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.