Evolution of Regulatory Motifs of Bacterial Transcription Factors

Article type: Research Article

Authors: Gorbunov, Konstantin Y. | Laikova, Olga N. | Rodionov, Dmitry A.^; | Gelfand, Mikhail S. | Lyubetsky, Vassily A.

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

Note: [] Corresponding author. E-mail: [email protected]

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

DOI: 10.3233/ISB-2010-0425

Journal: In Silico Biology, vol. 10, no. 3-4, pp. 163-183, 2010