Bioinformatics analysis of codon usage patterns and influencing factors in Penaeus monodon nudivirus

Codon usage bias analysis of the gene encoding NAD+-dependent DNA ligase protein of Invertebrate iridescent virus 6

The genome of Invertebrate iridescent virus 6 (IIV6) contains a sequence that shows similarity to eubacterial NAD+-dependent DNA ligases. The 615-amino acid open reading frame (ORF 205R) consists of several domains, including an N-terminal domain Ia, followed by an adenylation domain, an OB-fold domain, a helix-hairpin-helix (HhH) domain, and a BRCT domain. Notably, the zinc finger domain, typically present in NAD+-dependent DNA ligases, is absent in ORF 205R. Since the protein encoded by ORF 205R (IIV6 DNA ligase gene) is involved in critical functions such as DNA replication, modification, and repair, it is crucial to comprehend the codon usage associated with this gene. In this paper, the codon usage bias (CUB) in DNA ligase gene of IIV6 and 11 reference iridoviruses was analyzed by comparing the nucleotide contents, relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI), relative abundance of dinucleotides and other indices. Both the base content and the RCSU analysis indicated that the A- and T-ending codons were mostly favored in the DNA ligase gene of IIV6. The ENC value of 35.64 implied a high CUB in the IIV6 DNA ligase gene. The ENC plot, neutrality plot, parity rule 2 plot, correspondence analysis revealed that mutation pressure and natural selection had an impact on the CUB of the IIVs DNA ligase genes. Additionally, the analysis of codon adaptation index demonstrated that the IIV6 DNA ligase gene is strongly adapted to its host. These findings will improve our comprehension of the CUB of IIV6 DNA ligase and reference genes, which may provide the required information for a fundamental evolutionary analysis of these genes.

Codon Pattern and Compositional Constraints Determination of Genes Associated with Chronic Periodontitis

Genome-wide association studies showed the relationship of NIN, ABHD12B, WHAMM, AP3B2, and SIGLEC5 with chronic periodontitis. The study’s objective was to investigate different molecular patterns and evolutionary forces acting on the mentioned genes. The investigation of molecular patterns encompasses the study of compositional parameters, expression profile, physical properties of genes, codon preferences, degree of codon bias, determination of the most influential codons, and assessment of actions of evolutionary forces, such as mutations and natural selection. The overall compositional analysis revealed the dominance of A and G nucleotides compared to T and C. A relatively low codon usage bias is observed. The CTG codon is the most overused codon, followed by TCC. The genes, AP3B2 and SIGLEC5, preferred GC-ending codons, while NIN, ABHD12B, and WHAMM preferred AT-ending codons. The presence of directional mutational force and natural selection was found to operate codon usage in genes envisaged, and selective forces were dominant over mutational forces. Apart from mutation and selection forces, compositional constraints also played imperative roles. The study enriched our knowledge of specific molecular patterns associated with the set of genes significantly associated with chronic periodontitis. Further studies are warranted to identify more genetic signatures associated with the disease.

Genome dynamics, codon usage patterns and influencing factors in Aeromonas hydrophila phages

In the present study, genome characteristics and codon usage patterns of 44 Aeromonas hydrophila phages were studied. Phage genomes varied from 30.8 to 262.0 kb with mean±SD and median values of 111.3 ± 81.4 kb and 79.4 kb, respectively. Though the great variation in phage GC contents (35.1-62.2%) was observed, GC contents of all phages (except two phages) were significantly less than the GC content (62.4 ± 5.6%) of the host. The effective number of codons (ENC) values of phage genes ranged from 27.7 to 61 with a mean±SD value of 47.4 ± 6.8. Out of a total 5773 phage genes, 207 (3.6%), 3,528 (61.1%) and 2,012 (34.9%) genes had strong (ENC < 35), moderate (35 < ENC < 50) and low (ENC ≥ 50) codon usage bias, respectively. During relative synonymous codon usage (RSCU) analysis, shared usage of preferred codons was also observed between the phages and host. During codon adaptation index (CAI) analysis, 1028 (17.8%) phage genes showed significant adaptation towards the host. Among these genes, 797 (78.0%) genes encoded hypothetical proteins or proteins of unknown function; whereas 118 (12%) genes encoded the phage structural and packaging proteins. Segregation of ENC, RSCU and CAI analysis results based on genome size also indicated that codon usage bias was more prominent in phages with small genomes. Correlation, neutrality and GC3 versus ENC analyzes indicated a more dominant role of natural selection in shaping the codon usage patterns of A. hydrophila phages. The findings of the current study could be useful from evolutionary and host-pathogen interaction perspectives leading to efficient utilization of phages for therapeutic and other applications.

The effects of synonymous codon usages on genotypic formation of open reading frames in hepatitis E virus

Hepatitis E virus (HEV) infection has emerged as an important public health issue. As a zoonotic RNA virus, new strains are continuously discovered from human or various animal species. However, the capability of cross-species infection varies largely among different strains. Because the classical nucleotide-based genotyping system provides little functional insight, this study aimed to comprehensively investigate codon usage of the HEV coding regions for better understanding the evolutional orientation, virus-host interaction and cross-species transmission. We observed significant differences of the four nucleotide usages in the three open reading frames, indicating that the evolutional tendency of HEV caused by mutation pressure is modified by the evolutional dynamic related to positive selection. Furthermore, significant differences of nucleotide usages were found among HEV isolated from different host species, suggesting an important role of natural selection related to the host. Analysis of effective number of codons revealed distinct degrees of biased codon usage caused by mutation pressure or the host. Finally, we have mapped the similarity levels of the overall codon usage between the virus and the host to assess the potential of cross-species infection. Thus, this study has provided a novel aspect for better understanding the HEV genetic orientation and the zoonotic nature.

Molecular characterization of a novel white spot syndrome virus response protein (dubbed LvWRP) from Litopenaeus vannamei

White spot syndrome, which is caused by white spot syndrome virus (WSSV), is a highly contagious disease of penaeid shrimp. However, there is currently incomplete understanding of the infection mechanism and pathogenesis of WSSV. In this study, a novel gene of a previously uncharacterized WSSV response protein (LvWRP) in Litopenaeus vannamei was identified and characterized. The LvWRP gene has an open reading frame (ORF) of 879 bp encoding a putative protein of 292 amino acids. Sequence analysis revealed that LvWRP shared 24.9% identity with an uncharacterized protein of Penaeus monodon nudivirus. Real-time qPCR analysis showed that LvWRP was ubiquitously expressed in shrimp tissues, with transcript levels induced in hemocytes upon immune challenge with Vibrio parahaemolyticus, Streptoccocus iniae, lipopolysaccharide (LPS), and WSSV. In addition, RNA interference-mediated knockdown of LvWRP followed by WSSV challenge revealed significant decrease in the transcript levels of WSSV IE1 and VP28 genes coupled with a reduction in WSSV copies in shrimp hemocytes. Moreover, depletion of LvWRP followed by WSSV challenge significantly increased the transcript levels of Vago4 and Vago5 as well as increased the phosphorylation of STAT, while hemocytes apoptosis in terms of caspase 3/7 activity was decreased. These results suggest that LvWRP is important for WSSV replication in shrimp, and therefore one of the vital host factors in WSSV infection.

New insights into the factors affecting synonymous codon usage in human infecting Plasmodium species

Codon usage bias is due to the non-random usage of synonymous codons for coding amino acids. The synonymous sites are under weak selection, and codon usage bias is maintained by the equilibrium in mutational bias, genetic drift and selection pressure. The differential codon usage choices are also relevant to human infecting Plasmodium species. Recently, P. knowlesi switches its natural host, long-tailed macaques, and starts infecting humans. This review focuses on the comparative analysis of codon usage choices among human infecting P. falciparum and P. vivax along with P. knowlesi species taking their coding sequence data. The variation in GC content, amino acid frequencies, effective number of codons and other factors plays a crucial role in determining synonymous codon choices. Within species codon choices are more similar for P. vivax and P. knowlesi in comparison with P. falciparum species. This study suggests that synonymous codon choice modulates the gene expression level, mRNA stability, ribosome speed, protein folding, translation efficiency and its accuracy in Plasmodium species, and provides a valuable information regarding the codon usage pattern to facilitate gene cloning as well as expression and transfection studies for malaria causing species.