In silico identification of a new group of specific bacterial and fungal nitroreductases-like proteins

The nitroreductase family comprises a group of FMN- or FAD-dependent and NAD(P)H-dependent enzymes able to metabolize nitrosubstituted compounds. The nitroreductases are found within bacterial and some eukaryotic species. In eukaryotes, there is little information concerning the phylogenetic position and biochemical functions of nitroreductases. The yeast Saccharomyces cerevisiae has two nitroreductase proteins: Frm2p and Hbn1p. While Frm2p acts in lipid signaling pathway, the function of Hbn1p is unknown. In order to elucidate the function of Frm2p/Hbn1p and the presence of homologous sequences in other prokaryotic and eukaryotic species, we performed an in-depth phylogenetic analysis of these proteins. The results showed that bacterial cells have Frm2p/Hbn1p-like sequences (termed NrlAp) forming a distinct clade within the fungal Frm2p/Hbn1p family. Hydrophobic cluster analysis and three-dimensional protein modeling allowed us to compare conserved regions among NrlAp and Frm2/Hbn1p proteins. In addition, the possible functions of bacterial NrlAp and fungal Frm2p/Hbn1p are discussed.