Non-canonical RNA caps - cellular reaction to environment and stress

Introduction

The goal of this project is to understand the role of non-canonical RNA caps (mainly dinucleoside polyphosphates = NpnNs) in prokaryotes and eukaryotes. The 5' termini of the RNA are critical structures and are the least characterized among RNA modifications. In this project, we will develop selective capturing techniques for identification of NpnN-RNA sequences and identify the interacting partners of NpnN-RNA. Furthermore, we will reveal their metabolism and their role in cellular reaction to stress conditions in prokaryotes and eukaryotes.

Background

Until recently, only canonical structures, NAD or CoA, have been known as 5' RNA caps. We discovered an entirely new class of 5' RNA caps - dinucleoside polyphosphates (NpnN) in prokaryotic and eukaryotic cells. Based on our preliminary data, we know that methylated NpnN caps stabilize RNA of E. coli in the stationary phase and that some NpnN caps can also be found in mammalian cells.

Research Questions

We do not yet know:

1. The sequence of RNAs capped with NpnNs.
2. How many types of NpnN RNA caps exist in eukaryotes.
3. Whether RNA stabilization is their only role.
4. Why there are so many types of NpnN RNA caps (we identified nine in E. coli).
5. Whether NpnN-RNA can be translated, etc.

Alarmones and Their Mechanism

The role of free NpnNs, identified fifty years ago, is yet to be elucidated. NpnNs are called alarmones, as their concentration increases under stress conditions. The mechanism by which the alarm is recognized in cells is unknown.

Hypothesis

I presume that their cellular effects are mediated by the RNA, where they serve as RNA caps. As such, they become an important part of RNA metabolism and can be recognized by various RNA interacting proteins, triggering additional effects in cellular metabolism.

Potential Impact

The presented project has the potential to solve the puzzle of the role of NpnNs and clarify the connection between RNA metabolism and immune response or virulence factors of viruses and bacteria.