decay
pathway triggered by modification of the 5¢ end of the mRNA transcript by RppH and other enzymes. A better
understanding of this pathway could enable the development of new strategies to impede bacterial invasion
and survival in hosts. A recently discovered 5¢-end modification of E. coli mRNAs is nucleoside tetraphosphate
(Np4) caps, originated from stress-induced “alarmones”, such as Ap4A, present in all domains of life. Despite
the identification of capping and decapping enzymes in E. coli, practically nothing is known about mechanisms
of cap addition and removal. This proposal details a research plan to elucidate the mechanisms of Np4 capping
and decapping and the connection between cellular metabolism and RNA degradation in E. coli. Aim 1
addresses how the RNA polymerase adds Np4A cap precursor to mRNA molecules by using cryogenic
electron microscopy, X-ray crystallography, and biochemical experiments to reveal the mechanism and
specificity of incorporation. Aim 2 will uncover how the Np4 cap is removed by RppH, using X-ray
crystallography and biochemistry to understand the specificity and the catalytic mechanisms of decapping. Aim
3 elucidates the molecular basis of Np4 cap removal by ApaH, using X-ray crystallography and biochemistry to
understand the catalytic mechanism and RNA binding rules of this enzyme. Aim 4 reveals a relationship
between cellular metabolism and mRNA degradation. This aim uses structure-based genetic uncoupling to
identify how the metabolic enzyme DapF affects RNA degradation under various growth conditions. The results
of these studies will significantly advance our knowledge of the steps leading to 5¢-end-dependent mRNA
degradation and how modulation of this pathway affects the viability of bacteria.

## Key facts

- **NIH application ID:** 10058513
- **Project number:** 2R01GM112940-06
- **Recipient organization:** NEW YORK UNIVERSITY SCHOOL OF MEDICINE
- **Principal Investigator:** Alexander Serganov
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $355,950
- **Award type:** 2
- **Project period:** 2015-09-21 → 2024-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10058513

## Citation

> US National Institutes of Health, RePORTER application 10058513, Molecular Basis for mRNA Decay in Bacteria (2R01GM112940-06). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10058513. Licensed CC0.

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