Method Developed to Decipher Alternative Genetic Codes

In a paper published in eLife today, Harvard researchers describe a new computational method that can read the genome sequence of any organism and then determine its genetic code. The program, called Codetta, has the potential to help scientists expand their understanding of how the genetic code evolves and correctly interpret the genetic code of newly sequenced organisms.

Almost every organism, from E. coli to humans, uses the same genetic code. It’s why the code was once thought to be set in stone. But scientists have discovered a handful of outliers—organisms that use alternative genetic codes—exist where the set of instructions are different. This is where Codetta can shine. The program can help to identify more organisms that use these alternative genetic codes, helping shed new light on how genetic codes can even change in the first place.

“Understanding how this happened would help us reconcile why we originally thought this was impossible… and how these really fundamental processes actually work,” first author Yekaterina Shulgina explained.

Already, Codetta has analyzed the genome sequences of over 250,000 bacteria and other single-celled organisms for alternative genetic codes, and has identified five that have never been seen. In all five cases, the code for the amino acid arginine was reassigned to a different amino acid. It’s believed to mark the first-time scientists have seen this swap in bacteria and could hint at evolutionary forces that go into altering the genetic code.

Codetta works by reading the genome of an organism and then tapping into a database of known proteins to produce a likely genetic code. It differs from other similar methods because of the scale at which it can analyze genomes. The researchers say the next step of the work is to use Codetta to search for alternative codes in viruses, eukaryotes, and organellar genomes like mitochondria and chloroplasts.