Bioinformatic analysis of multi-drug resistant class 1 integron-coded protein of <i>Citrobacter freundii</i>

Abstract

Background: The understanding of the secondary structure of the class 1 integron coded protein is necessary to decipher potential drug target and also to infer evolutionary ancestry at the proteomic level. This study was therefore aimed at determining the secondary structure of class 1 integron-coded protein and also to provide information on their evolutionary ancestry.

Methodology: Five different sequences of Citrobacter freundii with the following accession numbers; KP902625.1, KP902624.1, KP902623.1, KP901093.1 and KP902609.1 were obtained using nucleotide BLAST (http://blast. ncbi.nlm.nih.gov/Blast.cgi) and subjected to evolutionary analysis, pairwise distance calculation, secondary structure and neutrality test using MEGA explorer, Kimura 2 parameter, SOPMA tool and Tajima’s test respectively.

Results: Results of the NCBI queries revealed significant identity with class 1 integron of the studied Citrobacter freundii. The nucleotide sequence alignment depicted several conserved regions with varying degree of transitions, transversions, insertions, and deletions while the amino acid sequences of the nucleotides showed 42 conserved sites among all the sequences. The secondary structure of the class 1 integron coded protein depicted significant representation of the random coil (43.74±3.24), alpha helix (25.69±6.29) and the extended strands (22.42±2.41) than the beta turns (8.15±1.12). The Tajima’s Neutrality test of five nucleotide sequences of Citrobacter freundii analyzed by considering the first, second and third codons as well as the non-coding regions revealed a total of 127 positions in the final datasets while the Tajima’s Neutrality test was estimated to be -0.1038.

Conclusion: The study confirmed common evolutionary ancestor for the class 1 integron coded protein found in Citrobacter freundii. Our study also documents the higher representation of random coil, alpha helix and extended strands than the beta turns. The negative value of the Tajima’s neutrality test suggests higher levels of both low and high frequency polymorphisms thus indicating a decrease in the class 1 integron population size and balancing selection

Keywords: Evolutionary, Protein structure, Class 1 integrons, Citrobacter freundii