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Open Access Research article

Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteria

Abel D González Pérez1, Evelyn González González1, Vladimir Espinosa Angarica23, Ana Tereza R Vasconcelos4* and Julio Collado-Vides5

Author Affiliations

1 Centro Nacional de Bioinformática. Industria y San José, Capitolio Nacional, CP. 10200, Habana Vieja, Ciudad de la Habana, Cuba

2 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza. Pedro Cerbuna 12, 50009 Zaragoza, España

3 Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza. Corona de Aragón 42 Edificio Cervantes, 50009 Zaragoza, España

4 Laboratório Nacional de Computação Científica. Av. Getulio Vargas 333, Quitandinha, CEP 25651-075, Petropolis, Rio de Janeiro, Brasil

5 Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México. Av. Universidad s/n., Colonia Chamilpa 62210, Cuernavaca, Morelos, México

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BMC Genomics 2008, 9:128  doi:10.1186/1471-2164-9-128

Published: 17 March 2008

Abstract

Background

In the past years, several studies begun to unravel the structure, dynamical properties, and evolution of transcriptional regulatory networks. However, even those comparative studies that focus on a group of closely related organisms are limited by the rather scarce knowledge on regulatory interactions outside a few model organisms, such as E. coli among the prokaryotes.

Results

In this paper we used the information annotated in Tractor_DB (a database of regulatory networks in gamma-proteobacteria) to calculate a normalized Site Orthology Score (SOS) that quantifies the conservation of a regulatory link across thirty genomes of this subclass. Then we used this SOS to assess how regulatory connections have evolved in this group, and how the variation of basic regulatory connection is reflected on the structure of the chromosome. We found that individual regulatory interactions shift between different organisms, a process that may be described as rewiring the network. At this evolutionary scale (the gamma-proteobacteria subclass) this rewiring process may be an important source of variation of regulatory incoming interactions for individual networks. We also noticed that the regulatory links that form feed forward motifs are conserved in a better correlated manner than triads of random regulatory interactions or pairs of co-regulated genes. Furthermore, the rewiring process that takes place at the most basic level of the regulatory network may be linked to rearrangements of genetic material within bacterial chromosomes, which change the structure of Transcription Units and therefore the regulatory connections between Transcription Factors and structural genes.

Conclusion

The rearrangements that occur in bacterial chromosomes-mostly inversion or horizontal gene transfer events – are important sources of variation of gene regulation at this evolutionary scale.