Codon Bias

The phenomenon of codon bias has been widely studied in the contemporary genetic science field. Since its discovery, scientists have made great strides at making the topic well known especially with regard to the study of microorganisms. This has led to numerous attempts to replicate the process of codon bias in ex-situ settings in order to further develop a synopsis and explanation of the events leading to its emancipation. The study of codon bias is therefore relevant in explaining evolutionary aspects regarding gene structures of organisms, for instance, mutational aspects in genetics explanation.What is Codon Bias?Codon essentially describes a cell mediated process whereby the events leading to the formation of particular amino acid combinations change in terms of specifity during protein formation. This occurs when a particular codon used to code for an amino acid is replaced by a different code, which normally codes for the same amino acid. "The genetic code is degenerate and thus allows different codons to be used to specify the same amino acid" (Balding, Bishop, & Cannings, 2007). This explains the existence of variation in terms of the selection for the respective codons, elementally coding for the amino acid in focus leading to the formation of structurally similar protein structures going by the functional component.Theia is a term which has been used in the contemporary field of astrobiology which usually entails the description of various aspects of the evolutionary perspectives. In essence, it has been borrowed from a mythological aspect and therefore has variations of meanings depending on its contextual description. In reference to mythology, it is a name provided by certain authors as a 'mars-sized object' which after its interaction with the earth through impacting the young earth, led to the moon formation" (Barbier, Gargaud, Martin, & Reisse, 2006).

Do the new genomes exhibit oligonucleotide frequencies?The oligonucleotide frequencies focusing on codons are essentially established after an analysis of the amino acid-coding regions or sites, inclusive of the non-coding sites. The orientation in the two sites relatively determines the expressed frequencies in the long run. "The order of nucleotides is governed not only by the encoded information, but also by physical and biological constraints, with the exception of long-range physical forces on DNA structure, all sections of the genome should be exposed to the same constraints and consequently should have the same fingerprints of oligonucleotide frequencies, i.e. frequencies being consistently either low or high for the same oligonucleotide (Cornelis, 2008). This establishes the fact that the expression of the oligonucleotide frequencies in the newly formed genomes is elementally based upon the identification of different finger print forms of the formed oligonucleotides. Furthermore, "The local G+C content and oligonucleotide frequencies are measures of variability in bacterial genomes (Cornelis, 2008). This fundamentally represents the different occurring structural as exhibited during codon formulation in terms of frequencies in combination. In essence, "Oligonucleotide bias is a signature of a microbial genome and carries a phylogenetic signal" (Cornellis, 2008). This provides meaningful evidence in a bid to establish the occurring codon frequencies emanating from the genomes.Do the phage sequence biases match those of their presumed bacterial hosts?

Previous research has established the fact that bacterial genomes are elementally plastic compared to those of eukaryotic organisms. This can be determined though the performance of properly configured plaque assays aimed at establishing the occurring diversification observed in the two potential different organisms in terms of their genetic structures. "Phage have long been known to induce phage conversion of their host, in which the surface molecules are altered. Phages are also known to exclude one another, indicating that phage identity systems can be intended to affect other genetic competitors, not simply their host" (Villarreal, 2008). This therefore provides a basis on which the variation in phages in the bacterial hosts may potentially be attributed to the occurring interaction dynamics. "Prophages also have much more direct and immediate effects on their hosts, which in turn will have an effect on the evolution of the host's genome" (Higgins, 2005).How T-RNA relate to codon bias?It has been observed that in cases where the anticodon binding to a tRNA, in which the anticodon matching the adjacent depend on the number of the bases, will follow the order of magnitude (Cohn, 1979). This explains the existence of the relative affinities of tRNAs to their respective codons to which they are elementally supposed to pair up. "However, irrespective of the evolutionary reasons underlying the existence of codon bias, there is a relationship between codon bias and relative tRNA abundance. It is clear that the translational apparatus, for at least the set of tRNAs used for mRNA decoding, has adapted to these biases, since higher codon biases associate with conserved and highly expressed genes" (Atkins, 2009). This kind of adaptation behaviour of the tRNA is associated with the decreased factor in terms of accuracy during actual mRNA translation that is essentially not linked to the occurrence of biasness. This phenomenon of tRNA translation is well manifested in terms of high degree of error occurrence during the expression of the translation factor especially during human amino acid chain synthesis. "Moreover, accuracy of translation depends not only on simple codon bias but also on a bias among co-occurring codons in mRNA" (Atkins, 2009). This therefore serves to establish the fundamental fact that tRNA plays a significant role in establishing the codon bias occurrence.

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