05/23/2014
Microbes Disprove Long-Held Assumption that All Organisms Share a Common Vocabulary
Certain bacteria and bacteriophages exhibited lineage-specific recoding of their stop codons.
The Science
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.
Summary
The genetic code appears to be largely conserved across all domains of life. Although limited deviations have been reported, these researchers used metagenomics to survey the prevalence of stop codon reassignment in naturally occurring microbial populations. Certain bacteria and bacteriophages exhibited lineage-specific recoding of their stop codons. In one specific phage, the genome was restructured into two genetic sets. One set of genes was encoded in a way that didn’t gel with the host genome and probably helped with infection. A second set of more host-compatible sequences encoded proteins expressed in the later stages of infection.
BER Program Manager
Ramana Madupu
U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]
References
Ivanova, N., P. Schwientek, H. J. Tripp, C. Rinke, A. Pati, M. Huntemann, A. Visel, T. Wokye, N. C. Kyrpides, and E. M. Rubin. 2014. “Stop Codon Reassignments in the Wild,” Science 344, 909–13. DOI:10.1126/science.1250691.