Ribosome-Related Proteins:
Alignments, Phylogeny and Structure

Introduction

The ever expanding wealth of genomic data is providing new opportunities for more consistent and reliable phylogenetic reconstructions. While many of the translation- related proteins, such as the tRNA synthetases, appear to lack consistent phylogenetic relationship, perhaps due to horizontal gene transfer and convergent evolution, we have shown that there are a number of translational proteins which provide clear and very consistant phylogenetic implications (Vishwanath et al. " Ribosomal Protein Sequence Block Structure Suggests Complex Prokaryotic Evolution with Implications for the Origin of Eukaryotes." Molecular Phylogenetics and Evolution 2004 Dec;33(3):615-25 ; Hartman et al. Archaea v.2 pXXXX 2006 entitled: " The archaeal origins of the eukarkotic translational system" ). Among these proteins are the ribosomal proteins, some initiation and elongation factors, some RNA polymerase subunits, the SRP proteins and a few others. The phylogenetic implications are in large part the result of a taxon- specific block structure, with blocks unique to, and distinctive of, all sequenced bacterial and separately of all sequenced archaeal genomes. The proteins common to the prokaryotes and the eukaryotes share the archaeal signature blocks, along with various N- and C-terminal additions. This is in parallel with what is seen in the eukaryotic rRNAes, which appear most similar to the archaeal rRNA with multiple insertions.

Overview

One of the main objectives of this study was to gain a deeper understanding of the Evolution of living organisms (Bacteria, Archaea and Eukarya). In order to achieve this goal, we analyzed the molecules that play an important role in the biological information system, specifically ribosomal proteins, polymerase and translation factors. Through profile methods, Blast and Psi Blast, we identified taxa containing representative proteins encompassing the widest taxonomic and ecological range possible and so as to include organisms for which structural and functional information was available. Initial Multiple sequence alignments were generated using various software and then refined so that the hydrophobicity, polarity and turn induction amino acid patterns were preserved in so far as possible. In addition, alignment gaps were restricted to positions between secondary structure elements. Finally amino acid making RNA contacts or involved in protein-protein interactions were aligned to produce conserved positions across the entire alignment if possible without additional gaps.

The blocks identified in the alignments have a length varying from 6 to 70 aa, have no consistent correlation with RNA contacts or protein protein interaction sites, are shorter than typical protein domains but longer than segments associated with enzyme active-sites, and their transitions are clear and well defined.

To investigate deeply the implications of the unusual block structure found, maximum likelihood and maximum parsimony phylogenetic trees were built by concatenating each type of blocks separately for all ribosomal and translation factor proteins respectively. The core branching obtained from the sequence alignments is the same: the trees clearly resolves not only the three domains, but also the separation between Crenarchaea and Euryarchaea, with an implied Crenarchaea "origin" for the eukaryotic translational system. More interesting is the suggested single last common ancestor for all extant Bacteria and all extant Archaea, which in turn opens the possibility of a very ancient and major prokaryotic bottleneck around two billion years ago!

Contact

BMERC - BioMolecular Engineering Research Center
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Boston University
Boston MA 02215 - USA