Understanding the commonalities and differences in genomic organizations across closely related bacteria from an energy perspective

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 Escherichia 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. genomic organization, transcription activation frequency, pathway modeling, comparative genomics analysis Citation:Ma Q, Chen X, Liu C, Mao XZ, Zhang HY, Ji F, Wu CG, Xu Y. Understanding the commonalities and differences in genomic organizations across closely related bacteria from an energy perspective. Sci China Life Sci, 2014Sci, , 57: 1121Sci, -1130Sci, , doi: 10.1007 Escherichia coli is by far the best-studied group of organisms on earth.

DOOR: a prokaryotic operon database for genome analyses and functional inference

“…Our postulation is that prokaryotes have evolved to minimize the total energy needed for folding and unfolding supercoils to enable transcription of operons that need to be activated throughout the life cycle of the organism. Our computational simulation analyses through randomly reshuffling a genome strongly confirmed our hypothesis [9,13,38]. This represents the first determinant for the global arrangements of operons in a prokaryotic genome.…”

“…The availability of genome-scale operons has also made it possible to study whether the global arrangement of operons in a prokaryotic genome is arbitrarily determined or follows some organizing rules, beyond functional studies of prokaryotic genomes. We have previously conducted a series of studies on potential determinants in the global arrangement of operons in a genome [9,13,38]. One observation is that operons for pathways with higher frequencies of transcriptional activation tend to be more closely clustered together in the host genome [13].…”

Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses

“…We used E. coli K12 as the target genome for assessing our algorithms and other selected 216 bacterial genomes as its reference genomes, which were downloaded from the NCBI (released as of November 2011). These reference genomes belong to the same phylum and different genus of E. coli , which were used to identify orthologous genes as in literatures 45 46 . To evaluate predicted regulons, we downloaded gene expression data of E. coli collected under 466 conditions from the M3D database 47 .…”