RecA gene genetic diversity and its regulatory element analysis: The case of Vibrio cholerae

Abstract

In conventional systems, indicator organisms are used to monitor drinking water quality which is unspecific in detecting pathogens. On the contrary, molecular techniques play vital role in these aspects by providing precise genetic information about particular pathogen of interest via proper biomarkers. The aim of this study was to undertake genetic relatedness and promoter region analysis for V. cholerae strains based on recA gene sequences which were retrieved from NCBI. Sequences homologous were ensured using BLASTn from RefSeq sequence in the NCBI using V. cholerae serotype O1 strain N16961 as a reference. Accordingly, considering only complete and coding sequences with query coverage of greater than 90% and E-value of less than 5%, a total of 109 sequences were recovered from NCBI. The genetic diversity analysis was carried out using MEGA X. The analysis revealed more than 99% sequence similarity among V. cholerae strains. From promoter regions analyses, five motifs shared by all (100%) of the promoter input sequences were identified. Using TOMTOM web application, motif_1was compared to a known prokaryotes' transcription factor database to search for its similarity with known regulatory motifs and was shown to serve as abundant binding site for helix-turn-helix (HTH) transcription factor gene family to regulate expression of V. cholerae recA genes. Furthermore, our analysis revealed that the V. cholerae recA gene promoter regions are CpG islands rich. In conclusion, all V. cholerae strains shared a very high degree of recA gene sequence similarity apart from other vibrios, which indicates that these non-virulent strains may be the remnant of pathogenic strains with the loss of toxin encoding genes.