Friday, October 12, 2012
Research interests
Our work contribute significantly in the understanding of gene
regulation and metabolism evolution in prokaryotes, and can be used as a base
stone to genetic modeling in bacteria and most importantly in archaea, where
few information is available.
Transcriptional Regulation
We are devoted to the analysis of DNA-binding
transcription factors in prokaryotic genomes (Archaea and Bacteria). In brief,
the analysis has been centered in the identification of the DNA-binding
domains, a discrete region of around 60 amino acid length. The identification
is achieved by the design of family specific HMM models and by the search with
models deposited in diverse databases (Superfamily and PFAM). In this regard,
we have identified and evaluated the repertories of TFs in two bacterial
models, as Escherichia coli K12 and Bacillus subtilis 168, and
more recently in 52 archaeal genomes. In archaeal genomes with similar sizes to
bacterial genomes, we identified a minor proportion of TFs and a large
proportion of small TFs. Hence, we proposed that archaeal TFs exhibit a modular
activity as occurs in eukarya, where archaeal TFs can act as hetero or homo
oligomers and they can form diverse multiple complexes.
Evolution of metabolism
By
using computational approaches, in a previous work eleven different amino acid
pathways have been proposed as ancestral to bacteria, archaea and eukarya,
closer to LUCA. In addition, in a recent work we suggest that metabolic
pathways have evolved by recruitment of blocks of enzymes sharing catalytic
activities.
People/Research Interests
Actual Members
Welcome to our new member, Aniel Brambila.
- Aniel Brambila Tapia / Postdoctoral research / Comparative Genomics --> New member.
- Nancy Rivera Gomez */ Gene Regulation, Evolution
- Dagoberto Armenta Medina * / Evolution of metabolism
- Cesar Poot Hernandez / Evolution of metabolism, Bioinformatics
- Mashenka Garcia Saiz / Pathogenesis, Genomics
Past Members
- Patricia Ortegon Cano / Evolution of metabolism/ Honours
- Monica Peñaloza / Identificacion of functional residues
- Eduardo Estrada / Protein structure modelling
- Gerardo May / Evolution of metabolism
- Alberto Santos Zavaleta / RpoS regulon / Honours
Selected Papers
- Knodle
LA, et al 2011. Coiled-coil domains mediate the association of Salmonella type III effectors with host
cell membranes. Cellular Microbiology.13,
1497-1517
- Rivera-Gomez
N, et al 2011. The transcriptional machinery in bacteria is modified by the
repertoire of Partner Domains associated to Transcription Factors. Microbiology. 157,2308 – 2318
- Armenta-Medina
D., et al 2011. Identification of functional motions in the adenylate kinase
(ADK) protein family by computational hybrid approaches. PROTEINS:
Structure, Function, and Bioinformatics. 79(5): 1662–1671.
- Perez-Rueda & Chandra Janga S. 2010.
Identification and genomic analysis of transcription factors in archaeal
genomes exemplifies their functional architecture and evolutionary origin. Molecular Biology and Evolution. 27,1–11.
- Martinez-Nuñez
MA, et al 2010. New insights into the Regulatory Network of Paralogous
Genes. Microbiology 156,14-22.
- Hernandez-Montes
G, et al 2008. The hidden universal distribution of amino acids biosynthetic
networks: a genomic perspective on its origins and evolution. Genome Biology. 9:R95.
- Diaz-Mejia JJ, et
al 2007. A network perspective on the evolution of metabolism by gene
duplication. Genome Biology. 8:R26.
- Moreno-Campuzano
S, et al 2006. Identification and analysis of DNA-binding Transcription Factors
in Bacillus subtilis and other
Firmicutes- A genomic approach. BMC
Genomics 7 147.
- Perez-Rueda & Collado-Vides. 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.
- Perez-Rueda & Collado-Vides 2000. The
repertoire of DNA-binding transcriptional regulators in Escherichia coli. Nucleic
Acids Research. 28,1838-1847.
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