Comparative and evolutionary analyses of gene regulation

Context and History

Ernesto Pérez-Rueda brought evolutionary analyses of gene regulation to this lab, when he expanded the repertoire of transcription factors of E.coli (Pérez-Rueda and Collado-Vides, 2000) to all the bacterial and archeal
genomes (Pérez-Rueda and Collado-Vides, 2001), showing that in fact some ancient families are shared between bacteria and archea.

In a similar transition, based on the high capacity to predict operons initially in E.coli (Salgado et al., 2000), Gabriel Moreno-Hagelsieb analyzed the conservation and flexibility in the organization of operons across all bacteria (Moreno-Hagelsieb et al., 2001). This provided the basis for a non-orthologous comprehensive method to
predict operons in bacteria (Moreno-Hagelsieb and Collado-Vides 2002).

Nebulon: Predicting Functionally associated genes

The flexibility in operon organization and rearrangement across Prokaryotes is the basis for a method to predict functionally associated genes in bacteria that we named Nebulon (Janga et al., 2005).

A radical new type of bioinformatic studies enriched our laboratory with the Ph.D. thesis of Arturo Medrano-Soto, who, while working with Gabriel Moreno-Hagelsieb, got interested in horizontal gene transfer in association with his studies in collaboration with Andrés Christen on clustering methods of heterogeneous variables (Medrano-Soto et al., 2005). Arturo's paper challenges the view that successfully transferred genes have a poor codon usage within the recipient genome (Medrano-Soto et al., 2004).

References.

Janga SC , Collado-Vides J., Moreno-Hagelsieb G. (2005) "Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons" Nucleic Acids Res. 33 : 2521-2530.

Medrano-Soto A., Moreno-Hagelsieb G , Vinuesa P., Christen J.A. and Collado-Vides J. (2004) "Successful Lateral Transfer Requires Codon Usage Compatibility Between Foreign Genes and Recipient Genomes" Molecular Biology and Evolution 21 :1884-1894

Medrano-Soto, A. Christen, J.A. and Collado-Vides, J. (2005) "BClass: A Bayesian Approach Based on Mixture Models for Clustering and Classification of Heterogeneous Biological Data" Journal of Statistical Software 13 (2):1-18.

Moreno-Hagelsieb, G., Treviño, V., Pérez-Rueda, E., Smith, T.E., and Collado-Vides, J. (2001) "Transcription unit conservation in the three domains of life: a perspective from Escherichia coli " Trends in Genetics , 17 : 175-177.

Moreno-Hagelsieb G. and Collado-Vides J. (2002) "A powerful non-homology method for the prediction of operons in prokaryotes" Bioinformatics (ISMB-02) 18: Suppl.1 S329-S336

Pérez-Rueda E., and Collado-Vides J. (2000) "The Repertoire of DNA-Binding Transcriptional Regulators in Escherichia coli" Nucleic Acids Research 28 : 1838-1847

Pérez-Rueda E., and Collado-Vides J. (2001) "Common History at the Origin of the Position-Function Correlation in Transcriptional Regulators in Archaea and Bacteria" J. Mol. Evol . 53 : 172-179

Salgado H., Moreno-Hagelsieb G., Smith T.F., and Collado-Vides J. (2000) "Operons in Escherichia coli : Genomic Analyses and Predictions" Proc.Natl.Acad.Sci.USA 97 : 6652-6657