FEBS Letters
Volume 584, Issue 2 , Pages 325-333, 21 January 2010

Computational analysis of tRNA identity

Edited by Manuel Santos

School of Natural Sciences and UC Merced Center for Computational Biology, University of California, Merced, CA 95343, USA

Received 3 November 2009; received in revised form 20 November 2009; accepted 20 November 2009. published online 27 November 2009.

Abstract 

I review recent developments in computational analysis of tRNA identity. I suggest that the tRNA–protein interaction network is hierarchically organized, and coevolutionarily flexible. Its functional specificity of recognition and discrimination persists despite generic structural constraints and perturbative evolutionary forces. This flexibility comes from its arbitrary nature as a self-recognizing shape code. A revisualization of predicted Proteobacterial tRNA identity highlights open research problems. tRNA identity elements and their coevolution with proteins must be mapped structurally over the Tree of Life. These traits can also resolve deep roots in the Tree. I show that histidylation identity elements phylogenetically reposition Pelagibacter ubique within alpha-Proteobacteria.

Keywords: Proteobacteria, tRNA, Determinant, Logo, Coevolution, Phylogeny

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PII: S0014-5793(09)01001-1

doi:10.1016/j.febslet.2009.11.084

FEBS Letters
Volume 584, Issue 2 , Pages 325-333, 21 January 2010

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