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.

Figure 1. Schematic representation of COMODO output for the first detected module across E. coli, B. subtilis, and S. enterica.

Modules in conserved co-expressed triplets are composed of homologous triplets between three organisms (core part). In addition, homologous pairs can be detected which are conserved only between two organisms, that share a mutual co-expression in each of the species. Furthermore, additional genes can also be detected for which the co-expression with the homologous linker genes was found to be species-specific.

Figure 2. Selected co-expressed conserved modules across E. coli and S. enterica.

A. Core part of co-expressed conserved module regulated by transcription factor CysB in E. coli. Existence of orthologous transcription factors CysB in S. enterica makes it highly probable that CysB is responsible for observed co-expression in module 181 of S. enterica. In addition, co-expression conservation of ydjN in both organisms may imply that this gene is also a target of CysB, and ydjN is involved in the same biological process as the other genes (cysteine metabolism). B. Co-expression conservation of motility and flagerlla synthesis (module 162). Transcription factor FlhCD and sigma factor FliA is known to be responsible for the co-expression of genes involved in this biological process in both organisms. Co-expression conservation of sigma factors FliA and FliZ, anti-sgima factor FlgM, and transcription factor YcgR may also imply the similarity in regulatory interaction conservation. From 20 genes detected as variable part in S. enterica just four genes (srfB, srfC, STM1300, STM2314) has not previously been identified as motility and flagerlla synthesis in E. coli. The other 16 genes could be detected in E. coli if the lower threshold would be used, but using lower threshold could also introduce many new non-linking genes this time in the variable part of E. coli. C. Co-expression conservation of two anti-sigma factor RseA and RseB in module 193. We expect that sigma factor RpoE is also conserved in co-expression as all these genes are in one operon in both E. coli and S. enterica (see also Figure 3B ). D. Homologous transcription factors CsgD and STM0347 are co-expressed in linked co-expressed module 166. CsgD also exist in S. enterica and probably not detected as co-expressed gene in S. enterica because of available condition set in this organism (see also Figure 3A ).

Figure 3. Expression behavior of genes in co-expressed modules 166 (Panel A) and 193 (Panel B) of Table S1 in S. enterica.

Genes in black are the genes which are found as the co-expressed modules by COMODO. While genes in red (csgD and rpoE) are the ones which are not found in the co-expressed modules, but their ortholgous pair are co-expressed with the E. coli counterpart modules. We expect that genes in red (csgD and rpoE) should also be part of their modules as they are in the same operon with some genes of their modules. Shaded areas correspond to conditions not shared for the genes which were not detected as co-expressed in S. enterica (red genes). The fact that these conditions are much smaller in number than the conditions genes in red (csgD and rpoE) show co-expression with the rest of the modules genes increases the probability that these genes are actually in those modules.

Figure 4. Phylogenetic tree of STM0347 and CsgD.

Both proteins were used as queries for BLAST searches to retrieve their closest relatives. Collected sequences were aligned using CLUSTALW and the resulting alignment file used as input for the program ‘neighbor’ of the PHYLIP tree to derive the tree. A total of 100 bootstrap replicates were generated (numbers on the branches). STM0347 and CsgD (Salmonella enterica) are far apart on the tree suggesting they have evolved from each other long time ago and might be involved in different functions.