Pathway analysis of Acinetobacter baylyi: a combined bioinformatic and genomics approach

Acinetobacter spp., source of numerous nosocomial infections, deserves a close attention as various multidrug resistance strains are being discovered worldwide. Acinetobacter baylyi is chosen because of its high competence for natural transformation, and its ability to undergo direct homology-based recombination. An in silico comparative analysis of the metabolic pathways of the host Homo sapiens and the pathogen Acinetobacter baylyi was performed by using BLASTp search. This search is against the non-redundant database restricted to the Homo sapiens subset. Sixteen unique pathways identified enlisted a total of 183 drug targets of which 31 belong to the metabolic pathways unique to pathogen having no human homolog. Of these potential drug targets enlisted, RmlA enzyme (d-glucose-1 phosphate thymidylyltransferase) is the first enzyme in the polyketide sugar unit synthesis metabolic pathway, which leads to the formation of l-rhamnose. In gram-negative bacteria, l-rhamnose is one of the important residues of the O-antigen of lipopolysaccharide, a key determinant factor for the virulence of these species. Moreover, these proteins are highly conserved among microorganisms, and therefore, conclusions drawn from the structure of a protein from one species will have strong implications for the corresponding enzyme structure of another origin. Homology modeling of RmlA was performed by MODELLER and the PMDB ID obtained is PM0076419. Further, molecular docking studies were performed for RmlA, which might aid drug design for nosocomial infections.