Comprehensive Analysis and Assessment on Codon Usage Pattern of Hemolytic Genes from Different Strains of Leptospira interrogans

Abstract

Background: Leptospirosis is a disease that is zoonotic in nature. It is easily able to survive in the environment and gets transmitted from the reservoir hosts such as rat to humans. Though the cause of Leptospira interrogans virulency is not determined, these studies expresses that the product of a Leptospira interrogans gene sphH is hemolytic in nature and is capable of lysing the erythrocyte cells and also few epithelial cell membranes. Aim: In this study, we have analyzed the codon usage bias of the gene sphH, taken from 49 strains of Leptospira interrogans. Materials and Methods: Data Collection: The full CDSs nucleotide of the gene sphH from 49 Leptospira interrogans was downloaded separately in FASTA format from the NCBI nucleotide database. Molecular Evolutionary Genetics Analysis (MEGA) program was used to edit and align the coding sequences. With the help of statistical techniques such as RSCU and ENC we have determined the codons mostly used to express the gene sphH and source of the bias with methods such as parity rule 2, neutrality plots. Result: The nucleotide content of the , gene across 49 variants of leptospira divulged that the usage of A (36.03% ± 0.74) and T (31.81% ± 0.65) occurred more frequently than the usage of G (17.88% ± 0.57) and C (14.28% ± 0.66) making the gene composition AT more than GC. The composition of bases in the 3rd position saw base T most frequent than base A. Conclusion: The codon and amino acid use patterns reflect this bias in genetic composition. Leptospiral strains have a similar general codon usage pattern and are slightly biassed. The majority of the frequently occurring codons are A- and U-ending, showing that mutational bias is the primary driver determining codon usage in this bacterium. There were significant changes in synonymous codon usage frequencies between Leptospira interrogans and with other virulent strains. Codon use preferences to account for these differences.