# Segmental amplification: the collateral effects of co-amplifying genes near a gene under selection for higher dosage

> **NIH NIH F32** · UNIVERSITY OF COLORADO · 2022 · $67,582

## Abstract

PROJECT SUMMARY/ABSTRACT
All organisms must adapt to new and changing environments. The evolution of new molecular functions by gene
duplication and divergence commonly drives this adaptation, allowing organisms to colonize new niches or
consume novel compounds. The inefficient and physiologically irrelevant side activities of enzymes, referred to
as “promiscuous” activities, can serve as the source material for evolving new functions by gene duplication and
divergence. If a promiscuous activity becomes important for fitness due to an environmental change, gene
duplication/amplification can rapidly increase the dosage of the now critical promiscuous activity. However, gene
duplication/amplification events usually duplicate many genes surrounding the gene under selection for higher
dosage. These duplicated genome segments can contain hundreds of genes. Thus, the co-amplified neighboring
genes can potentially cause collateral consequences for the organism depending on their function. While the
expression of amplified genes typically scales with copy number, the extent to which regulatory mechanisms
modulate the expression of recently amplified genes is largely unknown. I hypothesize that the expression and
functions of co-amplified neighboring genes influence the evolution of new enzymes by perturbing physiology
and impacting fitness after segmental amplification. My sponsor’s lab has developed a model system to study
gene duplication/amplification. In this system, an ΔargC Escherichia coli mutant is unable to produce arginine.
A point mutation in the gene proA (proA*) increases the promiscuous ArgC activity of the mutant enzyme ProA*,
weakly restoring arginine synthesis. Amplification of proA* improves fitness because the inefficient ArgC activity
of ProA* is the growth-limiting “weak-link” in metabolism. Previous work from my sponsor’s lab has shown that
proA* rapidly amplifies at its native locus (up to 50 copies) within a few hundred generations and that these
segmental amplifications typically include dozens to hundreds of other neighboring genes. To address the
immediate consequences of segmental amplification, I will modify the ΔargC proA* E. coli model system by
deleting the proBA* operon from its native locus and relocating it to five ectopic sites next to genes predicted to
perturb physiology if overexpressed and evolve these strains for ≤ 300 generations under conditions selecting
for proA* amplification. In Aim 1, I will determine the degree to which mRNA and protein levels expressed from
recently amplified genes scale with gene copy number. In Aim 2, I will characterize how the functions of genes
within an amplified segment affect global gene expression, physiology, and fitness after amplification but before
compensatory mutations can alleviate these effects. Our work will elucidate the extent to which homeostatic
mechanisms can regulate the expression of amplified genes. The results will improve our understanding of how
the functions ...

## Key facts

- **NIH application ID:** 10463583
- **Project number:** 5F32GM143927-02
- **Recipient organization:** UNIVERSITY OF COLORADO
- **Principal Investigator:** Ryan K Fritts
- **Activity code:** F32 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $67,582
- **Award type:** 5
- **Project period:** 2021-09-01 → 2023-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10463583

## Citation

> US National Institutes of Health, RePORTER application 10463583, Segmental amplification: the collateral effects of co-amplifying genes near a gene under selection for higher dosage (5F32GM143927-02). Retrieved via AI Analytics 2026-05-21 from https://api.ai-analytics.org/grant/nih/10463583. Licensed CC0.

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