Zinc binuclear cluster proteins (ZBC; Zn(II)2Cys6) are unique to the fungi kingdom and associated with a series of functions, viz., the utilization of macromolecules, stress tolerance, and most importantly, host–pathogen interactions by imparting virulence to the pathogen. Codon usage bias (CUB) is the phenomenon of using synonymous codons in a non-uniform fashion during the translation event, which has arisen because of interactions among evolutionary forces. The Zn(II)2Cys6 coding sequences from nine Ascomycetes plant pathogenic species and model system yeast were analysed for compositional and codon usage bias patterns. The clustering analysis diverged the Ascomycetes fungi into two clusters. The nucleotide compositional and relative synonymous codon usage (RSCU) analysis indicated GC biasness toward Ascomycetes fungi compared with the model system S. cerevisiae, which tends to be AT-rich. Further, plant pathogenic Ascomycetes fungi belonging to cluster-2 showed a higher number of GC-rich high-frequency codons than cluster-1 and was exclusively AT-rich in S. cerevisiae. The current investigation also showed the mutual effect of the two evolutionary forces, viz. natural selection and compositional constraints, on the CUB of Zn(II)2Cys6 genes. The perseverance of GC-rich codons of Zn(II)2Cys6 in Ascomycetes could facilitate the invasion process. The findings of the current investigation show the role of CUB and nucleotide composition in the evolutionary divergence of Ascomycetes plant pathogens and paves the way to target specific codons and sequences to modulate host–pathogen interactions through genome editing and functional genomics tools.

/pdf/composition-and-codon-usage-pattern-results-in-divergence-of-1hsu575t.pdf

Composition and Codon Usage Pattern Results in Divergence of the Zinc Binuclear Cluster (Zn(II)2Cys6) Sequences among Ascomycetes Plant Pathogenic Fungi

Abstract Codon usage bias (CUB) is a ubiquitous phenomenon perseveres in genome of all the organisms. It impinges the gene expression and other genetic intricacies within a genome. The present study explicates the pattern of codon usage in the protein coding sequence of Crocus sativus and its relation with gene expression. Gene expression analysis in C. sativus showed genes with high expression had a preference of G base at third position. CUB had an inverse relation with gene expression. Coding sequences with ENC &lt; 50 had low FPKM value while low codon bias group (ENC &gt; 50) possessed high FPKM value. The low tAI values showed the low translation efficiency of genes in C. sativus . The non-significant MELP and ENC correlation analysis suggested that expression of genes might not be associated with CUB. ENC and PR-2 plot revealed mutation pressure and natural selection played role in shaping CUB. However, neutrality plot conclusively depicted the dominance of natural selection in regulating the configuration of codons in all three species. In addition, the role of CUB regarding the predilection of fungal pathogens Aspergillus fumigatus and Fusarium oxysporum towards host plant C. sativus has also been expounded. We found a similar trend of codon usage pattern operative in plant and fungal pathogens as both the fungal pathogens and host plant showed similar GC rich genomic content as well as preference for GC ending codons at third codon position. This concurrence might be attributed for the colonization of fungal pathogens in C. sativus . Overall, different CUB indices reflected a weak codon bias in the C. sativus , F. oxysporum and A. fumigatus genome. 

/pdf/deciphering-the-role-of-codon-usage-bias-on-gene-expression-14xdsz4m.pdf

Deciphering the role of codon usage bias on gene expression and pathogen colonization in Crocus sativus

Exploring the relationship between codon usage and gene expression in the Meloidogyne incognita genome: Implications for environmental adaptability

Hepatitis C virus (HCV) is enveloped RNA virus, encoding for a polyprotein that is processed by cellular proteases. The virus is responsible for liver cirrhosis, allograft rejection, and human hepatocellular carcinoma. Based on studies including compositional analysis, odds ratio analysis, parity analysis, skew analysis, relative synonymous codon usage, codon bias, and protein properties, it was evident that codon usage bias in HCV is dependent upon the nucleotide composition. Codon context analysis revealed CTC-CTG as a preferred codon pair. While CGA and CGT codons were rare, none of the codons were rare in HCV-like viruses envisaged in the present study. Many of the preferred codon pairs were valine amino acid-initiated, which possibly infers viral infectivity; hence the role of selection forces appears to act on the HCV genome, which was further validated by neutrality analysis where selection accounted for 87.28%, while mutation accounted for 12.72% force shaping codon usage. Furthermore, codon usage was correlated with the length of the genome. HCV viruses prefer valine-initiated codon pairs, while HCV-like viruses prefer alanine-initiated codon pairs. The HCV host range is very narrow and is confined to only humans and chimpanzees. Based on indices including codon usage correlation analysis, similarity index, and relative codon deoptimization index, it is evident in the study that the chimpanzee is the primary host of the virus. The present study helped elucidate the preferred host for HCV. The information presented in the study paved the way for generating an attenuated vaccine candidate through viral recoding, with finely tuned nucleotide composition and a perfect balance of preferred and rare codons.

/pdf/insights-into-synonymous-codon-usage-bias-in-hepatitis-c-1hpk25b3.pdf

Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts

Abstract Meloidogyne incognita (Root-knot nematode) and Alternaria alternata (fungus) were among the dominant parasites of the medicinal plant Withania somnifera . Despite the fatal nature of their infection, a comprehensive study to explore their evolution and adaptation is lacking. The present study elucidates evolutionary and codon usage bias analysis of W. somnifera (host plant), M. incognita (root-knot nematode) and A. alternata (fungal parasite). The results of the present study revealed a weak codon usage bias prevalent in all the three organisms. Based on the nucleotide analysis, genome of W. somnifera and M. incognita was found to be A-T biased while A. alternata had GC biased genome. We found high similarity of CUB pattern between host and its nematode pathogen as compared to the fungal pathogen. Inclusively, both the evolutionary forces influenced the CUB in host and its associated pathogens. However, neutrality plot indicated the pervasiveness of natural selection on CUB of the host and its pathogens. Correspondence analysis revealed the dominant effect of mutation on CUB of W. somnifera and M. incognita while natural selection was the main force affecting CUB of A. alternata . Taken together the present study would provide some prolific insight into the role of codon usage bias in the adaptability of pathogens to the host’s environment for establishing parasitic relationship. 

/pdf/comprehensive-analysis-of-codon-usage-pattern-in-withania-2h327vai.pdf

Comprehensive analysis of codon usage pattern in Withania somnifera and its associated pathogens: Meloidogyne incognita and Alternaria alternata

GeoSteering Through Challenging Fractured Limestone Reservoir becomes Achievable Utilizing High Definition Multi-Layer Boundary Mapping Technology - A Case Study from a Deep Gas Reservoirs

J. Keot Chandan

Papers

Comprehensive analysis of codon usage pattern in Withania somnifera and its associated pathogens: Meloidogyne incognita and Alternaria alternata

GeoSteering Through Challenging Fractured Limestone Reservoir becomes Achievable Utilizing High Definition Multi-Layer Boundary Mapping Technology - A Case Study from a Deep Gas Reservoirs

Exploring the relationship between codon usage and gene expression in the Meloidogyne incognita genome: Implications for environmental adaptability