Recoded E. coli: Constructive Bio Transforms Biomanufacturing with Synthetic Genomes

Biomanufacturing is becoming competitive with traditional chemical synthesis, but there’s still work to do. Can E. coli with fully synthetic genomes reach the places where synthetic chemistry becomes too complex?

Well, Constructive Bio thinks so! And in this issue of the Deep Tech Breakdown, we go deep into their technology.

PS: This is a long one, so get yourself a drink and let’s start!

Constructive Bio was founded in 2022 in Cambridge, UK, in 2022. They’re transforming E. coli into biofactories for making new classes of biological polymers.

Biologics are some of the biggest advances in modern biomedicine.

They’re complex medicines produced using biological systems, from bacterial and yeast to mammalian cells. We’ve seen an explosion of them in recent years:

So, biologics are cool. But all of these approaches come with manufacturing challenges, and the specific challenges vary by molecule.

Some biologics, like antibodies, are already produced efficiently using cell culture, although it’s still expensive and time-consuming. Others, especially complex peptides and molecules containing non-canonical chemistry, are much harder to manufacture.

Therapeutic peptides are an interesting example.

Many are made using chemical synthesis, especially solid-phase synthesis. It works, but it can get expensive, requires large quantities of organic solvents, and the chemistry limits what you can build when the molecules get longer or more complex.

You can also make simple peptides biologically, but many therapeutic peptides are chemically modified to improve stability, half-life, or bioavailability. These modifications are still done using synthetic chemistry, with the same problems.

What if you could move more of that manufacturing process into a cell? Grow peptides in bacteria, with fewer organic solvents, and the ability to build molecules that conventional chemistry or biology can’t easily make?

That would transform biomanufacturing. It wouldn’t just make existing drugs cheaper and cleaner, but it could enable entirely new materials. Biomaterials with properties that you can’t find in nature, or pharmaceuticals with functions that were impossible before!

That’s the problem Constructive Bio is trying to solve.

Using biology to create products that chemistry can’t make.

That’s essentially Constructive Bio’s mission. Their solution? A combination of a completely recoded E. coli genome, programmable translation, and industrial-scale fermentation creates BioForge, their manufacturing platform.

Constructive is built on over 20 years of research from the lab of Jason W. Chin, currently Executive Director of the Generative Biology Institute, Oxford, and CSO of Constructive Bio.

The idea is to take control of bacterial protein production by controlling translation. Why? To create biological polymers with chemical functionality that isn’t available to normal cells.

And the key tools for doing this are non-canonical amino acids.

Most proteins in nature are built from the same 20 canonical amino acids. There are a few exceptions, but the standard genetic code is built around these canonical 20. Everything outside of them is generally referred to as a non-canonical amino acid (ncAA). There are hundreds of naturally occurring and synthetic ncAAs, with different chemical properties!

And ncAAs are incredibly useful in biotech.

They can add chemical handles for attaching molecules such as fluorophores or other functional groups, or be used in therapeutic proteins and peptides to improve properties such as stability, half-life, or resistance to degradation.

But the really cool possibility goes beyond modifying existing proteins. What if we could use ncAAs to create proteins with new chemical functions, or even entirely new polymers? That’s where the limitations of the normal genetic code become a problem.

Constructive’s answer? Codon recoding.

A codon is a sequence of 3 DNA or RNA bases that specifies an amino acid or signals the termination of protein synthesis during translation. There are 64 possible triplet codons, but they don’t all encode different amino acids; many are synonymous.

But what if we could use fewer codons?

We could free some of them up and reassign them to completely different building blocks: non-canonical amino acids! This is exactly what the Chin lab did, and it’s the base of Constructive’s technology.

Constructive uses large-scale DNA assembly to build bacterial genomes from scratch. The Chin lab has been a pioneer in methods for genome-scale DNA synthesis and assembly!

The process starts by computationally redesigning the complete ~4 Mb E. coli genome. The redesigned genome was divided into large fragments, assembled in yeast, and then progressively used to replace the original genome inside E. coli!

And I’m keeping it short here, but it’s an incredibly impressive feat! And a lot of work. The result was Syn61, an E. coli strain with a 61-codon genetic code. Three codons that were previously used by the cell were removed from the genetic code, freeing them for reassignment.

And the bacteria didn’t seem to mind. Syn61 does grow more slowly than the original strain, but the fact that a cell can work with such a radically redesigned genetic code is an extraordinary result!

And in 2025, they doubled down.

Using a similar approach, the team recoded additional codons, obtaining an E. coli strain that uses a 57-codon genetic code: Syn57! This frees seven codons that can potentially be reassigned to new functions.

This time, the bacteria do mind: their doubling time is 4x longer! But each free codon could, in principle, be reassigned to a different ncAA. Syn61-derived strains demonstrated incorporation of multiple ncAAs into the same proteins. Syn57 expands the coding capacity even further!

But it’s important to keep in mind that seven available codons doesn’t mean that Syn57 can manufacture a finished product containing seven different ncAAs. It means that the chassis has the potential to support a much larger expansion of the genetic code.

The other essential component for incorporating ncAAs into proteins is a set of orthogonal tRNA/synthetase pairs.

Each reassigned codon needs a matched pair: the tRNA recognizes the reassigned codon, while aminoacyl-tRNA synthetase loads that tRNA with the correct ncAA. This new pair needs to work with the ncAA and its reassigned codon without interfering with the normal cell machinery. That’s what “orthogonal” means here.

This process can be a major bottleneck. You need to find tRNAs that work in the host, synthetases that recognize the desired ncAA, and combinations that don’t cross-react with the cell’s existing machinery.

To make this process more efficient, the Chin lab has developed automated computational and experimental approaches to discover orthogonal tRNAs and identify compatible synthetases.

Without the tRNA/synthetase pairs, recoding the genome only gives you empty codons! But put the two pieces together, and you get something more powerful than a conventional production strain.

Constructive combines them with industrial-scale fermentation to build its biomanufacturing platform.

Okay, but what are the advantages of using this tech over conventional manufacturing?

There are two main ones:

So, Constructive has built an interesting platform, based on solid science and a clear first application (therapeutic peptides with non-canonical amino acids). But there’s always something that might go wrong with commercializing science.

Constructive isn’t the only one trying to improve how complex biological molecules are manufactured.

I think their competition can be divided into 2 buckets:

To me, it looks like Constructive is doing a lot of things well:

The science here is impressive!

We have seen E. coli with a redesigned genetic code that reassigns codons, introduces non-canonical amino acids, and uses the resulting cells to manufacture molecules that conventional chemistry or biology can’t easily make.

Aside from the potential applications, that’s the part I find most impressive!

That a synthetic, radically recoded genome can work at all is amazing. It shows how far synthetic biology has come: we’ve gone from changing individual genes to rewriting the whole genome of a bacterium so that its genetic code can support functions that weren't available to the original.

Now, can this cool technology create a better biofactory?

For me, the biggest questions are 3:

If Constructive answers those questions, the same technology could give us proteins, peptides, and more biological polymers with chemistry we simply don’t have nowadays! And potentially prove that synthetic biology can compete with chemistry on cost and reliability.

If you made it this far, thank you! What do you think of biomanufacturing? Do you think it will replace chemistry, or live alongside it? Reply and let me know!