Genome-Scale Co-Expression Network Comparison across Escherichia coli and Salmonella enterica Serovar Typhimurium Reveals Significant Conservation at the Regulon Level of Local Regulators Despite Their Dissimilar Lifestyles

Abstract

Availability of genome-wide gene expression datasets provides the opportunity to study gene expression across different organisms under a plethora of experimental conditions. In our previous work, we developed an algorithm called COMODO (COnserved MODules across Organisms) that identifies conserved expression modules between two species. In the present study, we expanded COMODO to detect the co-expression conservation across three organisms by adapting the statistics behind it. We applied COMODO to study expression conservation/divergence between Escherichia coli, Salmonella enterica, and Bacillus subtilis. We observed that some parts of the regulatory interaction networks were conserved between E. coli and S. enterica especially in the regulon of local regulators. However, such conservation was not observed between the regulatory interaction networks of B. subtilis and the two other species. We found co-expression conservation on a number of genes involved in quorum sensing, but almost no conservation for genes involved in pathogenicity across E. coli and S. enterica which could partially explain their different lifestyles. We concluded that despite their different lifestyles, no significant rewiring have occurred at the level of local regulons involved for instance, and notable conservation can be detected in signaling pathways and stress sensing in the phylogenetically close species S. enterica and E. coli. Moreover, conservation of local regulons seems to depend on the evolutionary time of divergence across species disappearing at larger distances as shown by the comparison with B. subtilis. Global regulons follow a different trend and show major rewiring even at the limited evolutionary distance that separates E. coli and S. enterica.

Phylogenomic analysis of gene co‐expression networks reveals the evolution of functional modules

“…Recently, the analyses were also extended to several plant crop species (Ficklin and Feltus, ; Movahedi et al ., ; Mutwil et al ., ; Tzfadia et al ., ). Co‐expression networks are conserved across species and even across distinct kingdoms of life, indicating that essential cellular processes, such as cell cycle, ribosome biogenesis and the proteasome are implemented by the same orthologous modules in different species (Stuart et al ., ; Gerstein et al ., ; Zarrineh et al ., ). These conserved modules can therefore be used to transfer knowledge obtained from better‐investigated model species to crop plants, for example (Mutwil et al ., ; Ruprecht et al ., ; Heyndrickx and Vandepoele, ; Park et al ., ; Tzfadia et al ., ).…”

Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon

“…Apart from predicting gene function, coexpression networks can be used to identify gene modules (i.e. groups of coexpressed genes) that may be conserved across species and even across different kingdoms of life, as exemplified by cell cycle, ribosome biogenesis and proteasome gene modules (Stuart et al ., ; Gerstein et al ., ; Zarrineh et al ., ). Such conserved gene modules are useful to transfer knowledge about pathways or co‐functional processes from better characterised model species to crop plants, as functionally equivalent genes are found by combining DNA sequence and coexpression contexts (Mutwil et al ., ; Ruprecht et al ., ; Park et al ., ; Tzfadia et al ., ).…”

PhytoNet: comparative co-expression network analyses across phytoplankton and land plants

“…The combination of gene families, Pfam domains, and co-expression modules allows detection and analysis of gene modules that are present in multiple species ( 13 , 46 , 47 ), and this property can be used to transfer functional knowledge from one species to another ( 48–51 ). Such conserved modules indicate that the biological process captured is present in the investigated species, and provides additional confidence that the homologous genes present in these modules are needed for the process and perform the same function ( 48 ).…”