Experimental Verification of the Evolutionary Neutrality of the 16S rRNA Gene, an Indicator for Evolutionary Taxonomy

– Another important finding is also relevant to consideration of the gene's fitness as an indicator –

Researcher) Kentaro Miyazaki, Leader, the Synthetic Bioengineering Research Group, the Bioproduction Research Institute

Main points

  • Discovered that the 16S rRNA genes of two types of bacteria widely separated in terms of evolutionary taxonomy have identical functions
  • Verified for the first time that the 16S rRNA gene, an indicator for the evolutionary taxonomy of prokaryotes, is evolving neutrally
  • Proposed a “cradle model” as the evolutionary pattern of the 16S rRNA gene
Figure 1
Cradle model of ribosome evolution based on comparative analysis involving substitution of 16S rRNA


Clarification of the phylogenic relationships among microorganisms offers important clues to the elucidation of the origin of life and subsequent evolutionary processes. However, unlike animals and plants, microorganisms have left almost no fossil record, and it is therefore extremely difficult to sketch out the history of their phylogenic evolution based on fossils. Because of this, the phylogenic relationships among microorganisms have to date been discussed based on phylogenic relationships among molecules. rRNAs are biopolymers that are present in all living things. The 16S rRNA gene is regarded as a molecular marker (or “molecular clock”) that accurately reflects the phylogenic evolution of living creatures. However, up to the present, there has been no experimental verification as to whether 16S rRNA satisfies the conditions required to serve as a molecular clock.


Researchers of AIST and the Faculty of Science, Hokkaido University, jointly conducted comparative analysis of the functions of 16S rRNA found in the ribosomes of two bacteria known to be distinct at the phylum level, the highest level of classification in bacteria taxonomy. It was found that the majority of the sequence differences between the analyzed 16S rRNA genes did not result in a significant effect on functions, verifying that the 16S rRNA genes evolve neutrally.

This outcome provides the first-ever experimental demonstration that the gene fulfill the condition of evolutionary neutrality, which is a basic requirement for use as a molecular clock in evolutionary phylogenic analysis. The results of the analysis suggest that the majority of mutations in base sequences specific to species do not affect ribosomal functions. At the same time, this fact suggests that the recombination of 16S rRNA genes among species is comparatively flexible, and this is expected to be used as an important finding in examining the fitness of 16S rRNA gene for use as a molecular clock.

▲ ページトップへ