Recoded Genome 2D: Engineering a Virus-Resistant Microbe

Genome Recoding

TAG→TAA sites recoded 0 / 30

Phage Challenge

Multiplicity of infection 4 phage

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Simulation speed 1.0×

Ready. Recode the genome, then decide when it is safe to delete RF1. Drag the ring to rotate it.

Live Readouts

Genome recoded

RF1 status

Present

Host viability

100%

Phage replication success (last run)

—

How it works

A genomically recoded organism (modelled on E. coli C321.ΔA) removes one of its 64 codons from ordinary use so it can be freed up as a synthetic firewall against viruses:

Step 1  Recode every native TAG (amber) stop → synonymous TAA
        (silent at the protein level — same amino acid sequence)
Step 2  Once TAG is used nowhere in the genome, delete
        release factor 1 (RF1), the protein that terminates
        translation at TAG
Step 3  TAG is now a "blank" codon — reassign it to a
        non-canonical amino acid via an orthogonal tRNA

The payoff is viral resistance: a bacteriophage genome still carries its own native TAG stop codons (it evolved for the *original* code). Without RF1, the host ribosome cannot terminate at TAG — it reads through into random near-cognate amino acids, so every phage protein comes out with a garbled, non-functional C-terminal extension. Translation still runs, but functional phage particles never assemble.

The catch is ordering: if RF1 is deleted before recoding finishes, the host's own unrecoded TAG stop codons fail exactly the same way — its own essential proteins misfold — which is why host viability in this simulator tracks the fraction of the genome recoded whenever RF1 is gone, and only reads 100% once recoding is complete first. Recoded (TAA) sites terminate correctly via release factor 2 regardless of whether RF1 is present, which is why they always read "safe" on the translation-tape panel below the ring.

Genome ring — 30 marked sites arranged around the circular chromosome (blue = recoded TAA, slate = native TAG). Drag it with the mouse or a finger to rotate the view.
Translation-tape panel — a live readout below the ring: a reading head sweeps across the same 30 sites, flashing green when translation terminates correctly and trailing a red garbled extension when it reads through instead.
Recoding slider — silently swaps TAG→TAA at each of 30 marked genome sites.
Delete RF1 — toggles the release factor off/on; safe only once recoding reads 30/30.
Launch Phage Challenge — spawns phage on the ring that home in on a genome site and attempt translation; outcome depends on whether RF1 is present to terminate at their native TAG codons.

Native TAG site Recoded (TAA) Bacteriophage RF1

drag to rotate