User:Ernesto Perez-Rueda

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Contact Info

Ernesto Perez-Rueda (an artistic interpretation)
  • Universidad Nacional Autonoma de Mexico
  • Avenida Universidad 1001, Col. Chamilpa
  • Cuernavaca, Morelos, Mexico
  • Email address:
  • Facebook : Laboratorio de Biologia Computacional [1]

I work in the "Instituto de Biotecnologia[2]" at Universidad Nacional Autonoma de Mexico[3]. I have interest on Gene Regulation, Genomics, Evolution of metabolism, and Bioinformatics.


  • 1999, PhD Biomedical Sciences, Centro de Investigacion Sobre Fijacion de Nitrogeno [4], UNAM
  • 1997, MS Biomedical Sciences, Centro de Investigacion Sobre Fijacion de Nitrogeno [5], UNAM
  • 1995, BS Biology, Facultad de Ciencias[6], UNAM

Lab Members / Research interests

  1. Aniel Brambila Tapia / Postdoctoral research / Comparative Genomics --> New member.
  2. Nancy Rivera Gomez [7]/ Gene Regulation, Evolution
  3. Dagoberto Armenta Medina [8] / Evolution of metabolism
  4. Patricia Ortegon Cano / Evolution of metabolism, Genetic algorithms design
  5. Cesar Poot Hernandez / Evolution of metabolism, Bioinformatics
  6. Mashenka Garcia Saiz / Pathogenesis, Genomics


  • 31. Ibarra JA, Perez-Rueda,E, Carroll RK, Shaw LN. 2013. Global Analysis of Transcriptional Regulators in Staphylococcus aureus. BMC Genomics. In press.

  • 30. Tenorio-Salgado S, Tinoco R, Vazquez-Duhalt R, Caballero-Mellado J, Perez-Rueda,E. 2013. Identification of volatile compounds produced by the bacterium Burkholderia tropica that inhibit the growth of fungal pathogens. Bioengineered. In press.[9]

  • 29. Ibarra JA, García-Zacarias CM, Lara-Ochoa C, Carabarin-Lima A, Tecpanecatl S, Perez-Rueda,E, Martínez-Laguna Y, Puente JL. 2013. Further characterization of functional domains of PerA, role of amino and carboxy terminal domains in DNA binding. PLoS One. In press.

  • 28. Huerta-Saquero A, Evangelista-Martínez Z, Moreno-Enriquez A,Perez-Rueda,E. 2013. Rhizobium etli asparaginase II: An alternative for acute lymphoblastic leukemia (ALL) treatment. Bioengineered. 4(1). [10]

  • 27. Perez-Rueda,E, Martinez-Nuñez M.A. 2012. The Repertoire of DNA-Binding Transcription Factors in Prokaryotes: Functional and Evolutionary Lessons. Science Progress. 95:315-329. [11]

  • 26. Moreno-Enriquez, A. Evangelista-Martínez, Z. González-Mondragón, E. Calderon-Flores, A. Arreguin, R. Perez-Rueda,E. Huerta-Saquero, A. 2012. Biochemical characterization of recombinant L-asparaginase (AnsA) from Rhizobium etli, a member of an increasing Rhizobial-type family of L-asparaginases. J. Microbiol. Biotechnol. 22:292–300. [12]

  • 25. Tenorio-Salgado,S. Huerta-Saquero,A. Perez-Rueda,E. 2011. New insights on gene regulation in archaea. Comput. Biol. Chem. 35, 341-346.[13].

A more detailed explanation about the archaeal TFs role is described.

  • 24.Knodler, L. Ibarra, JA.Perez-Rueda,E. Yip, C, Steele-Mortimer O. 2011. Coiled-coils domains enhance the membrane association of Salmonella type II effectors. Cellular Microbiology, 13, 1497-1517.[14].

  • 23. Rivera-Gomez,N. Segovia,L. Perez-Rueda,E. 2011. The diversity and distribution of TFs and their partner domains play an important role in the regulatory plasticity in bacteria. Microbiology, 157, 2308-2318.[15].

We evaluate the repertoire of winged helix-turn-helix domains (wHTHs), a class of DNA-binding TFs in bacterial sequence genomes. The repertoire of wHTHs in terms of their partner domains, or PaDos was evaluated. Based on the PaDos, we defined three main groups of families: i) monolithic, those families with little diversity of PaDos, such as LysR; ii) promiscuous, those families with a high diversity of PaDos; iii) monodomain, with families of small sizes, such as MarR. These findings suggest that PaDos have a very important role in the diversification of regulatory responses in bacteria, probably contributing to their regulatory complexity.

  • 22. Santos-Zavaleta A, Gama-Castro MS, Perez-Rueda,E. 2011. A comparative genome analysis of the RpoS Sigmulon. Microbiology, 157, 1393-1401. [16].

  • 21. Armenta-Medina, D. Perez-Rueda,E. Segovia, L. 2011. Identification of functional motions in the adenylate kinase (ADK) protein family by computational hybrid approaches Proteins, 79, 1662-1671. [17].

In this work we used an integrative computational hybrid approaches that combined statistical coupling analysis (SCA), molecular dynamics (MD), and normal mode analysis (NMA), to identify evolutionarily coupled residues involved in functionally relevant motion in the adenylate kinase protein family.

  • 20. Chavez-Calvillo,G. Perez-Rueda,E. Lizama,G. Zuniga Aguilar,J.J. Gaxiola,G. Cuzon,G. Arena-Ortiz,L. 2010. Differential gene expression in Litopenaeus vannamei shrimp in response to diet changes. Aquaculture, 300, 137-141. [18]

  • 19. Perez-Rueda,E. Janga,S.C. 2010. Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin Mol Biol Evol. 27, 1449-1459. [19]

We propose that archaeal TFs are significantly small compared with other protein-coding genes in archaea as well as bacterial TFs, suggesting that a large fraction of these small-sized TFs could form different combinations of monomers similar to that observed in eukaryotic transcriptional machinery.

  • 18. Martinez-Nunez,M.A. Perez-Rueda,E. Gutierrez-Rios,R.M. Merino,E. 2010. New insights into the regulatory networks of paralogous genes Microbiology, 156, 14-22. [20]

Our survey reinforces the notion that despite TFs being the most prominent components shaping the regulatory networks, other elements are also important. These include small RNAs, riboswitches, RNA-binding proteins, sigma factors, protein-protein interactions and DNA supercoiling, which modulate the expression of genes involved in particular metabolic processes or induce a more complex response in terms of the regulatory networks of paralogous genes in an integrated interplay with TFs

  • 17. Perez-Rueda,E. Janga,S.C. Martinez-Antonio,A. 2009. Scaling relationship in the gene content of transcriptional machinery in bacteria Mol Biosystems, 5, 1494-1501. [21]

Here, we show that sigma, transcription factors (TFs) and the number of protein coding genes occur in different magnitudes across 291 non-redundant eubacterial genomes. Clustering of the distribution of transcription and sigma families across genomes suggests that functional constraints could force their co-evolution, as was observed in sigma54, IHF and EBP families.

  • 16. Janga,S.C. Perez-Rueda,E. 2009. Plasticity of transcriptional machinery in bacteria is increased by the repertoire of regulatory families Comput Biol Chem, 33, 261-268. [22]

  • 15. Hernandez-Montes,G. Diaz-Mejia,J.J. Perez-Rueda,E. Segovia,L. 2008. The hidden universal distribution of amino acids biosynthetic networks: a genomic perspective on its origins and evolution Genome Biol, 9, R95.[23]

We predicted a core of widely distributed network branches biosynthesizing at least 16 out of the 20 standard amino acids, suggesting that this core occurred in ancient cells, before the separation of the three cellular domains of life. The distribution of two types of alternative branches to this core: analogs, enzymes that catalyze the same reaction (using the same metabolites) and belong to different superfamilies is described; and 'alternologs', herein defined as branches that, proceeding via different metabolites, converge to the same end product

  • 14. Ibarra,J.A. Perez-Rueda,E. Segovia,L. Puente,J.L. 2008. The DNA-binding domain as a functional indicator: the case of the AraC/XylS family of transcription factors Genetica, 133, 65-76. [24]

In this work, using the DNA binding domain of 58 experimentally characterized proteins from the AraC/XylS (A/X), 1974 A/X proteins were found in 149 out of 212 bacterial genomes. This domain was used as a template to generate a phylogenetic tree and as a tool to predict the putative regulatory role of the new members of this family based on their proximity to a particular functional cluster in the tree

  • 13. Sanchez-Flores,A. Perez-Rueda,E. Segovia,L. 2008. Protein homology detection and fold inference through multiple alignment entropy profiles PROTEINS: Structure, Function, and Bioinformatics, 70, 248-256. [25]

  • 12. Hernandez-Mendoza,A. Quinto,C. Segovia,L. Perez-Rueda,E. 2007. Ligand-binding prediction in the resistance-nodulation-cell division (RND) proteins Comput. Biol Chem, 31, 115-123. [26]

AcrB of Escherichia coli was used to predict the compounds transported by 47 RND proteins, based on 14 amino acids directly involved in substrate interactions. These residues provide enough information to identify 16 groups that correlates with the ligand they extrude, such as proteins expelling aromatic hydrocarbons or proteins expelling heavy metals

  • 11. Diaz-Mejia,J.J. Perez-Rueda,E. Segovia,L. 2007. A network perspective on the evolution of metabolism by gene duplication. Genome Biol, 8, R26. [27]

This work shows that metabolic networks have a high retention of duplicates within functional modules, and a preferential biochemical coupling of reactions. A high retention of duplicates between chemically similar reactions, as illustrated by fatty-acid metabolism, was also identified. The retention of duplicates between chemically dissimilar reactions is, however, also greater than expected by chance

  • 10. Hernandez-Lucas,I. Ramirez-Trujillo,J.A. Gaitan,M.A. Guo,X. Flores,M. Martinez-Romero,E. Perez-Rueda E. Mavingui,P. 2006. Isolation and characterization of functional insertion sequences of rhizobia FEMS Microbiol.Lett., 261, 25-31. [28]

  • 9. Moreno-Campuzano,S. Chandra,J.S. Perez-Rueda,E. 2006. Identification and analysis of DNA-binding Transcription Factors in Bacillus subtilis and other Firmicutes- A genomic approach BMC Genomics, 7, 147. [29]

A collection of 237 DNA-binding Transcription Factors (TFs) was identified in B. subtilis. 59% of them were predicted to be repressors, 17% activators, 17% were putatively identified as dual regulatory proteins and the remaining 6.3% could not be associated with a regulatory role. 56 TFs were found to be autoregulated, most of them negatively, though a significant proportion of positive feedback circuits were also identified. In addition, six global regulators were defined in B. subtilis based on the number and function of their regulated genes.

  • 8. Gonzalez AD, Espinosa V, Vasconcelos AT, Perez-Rueda E, Collado-Vides J. 2005. TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes. Nucleic Acids Research.33, 98-102. [30]

  • 7. Perez-Rueda E, Collado-Vides J, Segovia L. 2004. Phylogenetic Distribution of DNA-binding Transcription Factors in Bacteria and Archaea A genomic approach. Computational Biology and Chemistry. 28, 341-350 [31]

  • 6. Perez-Rueda E, Collado-Vides J. 2001. Common history at the origin of the position-function correlation in transcriptional regulators in Archaea and Bacteria. Journal of Molecular Evolution. 53,172-179. [32]

  • 5. Moreno-Hagelsieb G, Treviño V, Perez-Rueda E, Smith T, Collado-Vides J. 2001 Transcription unit conservation in the three domains of life: a perspective from Escherichia coli. Trends in Genetics. 17,175-177. [33]

  • 4. Perez-Rueda E, Collado-Vides J. 2000. The repertoire of DNA-binding transcriptional regulators in Escherichia coli. Nucleic Acids Research. 28, 1838-1847. [34]

A total of 314 regulatory DNA-binding proteins was identified in Escherichia coli, which might represent its minimal set of transcription factors. The collection is comprised of 35% activators, 43% repressors and 22% dual regulators. This work describes a full characterization of the repertoire of regulatory interactions in a whole living cell.

  • 3. Salgado H, Santos-Zavaleta A, Gama-Castro S, Millan-Zárate D, Diaz-Peredo E, Sanchez-Solano F, Perez-Rueda E, Bonavides-Martinez C, Collado-Vides J. 2001. RegulonDB (version 3.2): Transcriptional regulation and operon organization in Escherichia coli K12. Nucleic Acids Research. 29, 72-74. [35]

  • 2. Thieffry, D. Huerta AM, Perez-Rueda E, Collado-Vides J. 1998. From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. BioEssays, 20:1-8. [36]

  • 1. Perez-Rueda E, Gralla J, Collado-Vides J. 1998. Genomic Position Analysis and the Transcription Machinery. Journal of Molecular Biology. 27,165-170. [37]

In bacteria and eukaryotes, regulatory proteins are found to have their DNA-binding domains near termini.

Book Chapters

  • 4. Hernández-Montes, G. Armenta-Medina, D. Perez-Rueda, E. 2012. Evolution of metabolism: A network perspective of the amino acid biosynthesis pathways. Encyclopedia of Systems Biology. Springer. [38]

  • 3. Arena-Ortiz, L. Rojas-Herrera, R. Apodaca-Hernandez, J. Perez-Rueda E. 2012 Flora Bacteriana en Camarones. En Recursos Genéticos Microbianos en la zona Golfo-Sureste de México. Volumen I. Editores M. Gamboa, R. Rojas. In press.

  • 2. Perez-Rueda, E. Rivera-Gomez, N. Martinez-Nunez, MA. Tenorio-Salgado, S. 2012. Evolution of DNA-binding Transcription Factors and Regulatory Networks in Prokaryotes in: Evolution of regulatory networks in bacteria Horizon Scientific Press. [39]

  • 1. Collado-Vides J, Moreno-Hagelsieb G, Perez-Rueda, E. et al. 2002 Genomics of Gene Regulation: The view from Escherichia coli in: Gene Regulation and Metabolism: Post-Genomic Computational Approaches eds. Collado-Vides J. and Hofestadt R. MIT Press.

Papers of Dissemination

  • 2. Perez-Rueda E, Santos-Zavaleta A. Patino-Guerrero EA. 2012. Lo que hay detrás de las biopelículas bacterianas ¿perjudiciales o benéficas? Hypatia, 43. [40] In spanish.
  • 1. Perez-Rueda E 2011. Lo conocido de los desconocidos microbios llamados “Arqueas”. Hypatia. [41]. In spanish.

Useful links