Abstract
The availability of a large number of sequenced bacterial genomes facilitates in-depth studies about why genes (operons) in a bacterial genome are globally organized the way they are. We have previously discovered that (the relative) transcription- activation frequencies among different biological pathways encoded in a genome have a dominating role in the global arrangement of operons. One complicating factor in such a study is that some operons may be involved in multiple pathways with different activation frequencies. A quantitative model has been developed that captures this information, which tends to be minimized by the current global arrangement of operons in a bacterial (and archaeal) genome compared to possible alternative arrangements. A study is carried out here using this model on a collection of 52 closely related E. coli genomes, which revealed interesting new insights about how bacterial genomes evolve to optimally adapt to their environments through adjusting the (relative) genomic locations of the encoding operons of biological pathways once their utilization and hence transcription activation frequencies change, to maintain the above energy-efficiency property. More specifically we observed that it is the frequencies of the transcription activation of pathways relative to those of the other encoded pathways in an organism as well as the variation in the activation frequencies of a specific pathway across the related genomes that play a key role in the observed commonalities and differences in the genomic organizations of genes (and operons) encoding specific pathways across different genomes.
Highlights
The availability of a large number of sequenced bacterial genomes facilitates in-depth studies about why genes in a bacterial genome are globally organized the way they are
These sequenced genomes within the E. coli species have offered a unique opportunity for in-depth studies of the organizational principles of functional elements encoded in a genome, for example, the rules that may govern how operons are globally arranged in a genome
We have previously discovered one general organizational principle of bacterial genomes: that is, more frequently activated biological pathways tend to have their component operons localized into a smaller number of DNA-folding domains, termed supercoil domains or supercoils [9,10]
Summary
The availability of a large number of sequenced bacterial genomes facilitates in-depth studies about why genes (operons) in a bacterial genome are globally organized the way they are. Different strains of E. coli share a high proportion of the protein-encoding genes [8] These sequenced genomes within the E. coli species have offered a unique opportunity for in-depth studies of the organizational principles of functional elements encoded in a genome, for example, the rules that may govern how operons are globally arranged in a genome. We have defined a simple model for estimating this total energy along with a prediction of the set of supercoils, i.e., a partition of the whole genome into 10 100 kb genomic regions, that achieves the minimal energy [11], which is termed as the energy score of a genome throughout this paper This model explains very well the current global arrangement of operons in a variety of bacterial and archaeal genomes, which fall into a wide range of taxonomical groups, as we have previously demonstrated [11,12]. We present a study on elucidation of the possible reasons for the observed diversity in the genomic organizations of operons across the 52 E. coli genomes, using this model
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