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In Silico Biology 10, 0012 (2010); ©2009, Bioinformation Systems e.V.  



Evolution of regulatory motifs of bacterial transcription factors

Konstantin Y. Gorbunov*1, Olga N. Laikova2, Dmitry A. Rodionov1,3, Mikhail S. Gelfand1 and Vassily A. Lyubetsky1

1 Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia
2 State Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia
3 Burnham Institute, La Jolla, CA, USA


* Corresponding author
   Email: gorbunov@iitp.ru


Edited by E. Wingender; received August 18, 2009; revised November 16, 2009; accepted December 23, 2009; published March 09, 2010


Abstract

Unlike evolution of genes and proteins, evolution of regulatory systems is a relatively new area of research. In particular, little systematic study has been done on evolution of DNA binding motifs in transcription factor families. We suggest an algorithm that reconstructs the most parsimonious scenario for changes in DNA binding motifs along an evolutionary tree of transcription factor binding sites. The algorithm was validated on several artificial datasets and then applied to reconstruct the evolutionary history of the NrdR, MntR, LacI, FNR, Irr, Fur and Rrf2 transcription factor families. The algorithm seems to be sufficiently robust to be applicable in realistic situations. In most transcription factor families the changes in binding motifs are limited to several branches. Changes in consensus nucleotides proceed via an intermediate stage when the respective position is not conserved.


Keywords: evolutionary scenario, regulatory signal, frequency matrix, evolution along a tree, transcription factor tree