How Genetic Precision Is Revolutionizing Green Chemical Production
Imagine a future where the plastics we use daily, the fuels that power our vehicles, and the medicines that heal us are no longer derived from polluting fossil fuels but are instead manufactured by microscopic bacteria working with environmental precision. This isn't science fiction—it's the promise of industrial biotechnology that scientists are bringing closer to reality every day.
At the forefront of this revolution stands an unassuming bacterium called Actinobacillus succinogenes, a microbial superstar capable of producing succinic acid, a valuable platform chemical with wide-ranging applications. But until recently, scientists faced a formidable challenge: how to optimize this natural producer without the genetic tools needed to rewrite its internal code. That all changed with the development of highly efficient base editors—genetic precision tools that are accelerating our path toward sustainable manufacturing 1 3 .
Chemical structure of succinic acid
Succinic acid may not be a household name, but this versatile four-carbon dicarboxylic acid is quietly transforming how we manufacture everyday products.
Traditionally derived from petroleum-based chemicals through energy-intensive processes that require precious metal catalysts and often involve high temperatures and pressures, succinic acid serves as a crucial building block for everything from biodegradable plastics and paints to pharmaceuticals and food additives 3 8 .
The global market for bio-based succinic acid is projected to reach
by 2026, expanding at an impressive compound annual growth rate of 19.6-27.4% 1 8 .
Producing succinic acid biologically instead of petrochemically can reduce
greenhouse gas emissions—from 1.94 kg CO₂ equivalent per kg to just 0.88 kg 8 .
Among microorganisms, Actinobacillus succinogenes stands out as a particularly promising candidate for industrial production. This bacterium is a natural succinic acid accumulator, capable of achieving high concentrations without the extensive genetic modification required by other industrial microbes like E. coli or yeast 3 .
What makes A. succinogenes especially remarkable is its ability to feast on diverse renewable feedstocks—from agricultural waste to industrial byproducts—while simultaneously capturing and utilizing CO₂ during fermentation 3 .
Despite these natural advantages, A. succinogenes had one significant drawback: the lack of efficient genetic modification tools hindered scientists' ability to optimize its production capabilities through metabolic engineering 1 . This limitation kept researchers from unlocking the bacterium's full potential—until now.
Traditional genetic engineering in bacteria often relies on methods that create double-strand breaks in DNA—the biological equivalent of cutting a sentence in half with scissors. While effective in some organisms, this approach proved problematic in A. succinogenes, where such breaks often proved lethal to the cells because of their weak DNA repair mechanisms 1 .
Earlier techniques based on homologous recombination—swapping genetic material between similar DNA sequences—suffered from inefficient mutation rates and typically left behind unwanted "scar" sequences or selection markers that prevented further engineering of the same strain 1 .
The discovery of the CRISPR-Cas system—a bacterial immune adaptation that can target specific DNA sequences—revolutionized genetic engineering across all fields of biology. But the standard CRISPR-Cas9 system still creates those problematic double-strand breaks.
The real breakthrough came with the development of base editors, which combine the targeting ability of CRISPR systems with enzymes that can directly change one DNA base into another without cutting the DNA backbone 1 .
Scissors and paste approach
Find-and-cut function
Find-and-replace function
In their groundbreaking study, researchers set out to develop the first base editing system specifically for A. succinogenes 1 . They designed four different base editors by fusing various Cas9 nickase proteins (which nick rather than cut DNA) with different deaminase enzymes (which convert one base to another):
The researchers cleverly used the lacZ gene—which produces an enzyme that turns bacteria blue in the presence of a specific chemical—as their initial test case. Successful editing of this gene would result in colonies losing their blue color, providing a simple visual indicator of editing efficiency 1 .
The initial results were disappointing—none of the editors worked well until the scientists made a crucial addition: the uracil DNA glycosylase inhibitor (UGI) from a bacteriophage 1 . This inhibitor prevents the bacterial cell from detecting and "correcting" the edits made by the base editors—much like preventing the autocorrect feature from undoing your intentional changes in a word processor.
With this enhancement, the ABE and Td-CBE systems achieved remarkable editing efficiencies of up to 100% for single targets, unprecedented in A. succinogenes 1 . The researchers didn't stop there—they successfully demonstrated multiplex base editing, simultaneously modifying six different sites with 100% efficiency for ABE and two sites with 10% efficiency for Td-CBE 1 .
With their powerful new genetic tools in hand, the researchers then targeted specific genes related to succinic acid production. They focused on transporters—cellular gatekeepers that control what enters and exits the cell:
These findings demonstrated how base editors could not only improve production but also help scientists understand the fundamental biology of A. succinogenes.
| Base Editor Type | Base Conversion | Single-Site Efficiency | Multiplex Editing |
|---|---|---|---|
| ABE | A → G | Up to 100% | 6 sites at 100% efficiency |
| Td-CBE | C → T | Up to 100% | 2 sites at 10% efficiency |
| Initial CBE | C → T | Very low | Not demonstrated |
| Enhanced CBE | C → T | Significant improvement | Not tested |
| Research Tool | Function in Base Editing | Specific Example/Component |
|---|---|---|
| Cas9 Nickase | DNA-targeting component that nicks rather than cuts DNA backbone | nCas9(D10A) mutant |
| Deaminase Enzymes | Catalyzes conversion of one DNA base to another | rAPOBEC1 (for C→T), TadA-8e (for A→G) |
| Uracil DNA Glycosylase Inhibitor (UGI) | Prevents cellular repair systems from reversing edits | PBS1 bacteriophage UGI |
| Guide RNA (gRNA) | Directs editing machinery to specific DNA sequences | Sequence targeting lacZ or transporter genes |
| Reporter Genes | Provides visual confirmation of editing success | lacZ gene (turns colonies blue when functional) |
| Expression Vectors | Delivers editing components into bacterial cells | Plasmid pLGZ922 with frd promoter |
Precisely targets DNA without creating double-strand breaks
Directly converts one DNA base to another
Protects edits from cellular repair mechanisms
The development of efficient base editors for A. succinogenes represents more than just a technical achievement—it opens up new possibilities for sustainable manufacturing. With these tools, scientists can now systematically optimize every aspect of succinic acid production, from enhancing carbon capture to redirecting metabolic fluxes toward desired products.
The implications extend far beyond succinic acid production alone. The same base editing approaches could be adapted for other industrial microorganisms, accelerating the development of bio-based alternatives to petrochemical processes across multiple sectors.
As these tools become more sophisticated and accessible, we move closer to a future where complex chemicals are manufactured by designed microorganisms working with minimal environmental impact, creating a true circular bioeconomy.
The story of base editor development in A. succinogenes exemplifies how fundamental advances in genetic engineering can transform industrial processes. What began as basic research into bacterial immune systems has evolved into a powerful technology that enables us to rewrite the genetic code of microorganisms with unprecedented precision.
As these genetic tools continue to improve and combine with advances in fermentation technology and downstream processing, the vision of a circular bioeconomy comes closer to reality—one where waste carbon streams become valuable resources, and manufacturing works in harmony with the environment rather than against it. The humble A. succinogenes, armed with its new genetic editors, stands ready to play a crucial role in this sustainable future.