Article summary, codon bias in E. Coli

The nature of the gene codon varies among organisms. Codon preferences have been considered on the perspectives of translational efficiency and fidelity and the selective and non selective biases operating during DNA transcription replication and repair processes. Variations in tRNA on codon bias of highly expressed genes during rapid growth phase of E. coli exist. Codon selectivity is influenced by codonanticodon interaction strength, site specific codon biases, time of replication, codon context, or evolutional age. Codon preferences among gene classes in E. coli are grouped according to the following comparisons correlation of codon biases with level of gene expression, organisation of genome according to genome partitions based on size, codons use for genes characterized by function and cellular localization of gene products, gene size, comparisons  that divide all genes by similarity of codon usage or amino acid usage or similarity of a reduced set of amino acid or codons and characterization of alien genes.

The Codon Adaptation Index (CIA) is a qualitative measure for assessing codon bias. Ribosomal protein (RP) genes and membrane genes are genes that are highly expressed during fast growth and CIA and codon bias (CB) values are inversely correlated with respect to RP genes. Most ribosomal proteins are highly expressed during the E. coli exponential growth phase during which most genes facilitating translation are highly expressed. Codon preferences differ among highly expressed genes relative to the average gene for certain amino acid types, especially disparities for alanine, aspartine, histidine, isoleucine, phenealanine, threonine and valine. There is a high correlation between optimal codons and level of gene expression. In relation to E. coli genes, codon biases generally increase with increasing protein molecular weight abundance. Codon usage differences generally decrease with respect to protein molecular abundance when compared to RP. Negative correlation in the degree of protein molar abundance relative to tRN genes or other sub classes of the translation functional category is not evident. The molar abundance and codon usage differences unequivocally correlate negatively with the RP gene family and positively with the average E. coli gene respectively.

The E. coli genome is homogeneous with relatively weak codon biases among the genes distributed over the genome. Codon bias does not depend on timing in the replication cycle except near the ter region. The deviation in codon usage from RP and tRN genes is most emphatic at ter region. Relative codon usage bias among 5 middle and 3 parts of genes in E. coli show that the middle and the last third of genes are more similar in codon usage than either is to the initial third of the gene. There also exists a difference in the frequencies of 3 GC near the oriC than near the ter region. Different bacterial genomes display variation in their overall G and C content, attributed to varying mutational mechanisms and processes. For eukaryotic genomes site 3 GC frequencies decrease with increasing gene length. Alien genes are characterized in terms of extreme codon bias relative to average E. coli genes and high relative to RPs. These genes are of unknown function and are either GC rich or AT rich. Extremes in codon bias are for identifying pathogenicity islands and developing gene classes reflecting difference expression levels in untypical events. When the genome is divided into contigs, gene classes and dicodon bias is most pronounced between the gene classes of the region about the oriC versus the ter region. Dicodon bias increases with gene size and compared to the average gene dicodon biases are constant throughout the genome. When genes are divided into thirds, the dicodon biases of the 5 third, middle third .3 third parts of genes are similar though level of bias is about twice that of straight codon bias.

Codon and dicodon bias correlations for E. coli genes were evaluated for level of expression, contrast along genes, size of contigs around genome and gene size classes. Explanations for codon bias have involved combinations of selection and mutational pressures. The RPs and amminoacyl tRNA synthetases are highly expressed gene classes during exponential growth of E. coli.  Codon biases for RP genes are much more extreme than for tRN genes. The greater the abundance a gene product, the more its codon usage resembles hat of RPs, but this is not the case for comparisons to tRN genes or protein genes essential to translational activities. For gene classes RP and tRN, the source of codon bias differs significantly. RP are among the most deviant from the average E. coli gene.  It is suggested that codon usage and tRNA abundance are correlated for highly expressed genes to match substrate levels with cellular demands. Hence RP genes which are small single domain proteins show high codon usage correlation with overall E. coli codon usage and tRNA do not show this bias although they are highly expressed. The middle and final 3 end of genes entail the same levels of codon biases. The rare codon hypothesis for domains and secondary structures argues that the use of repetitive rare codons might reduce translational rate and induce translation pauses allowing protein domains and suitable secondary structures to fold into native structural conformation. There are differences in prokaryotic and eukaryotic translational mechanisms. These differences may be important in translation initiation or early stages of translation. Highly biased slowly translated codon pairs are more closely correlated with levels of expression than with protein length. Understanding basis of codon usage is of interest with respect to fundamental evolutionary questions, gene prediction, gene classification and design of optimal expression vectors. Codon usage programs are essential for gene finding and analysis of prokaryotic and eukaryotic genomes.

Commentary on summary
Premise Audience consists of students undertaking course in genetics
Paragraph 1 Introduction of the topic.
I decided to explain the nature of codon variation among cells.
I explained what influences codon selectivity.
I listed the criteria codon preferences are grouped in.

Paragraph 2 Description of experiment and its findings
Explanation of the Codon Adaption Index.
I did not mention any specific results found but rather the general findings of all results.
I mentioned existence of highly expressed genes and average genes.
Discussed the relationship between codon bias and molecular weight with relation to E. coli.

Paragraph 3 Result
I discussed the E. coli genome with respect to codon variation along the genome.
I discussed the variation of other organism genomes from E. coli genome.
I described meaning of alien genes according to the text and relevance of their existence.
The importance of identifying regions with codon bias.
Discussion on dicodon bias.

Paragraph 4 Observations and conclusions
Rare codon hypothesis explanation of codon bias in genomes.
The significance of findings, understanding the importance of codon bias and how it can be implemented in other genetic programs.


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