# Mechanism of transcription and related gene expression processes in bacteria and human mitochondria

> **NIH NIH R35** · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2024 · $395,000

## Abstract

Project Summary
In the cell, the RNA made by RNA polymerase (RNAP) folds into its functional three-dimensional shape while it
is being synthesized by RNAP. The kinetics of RNA synthesis, which determine the RNA folding outcome, are
influenced by myriad factors, such as intracellular temperature, pH, concentrations of small molecules and
proteins in the cell, and the exact sequence of DNA being transcribed into RNA. Transcription is not a continuous
process: RNA synthesis by RNAP is interrupted by sequence-dependent pauses, during which RNAP remains
bound to the nucleic acids without active nucleotide addition occurring. These pauses create windows of time
for regulation of transcription to occur. Our research program will address the mechanisms of pausing at the
atomic level and the contribution of pausing to co-transcriptional events, such as folding of RNA, in bacteria and
human mitochondria. The first direction of the program aims to develop tools for capturing and visualizing RNA
folding intermediates during transcription and to understand the effect of pH on the kinetics of RNA synthesis by
RNAP, and thus the RNA folding pathway. The resulting tools will be of broad interest to the RNA community
because they can be applied to follow folding of other biologically important RNAs. A second direction will apply
those tools to map the differences in co-transcriptional RNA folding of “healthy” and mutated human
mitochondrial transfer RNAs (mt-tRNA), thus providing the structural basis for disease-causing mt-tRNA
mutations. We will assess the contribution of mitochondrial RNAP (mtRNAP) pausing to the differential folding
of unmutated vs. disease-variant mt-tRNA. Additionally, we will test another hypothesized function of mtRNAP
pausing: coupling of transcription of mitochondrial DNA (mtDNA) to its replication, which is critical for maintaining
enough mtDNA copies for production of protein components of the oxidative phosphorylation machinery. Finally,
a third research direction will address how the balance between transcription of mtDNA and its packaging is
achieved to cater to the ever-changing cellular needs for energy. The completion of the proposed research will
be transformative to the understanding of basic principles governing gene expression, the molecular
mechanisms of diseases linked to mtDNA, and to the applications of RNA-based tools in synthetic biology.

## Key facts

- **NIH application ID:** 10874512
- **Project number:** 5R35GM142785-04
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN DIEGO
- **Principal Investigator:** Tatiana Vladimirovna Mishanina
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $395,000
- **Award type:** 5
- **Project period:** 2021-07-21 → 2026-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10874512

## Citation

> US National Institutes of Health, RePORTER application 10874512, Mechanism of transcription and related gene expression processes in bacteria and human mitochondria (5R35GM142785-04). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10874512. Licensed CC0.

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