Global pleiotropic effects in adaptively evolved Escherichia coli lacking CRP reveal molecular mechanisms that define the growth physiology

Abstract

Evolution facilitates emergence of fitter phenotypes by efficient allocation of cellular resources in conjunction with beneficial mutations. However, system-wide pleiotropic effects that redress the perturbations to the apex node of the transcriptional regulatory networks remain unclear. Here, we elucidate that absence of global transcriptional regulator CRP in Escherichia coli results in alterations in key metabolic pathways under glucose respiratory conditions, favouring stress- or hedging-related functions over growth-enhancing functions. Further, we disentangle the growth-mediated effects from the CRP regulation-specific effects on these metabolic pathways. We quantitatively illustrate that the loss of CRP perturbs proteome efficiency, as evident from metabolic as well as ribosomal proteome fractions, that corroborated with intracellular metabolite profiles. To address how E. coli copes with such systemic defect, we evolved Δcrp mutant in the presence of glucose. Besides acquiring mutations in the promoter of glucose transporter ptsG , the evolved populations recovered the metabolic pathways to their pre-perturbed state coupled with metabolite re-adjustments, which altogether enabled increased growth. By contrast to Δcrp mutant, the evolved strains remodelled their proteome efficiency towards biomass synthesis, albeit at the expense of carbon efficiency. Overall, we comprehensively illustrate the genetic and metabolic basis of pleiotropic effects, fundamental for understanding the growth physiology.

A systems biology approach to disentangle the direct and indirect effects of global transcription factors on gene expression in Escherichia coli

“…previously that the gene expression changes in response to growth rate effects are consistent, despite the glucose-limited or glucose-excess conditions (Li et al, 2019;Pal et al, 2022;Utrilla et al, 2016). Thus, the DEGs identified under the chemostat conditions were then utilized to characterize the indirect targets as growth-rate mediated effects and the direct targets as regulation-specific effects by the dTF/s in batch-exponential growth conditions.…”

“…While the functions and the pleiotropic effects of the global TFs are well appreciated, the true direct targets and indirect effects on gene expression together with their underlying basis for a particular environment remain unclear. These genome-wide indirect effects are primarily mediated by alterations in growth rates or physiological state of the organism that encompass regulation by RNA polymerase associated sigma factors, ribosomes, intracellular metabolites as well as by other interacting global or local TFs (Berthoumieux et al, 2013; Gerosa et al, 2013; Klumpp et al, 2009; Li et al, 2019; Pal et al, 2022; Pan et al, 2021; Utrilla et al, 2016; Yu et al, 2021). For example, the growth rate was found to exert a significant effect on the gene expression patterns in a strain lacking the global regulator CRP (Pal et al, 2022).…”

“…These genome-wide indirect effects are primarily mediated by alterations in growth rates or physiological state of the organism that encompass regulation by RNA polymerase associated sigma factors, ribosomes, intracellular metabolites as well as by other interacting global or local TFs (Berthoumieux et al, 2013; Gerosa et al, 2013; Klumpp et al, 2009; Li et al, 2019; Pal et al, 2022; Pan et al, 2021; Utrilla et al, 2016; Yu et al, 2021). For example, the growth rate was found to exert a significant effect on the gene expression patterns in a strain lacking the global regulator CRP (Pal et al, 2022). This growth rate-mediated effect on the gene expression was consistent in the event of adaptive laboratory evolution to facilitate the emergence of cells with better fitness (Pal et al, 2022; Utrilla et al, 2016).…”

“…For example, the growth rate was found to exert a significant effect on the gene expression patterns in a strain lacking the global regulator CRP (Pal et al, 2022). This growth rate-mediated effect on the gene expression was consistent in the event of adaptive laboratory evolution to facilitate the emergence of cells with better fitness (Pal et al, 2022; Utrilla et al, 2016). Thus, apart from the known functions of the direct target genes, it is fundamental to investigate the functions of these indirect or growth-rate mediated genes and their relevance in overall cellular objectives for a particular environment.…”

“…The metabolite changes can often be attributed to the net effect of the metabolic flux as a result of the underlying proteome allocation (Iyer et al, 2021; Reznik et al, 2017; Scott et al, 2014; You et al, 2013). For instance, our previous studies have demonstrated the TF driven changes in proteome allocation that resulted in significant perturbations in the intracellular metabolite levels of the organism (Iyer et al, 2021; Pal et al, 2022). These intracellular metabolites not only constitute the biomass building blocks but also contribute as signalling molecules that confer metabolic plasticity to the organism (Chubukov et al, 2014; Erickson et al, 2017; Zampieri et al, 2019).…”