Research

The origin and evolution of the ribosome

Temple F Smith¹ , Jung C Lee^2,3 , Robin R Gutell^2,3,4 and Hyman Hartman⁵

¹BioMolecular Engineering Research Center, 36 Cummington Street, Boston University, Boston, MA 02215, USA

²Center for Computational Biology and Bioinformatics, University of Texas, Austin, TX 78712, USA

³Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA

⁴Section of Integrative Biology, University of Texas, Austin, TX 78712, USA

⁵Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

author email corresponding author email

Biology Direct 2008, 3:16doi:10.1186/1745-6150-3-16

Published:	22 April 2008

Abstract

Background

The origin and early evolution of the active site of the ribosome can be elucidated through an analysis of the ribosomal proteins' taxonomic block structures and their RNA interactions. Comparison between the two subunits, exploiting the detailed three-dimensional structures of the bacterial and archaeal ribosomes, is especially informative.

Results

The analysis of the differences between these two sites can be summarized as follows: 1) There is no self-folding RNA segment that defines the decoding site of the small subunit; 2) there is one self-folding RNA segment encompassing the entire peptidyl transfer center of the large subunit; 3) the protein contacts with the decoding site are made by a set of universal alignable sequence blocks of the ribosomal proteins; 4) the majority of those peptides contacting the peptidyl transfer center are made by bacterial or archaeal-specific sequence blocks.

Conclusion

These clear distinctions between the two subunit active sites support an earlier origin for the large subunit's peptidyl transferase center (PTC) with the decoding site of the small subunit being a later addition to the ribosome. The main implications are that a single self-folding RNA, in conjunction with a few short stabilizing peptides, formed the precursor of the modern ribosomal large subunit in association with a membrane.

Reviewers

This article was reviewed by Jerzy Jurka, W. Ford Doolittle, Eugene Shaknovich, and George E. Fox (nominated by Jerzy Jurka).