APR 13, 2015 8:07 AM PDT

Microbes Refute Belief All Organisms Share a Common Vocabulary

WRITTEN BY: Judy O'Rourke
The Science
Some wild microorganisms, found in nature and not grown in the laboratory, reinterpret the instructions coded into their DNA. Short segments of DNA that signal other organisms to stop adding building blocks or amino acids to a protein are instead interpreted as "add another amino acid."

The Impact
The data from these wild microbes helps researchers realize that some preconceived notions of microbial behavior may not be accurate because they are based on data from the small fraction of microbes that have been cultivated and studied in a laboratory.

Summary
Four letters - A, C, G, and T - represent the bases in DNA for all organisms on Earth. Because the particular order, or sequence, of these four letters genetically defines an organism, determining the sequence is a foundational starting point for many biological investigations.
Researchers have found that some wild organisms interpret a genetic sequence typically read as
Within this sequence are shorter, three-letter groups called codons that represent amino acids, the building blocks of proteins that carry out myriad functions critical to life. Of the 64 codons, 61 routinely code for the 20 known amino acids. Three codons function as stop signals and are used to mark the end of protein generation.

Given that all organisms have genetic material or genomes built on the same four letters, scientists have long assumed that organisms also share a common vocabulary and interpret the 64 codons the same. However, researchers from the Department of Energy (DOE) Joint Genome Institute (JGI) show that for many uncultivated microbes, the instructions for these three codons mean anything but stop.

The stop codons often were reassigned to code for amino acids. Led by Eddy Rubin, MD, PhD, director, DOE JGI, researchers studied a collection of viral sequences as well as uncultivated microbes whose genomes had been described through single-cell genomics and metagenomics. Nearly 6 trillion bases of sequence data were analyzed from 1,776 samples collected from the human body and several sites around the world. The team found that reassignment of all three stop codons was found but with different preferences by domain and habitat.

The team observed distinct patterns of stop codon reassignment (each stop codon has a name: amber, opal, and ochre.). Bacteria showed only opal reassignments. Eukaryotes showed ochre reassignments. Archaea were devoid of codon reassignments.

Among DNA viruses, the team found both amber and opal reassignments. This work builds on a previous study in which DOE JGI researchers successfully used single-cell genomics to shed insight on a plethora of microbes representing 29 "mostly uncharted" branches on the tree of life.

[Source: Department of Energy/Office of Science]
About the Author
  • Judy O'Rourke worked as a newspaper reporter before becoming chief editor of Clinical Lab Products magazine. As a freelance writer today, she is interested in finding the story behind the latest developments in medicine and science, and in learning what lies ahead.
You May Also Like
APR 24, 2020
Microbiology
How Syphilis Evades the Immune System
APR 24, 2020
How Syphilis Evades the Immune System
The incidence of syphilis has been rising for the past two decades, and over 115,000 new cases were diagnosed in the US ...
MAY 10, 2020
Cell & Molecular Biology
RNA Structure Informs RNA Function
MAY 10, 2020
RNA Structure Informs RNA Function
Proteins carry out many of an organism's critical functions, and they are coded for by genes. To make a protein from ...
MAY 14, 2020
Genetics & Genomics
Tracking Single Cells as They Build an Adult Organism
MAY 14, 2020
Tracking Single Cells as They Build an Adult Organism
Organisms develop from a single cell that gives rise to all the different kinds of tissues and structures that are found ...
JUN 11, 2020
Genetics & Genomics
Restoring Hearing by Editing Only One Base of a Gene
JUN 11, 2020
Restoring Hearing by Editing Only One Base of a Gene
Errors in genes can cause serious diseases. Some of those errors are large, while others are due to a change in only one ...
JUL 11, 2020
Genetics & Genomics
Cocaine Changes Gene Expression in a Specific Part of the Brain
JUL 11, 2020
Cocaine Changes Gene Expression in a Specific Part of the Brain
Scientists have begun to examine how cocaine exposure alters gene expression in a specific region of the brain, and the ...
JUL 13, 2020
Genetics & Genomics
New Therapeutic Targets For Lupus Are Identified
JUL 13, 2020
New Therapeutic Targets For Lupus Are Identified
Advances in computational and genetic technologies have enabled scientists to search the genome to look for places where ...
Loading Comments...