Deconstruction of Archaeal Genome Depict Strategic Consensus in Core Pathways Coding Sequence Assembly

Abstract

A comprehensive in silico analysis of 71 species representing the different taxonomic classes and physiological genre of the domain Archaea was performed. These organisms differed in their physiological attributes, particularly oxygen tolerance and energy metabolism. We explored the diversity and similarity in the codon usage pattern in the genes and genomes of these organisms, emphasizing on their core cellular pathways. Our thrust was to figure out whether there is any underlying similarity in the design of core pathways within these organisms. Analyses of codon utilization pattern, construction of hierarchical linear models of codon usage, expression pattern and codon pair preference pointed to the fact that, in the archaea there is a trend towards biased use of synonymous codons in the core cellular pathways and the Nc-plots appeared to display the physiological variations present within the different species. Our analyses revealed that aerobic species of archaea possessed a larger degree of freedom in regulating expression levels than could be accounted for by codon usage bias alone. This feature might be a consequence of their enhanced metabolic activities as a result of their adaptation to the relatively O2-rich environment. Species of archaea, which are related from the taxonomical viewpoint, were found to have striking similarities in their ORF structuring pattern. In the anaerobic species of archaea, codon bias was found to be a major determinant of gene expression. We have also detected a significant difference in the codon pair usage pattern between the whole genome and the genes related to vital cellular pathways, and it was not only species-specific but pathway specific too. This hints towards the structuring of ORFs with better decoding accuracy during translation. Finally, a codon-pathway interaction in shaping the codon design of pathways was observed where the transcription pathway exhibited a significantly different coding frequency signature.

Comparative in silico analysis of ftsZ gene from different bacteria reveals the preference for core set of codons in coding sequence structuring and secondary structural elements determination

“…On the other hand, Chlamydophila pneumoniae CWL 029, a pathogenic, Gram-negative bacteria exhibited the highest Nc value of 61. A higher Nc value indicates poor codon bias of the gene [94]. Analysing the mean genomic Nc value of all the organisms studied, it was observed that the lowest mean genomic Nc value (29.198) is depicted by the organism Kocuria kristinae , a pathogenic, Gram-positive bacteria whereas the maximum mean genomic Nc value (55.68) is depicted by a pathogenic, Gram-negative bacteria called Anaplasma marginale str.…”

Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes

“…About 52 species from different soil types were found to demonstrate Nc avg above 40. This is suggestive of a relatively lower codon bias existing within the genome of these species (Botzman and Margalit, 2011;Pal et al, 2015;Khandia et al, 2019). The lowest Nc avg value (29.99, SD = ±3.91) was observed in Micrococcus luteus NCTC 2665, a Gram positive soil bacterium indicating high level of codon bias within its genome.…”

“…The correlation between Nc and GC3 was plotted on a graph called Nc plot (Wright, 1990) for the 92 species considered in this study. Our previous study has shown that the Nc plots can be used as a valuable tool to detect intra-and inter-specific/genic synonymous codon usage patterns (Pal et al, 2015). Analyzing the Nc plots, three types of gene clustering on the Nc plot was evident-left centric, mid centric and right centric aggregation of coding sequences as shown in Figure 2.…”

“…It ranges from 20 to 61. A Nc value lower than 40 indicates codon usage bias and higher than 40 indicates equal likely usage of all synonymous codons (Botzman and Margalit, 2011;Pal et al, 2015;Wang et al, 2018;Khandia et al, 2019). GC3 has been reported to be linked with DNA flexibility and codon bias across prokaryotes (Babbitt et al, 2014) and also plays a regulatory role in gene expression and methylation (Tatarinova et al, 2013).…”

A comparative genomics-based study of positive strand RNA viruses emphasizing on SARS-CoV-2 utilizing dinucleotide signature, codon usage and codon context analyses

“…Codon pair utilization bias present in each of the different organisms can be better explored through this parameter to infer on phylogeny ( Moura et al, 2011 ). Codon context analysis was carried out using the software ANACONDA 2 to generate the frequency table of codon pair context ( Baha et al, 2019 ), and followed by subsequent statistical analysis, to identify preferred set of codon pairs in a coding sequence ( Nasrullah et al, 2015 ; Pal et al, 2015 ). Along with codon context analysis, the codon pair ratio or CP R was also calculated for each viral genome to find out how many codon pairs have been utilized in coding the different coding sequences relative to the number of codon pairs combinations that are feasible ( Pal et al, 2015 ).…”