Synthesis of a re-designed E. coli genome

Ygggdrasil

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Summary
Scientists redesigned a bacterial genome to omit three codons and synthesized the bacteria, which could be useful tools in biotechnology.
All organism on earth use a genetic code consisting of 64 three-letter codons to encode the 20 amino acids found in proteins. Scientists in the field of synthetic biology have long sought to expand the genetic code to allow encoding of more than 20 natural amino acids found in most organisms. Some synthetic biologists have worked toward this goal by engineering the ribosome to decode four-letter codons, while others have sought to add more letters to the DNA alphabet. Another approach to expand the genetic code involves removing some of the redundancy of the natural genetic code to make room for additional amino acids. Previous work had completely removed all 321 instances of one stop codon from the widely studied bacteria E. coli. Published today in the journal Nature, scientists report synthesis of a functional E. coli genome with all instances of three codons removed from the genome.

Fredens et al. Total synthesis of Escherichia coli with a recoded genome. Nature. Published online 15 May 2019. https://www.nature.com/articles/s41586-019-1192-5

Abstract:
Nature uses 64 codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon—out of up to 6 synonyms—to encode each amino acid. Synonymous codon choice has diverse and important roles, and many synonymous substitutions are detrimental. Here we demonstrate that the number of codons used to encode the canonical amino acids can be reduced, through the genome-wide substitution of target codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. Our synthetic genome implements a defined recoding and refactoring scheme—with simple corrections at just seven positions—to replace every known occurrence of two sense codons and a stop codon in the genome. Thus, we recode 18,214 codons to create an organism with a 61-codon genome; this organism uses 59 codons to encode the 20 amino acids, and enables the deletion of a previously essential transfer RNA.
The work was based a prior study by the same group published in 2016 that showed the feasibility of removing the three codons from a segment of the E. coli genome. In their new work, the scientists synthesize and assemble the full, re-coded E. coli genome. The bacteria with the redesigned genomes are functional and viable, though they grow somewhat more slowly than their natural counterparts. While the first bacterial genome (consisting of ~1 million base pairs) was synthesized back in 2010, the 4 Mb E. coli genome represents the largest full genome synthesized to date. The work now allows the researchers the freedom to insert genes to allow these engineered bacteria to produce proteins containing unnatural amino acids, which will likely be the subject of future work. Removal of additional codons may be difficult as demonstrated by previous studies, though more extensive re-coding could be possible in the future.

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Summary: Scientists redesigned a bacterial genome to omit three codons and synthesized the bacteria, which could be useful tools in biotechnology.

The work now allows the researchers the freedom to insert genes to allow these engineered bacteria to produce proteins containing unnatural amino acids, which will likely be the subject of future work.
What would be some applications?
 

Ygggdrasil

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What would be some applications?
1. With three unused codons, scientists could engineer the bacteria to use up to three additional unnatural amino acids, which it could then incorporate into proteins. These unnatural amino acids could be used to provide the proteins with new functions not found in nature.

2. Because the bacteria no longer use some of the same codons, they may be resistant to almost all viruses (bacteriophages) that might try to attack it (since presumably the virus genes would contain the unused codons and would not be produced correctly in the engineered bacteria). This would be very helpful to prevent problems associated with phage infections when bacteria are used in large-scale industrial settings.
 

BillTre

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2. Because the bacteria no longer use some of the same codons, they may be resistant to almost all viruses (bacteriophages) that might try to attack it (since presumably the virus genes would contain the unused codons and would not be produced correctly in the engineered bacteria). This would be very helpful to prevent problems associated with phage infections when bacteria are used in large-scale industrial settings.
Sounds like a challenge to the viruses' evolutionary abilities.
I would expect:
  1. phages would be selected to avoid using of the incorrect codons in the few proteins (relative to the bacteria) that they make
  2. phages would then be able to evolve utilization the novel codons to make new proteins that might incorporate the novel amino acids
These guys would in a sense be in a new evolutionary cyber-universe defined by their different codons.

The chemical nature of the new amino acids could be important.
Would they be naturally found pretty commonly but not genome encoded amino acids (such as posttranscriptionally modified amino acids found in some proteins (methylation, ubiquitination, ...))? In that case they should be easily metabolized. If not they might be poisonus or have some other effect. Of curse the modified bacteria would then have to have some novel way to deal with the novel amino acid, which would present an additional problem for the engineers.
 

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