Analyzing prokaryotic codon usage trends has become a crucial topic of study with significant ramifications for comprehending microbial genetics, classification, evolution, and the control of gene expression. This review study explores the numerous facets of prokaryotic codon usage patterns, looking at different parameters like habitat and lifestyle across broad groups of prokaryotes by emphasizing the role of codon reprogramming in adaptive strategies and its integration into systems biology. We also explored the numerous variables driving codon usage bias, including natural selection, mutation, horizontal gene transfer, codon-anticodon interaction, and genomic composition in prokaryotes through a thorough study of current literature. Furthermore, a special session on codon usage on pathogenic prokaryotes and the role of codon usage in the phylogeny of prokaryotes has been discussed. We also looked at the various software and indices that have been recently applied to prokaryotic genomes. The promising directions that lay ahead to map the future of codon usage research on prokaryotes have been emphasized. Codon usage variations across prokaryotic communities could be better understood by combining environmental, metagenomic, and system biology approaches.

Introduction: The escalating challenge of multidrug resistance among ESKAPE pathogens has become a prominent concern for global healthcare providers, leading to amplified morbidity and mortality rates. Methods: We conducted this study to elucidate the genetic architecture of ESKAPE constituents with the intent of ameliorating pathogenicity and facilitating drug development efforts. A comprehensive array of computational tools and statistical methodologies were employed to scrutinize the genomes of ESKAPE pathogens. Results: Translational selection profoundly influences the codon usage bias within this pathogenic cohort. Notably, leucine emerged as the predominant amino acid, except in the case of Acinetobacter baumannii, where arginine exhibited preeminence. There was a universal preference for at least one histidine codon across all ESKAPE pathogens. GpC emerged as the most prominently overrepresented dinucleotide at the codon pair junction in all ESKAPE pathogens. Furthermore, a comparison of gyrB gene sequences and phylogenic tree construction showed a distinct evolutionary relationship between AT-rich and GC-rich ESKAPE pathogens. Additionally, identification, characterization, and phylogenetic analysis of multiple antibiotic resistance genes revealed distinct evolutionary relationships. Conclusion: It was discerned that despite substantial variability amongst antibiotic resistance genes of pathogens, leucine emerged as the predominant amino acid.

Understanding codon usage has been vital for optimizing biotechnological applications across various domains. In response to this necessity, this review examines the impact of codon usage on protein expression systems, highlighting strategies to enhance yield and solubility in prokaryotic and eukaryotic hosts. We have discussed the role of codon usage in vaccine development, emphasizing how tailored codon sequences improve antigen expression and immune responses. In therapeutic protein production, optimizing codon preferences is shown to increase yields and reduce misfolding, facilitating the cost-effective manufacture of complex proteins. The review further explores the significance of codon usage in gene therapy, metabolic engineering, and synthetic biology, where precise codon design can drive innovations in genetic circuits and metabolic pathways. Additionally, we addressed emerging technologies and methodologies that enhance our understanding of codon optimization, paving the way for future advancements in biotechnology. By integrating insights from most recent studies, this paper underscores the importance of codon usage and its optimization, highlighting its transformative potential in enhancing the efficacy and scalability of biotechnological processes. Overall, we propose future directions for research, advocating for a multidisciplinary approach that combines computational tools and experimental validation to unlock the full potential of codon usage in biotechnology.