Microbes Disprove Long-Held Assumption that All Organisms Share a Common Vocabulary


Four letters—A, C, G, and T—make up the DNA bases in all organisms on Earth. The particular order, or sequence, of these same four letters genetically defines an organism and is a main reason that determining the genome sequence is now a foundational starting point for many biological investigations. Within this sequence are shorter, three-letter groups called codons that represent amino acids, the building blocks of proteins that carry out the myriad functions critical to life and biology. There are 64 of these codons and, routinely, 61 of them code for the 20 known amino acids. Three of these triplets function as stop signals and are used to mark the end of protein generation. Given that all organisms have genomes built on the same four letters, scientists had long assumed that they also all shared the same vocabulary and the 64 codons would be interpreted the same way across the board. However, a recent study from the U.S. Department of Energy’s (DOE) Joint Genome Institute (JGI) shows that for some organisms the instructions for these three codons mean anything but stop. The researchers focused on uncultivated microbes, whose genomes had been described through single-cell genomics and metagenomics, and on a collection of viral sequences. Nearly six trillion bases of sequence data were analyzed from 1,776 samples collected from the human body and several sites around the world. The study found that these stop codons often were reassigned to code for amino acids. This work builds on a previous study in which DOE JGI researchers successfully employed single-cell genomics to shed insight on a plethora of microbes representing 29 “mostly uncharted” branches on the tree of life.


Ivanova, N., et al. 2014. “Stop Codon Reassignments in the Wild,” Science 344, 909–13. DOI:10.1126/science.1250691.