Analysis of Codon Usage Pattern in the Genome of a Novel Bacterial Strain Isolated from Bakreswar Hot Spring

Abstract

BKH4, a novel bacterial strain discovered in a hot spring in Bakreswar (India), has proven to be useful in bio-concrete technology due to its alkaliphilic characteristics and extended survivability in the concrete. The study used bioinformatic analysis to investigate the pattern of codon usage in the protein-coding genes of BKH4 and the factors that might influence the translational efficiency of the bacterial genes. Genetic engineering is a promising tool in modern biotechnology, and the characterization of BKH4 genes is important for concrete technology. In this study, the protein coding genes of BKH4 were found to be AT rich. The GC content at first codon site was found to be higher than at the second and third codon sites. The effective number of codons in protein coding genes were observed to have a range of 21.5 to 61, with a mean value of 46.24 suggesting a moderate bias in the codon usage of BKH4 genes. The correspondence analysis was used to examine the bias in the use of synonymous codons. According to our study, compositional features, natural selection, and directed mutation pressure may all have an impact on the codon bias in BKH4 genes. GC12 and GC3_S were shown to have no meaningful relationship. The results revealed that natural selection primarily shaped codon usage in BKH4 genes. Our study is the first to investigate the sequencing properties of the genes of the BKH4 bacterial strain, which would be useful for future research in genetic engineering on the enhancement of bio-concrete properties.