Analysis of upstream region of antibiotic resistance genes to identify leader peptides

The main aim of this project was to analyze the upstream regions of antibiotic resistance genes in order to identify putative short open reading frames (ORFs) that are likely to regulate the expression of the resistance genes. The larger goal was to characterize the mechanism of programmed drug- and nascent peptide-dependent ribosome stalling wherein the leader peptides are responsible for the regulation of expression of the resistance genes. This study involved the analysis of genes known to confer resistance to the macrolide, lincosamide and streptogramin B (MLSB) classes of antibiotics. These genes are known to be inducible, so that the resistance gene is turned on only in the presence of the antibiotic. This study is a prelude to gain deeper insights into the diversity of short leader peptides involved in the regulation of genes causing MLSB resistance. A web-based short ORF (shORF) finding program was developed to identify all possible short ORFs in the upstream regions of antibiotic resistance genes. This tool was specifically developed to identify short ORFs, considering all the key sequence features pertinent to known leader peptides. The study revealed that around 30% of the known resistance genes possess shORFs, some which have been reported earlier while others are novel and have similarities to other known ORFs.