# An improved low-endotoxin Clean Genome E. coli strain for production of biological products

> **NIH NIH R44** · SCARAB GENOMICS, LLC · 2024 · $842,151

## Abstract

Abstract
E. coli has played a vital role in the production of recombinant proteins and plasmid DNA (pDNA) for therapeutic
use since the advent of the biopharmaceutical industry. E. coli remains the workhorse in the production of
heterologous proteins and pDNA because of its short doubling time, its ability to grow to high cell densities and
its relatively straightforward scale-up potential. About 30% of all approved therapeutic proteins and 70% of anti-
cancer agents continue to be made in E. coli. As the need for high quality pDNA has increased due to success
in gene therapy and mRNA vaccines, there is a growing need for high quality, low toxicity bacterial strains for
production of plasmids. The goal of this direct to Phase II application is to develop a versatile next-generation E.
coli strain built using Scarab Genomics’ Clean Genome® platform that combines low endotoxin levels with
enhanced genetic stability characteristics for nucleic acid and protein production. Specifically, we propose to use
genetic techniques to substantially lower the level of contaminating endotoxin in pDNA and recombinant protein
preparations.
Scarab Genomics has developed and patented its reduced genome E. coli strains, which has removed 650
potentially contaminating proteins and all transposable elements. We propose to further eliminate genes that are
responsible for the activation of the Toll-like receptor-4 (TLR-4). We propose that phosphorylation sites on lipid
A and on carbohydrates on the LPS side chains activate the Limulus amebocyte lysate (LAL) assay. These will
be removed and pDNA and protein products from this strain tested in a TLR-4 and LAL assay. Success of the
proposal will culminate in an E. coli strain that is low in endotoxin and increased genetic stability but continues
to generate high levels of nucleic acid and protein under fermentation conditions.

## Key facts

- **NIH application ID:** 11008247
- **Project number:** 1R44GM156147-01
- **Recipient organization:** SCARAB GENOMICS, LLC
- **Principal Investigator:** FREDERICK R BLATTNER
- **Activity code:** R44 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $842,151
- **Award type:** 1
- **Project period:** 2024-09-01 → 2027-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/11008247

## Citation

> US National Institutes of Health, RePORTER application 11008247, An improved low-endotoxin Clean Genome E. coli strain for production of biological products (1R44GM156147-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/11008247. Licensed CC0.

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