Effect of Global Regulators RpoS and Cyclic-AMP/CRP on the Catabolome and Transcriptome of Escherichia coli K12 during Carbon- and Energy-Limited Growth.

Alessandro G Franchini,Thomas Egli,Julian Ihssen,Patrick C Cirino

doi:10.1371/journal.pone.0133793

Alessandro G Franchini, Thomas Egli + Show 2 more

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https://doi.org/10.1371/journal.pone.0133793

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Abstract

For heterotrophic microbes, limited availability of carbon and energy sources is one of the major nutritional factors restricting the rate of growth in most ecosystems. Physiological adaptation to this hunger state requires metabolic versatility which usually involves expression of a wide range of different catabolic pathways and of high-affinity carbon transporters; together, this allows for simultaneous utilization of mixtures of carbonaceous compounds at low concentrations. In Escherichia coli the stationary phase sigma factor RpoS and the signal molecule cAMP are the major players in the regulation of transcription under such conditions; however, their interaction is still not fully understood. Therefore, during growth of E. coli in carbon-limited chemostat culture at different dilution rates, the transcriptomes, expression of periplasmic proteins and catabolomes of strains lacking one of these global regulators, either rpoS or adenylate cyclase (cya), were compared to those of the wild-type strain. The inability to synthesize cAMP exerted a strong negative influence on the expression of alternative carbon source uptake and degradation systems. In contrast, absence of RpoS increased the transcription of genes belonging to high-affinity uptake systems and central metabolism, presumably due to reduced competition of σD with σS. Phenotypical analysis confirmed this observation: The ability to respire alternative carbon substrates and to express periplasmic high-affinity binding proteins was eliminated in cya and crp mutants, while these properties were not affected in the rpoS mutant. As expected, transcription of numerous stress defence genes was negatively affected by the rpoS knock-out mutation. Interestingly, several genes of the RpoS stress response regulon were also down-regulated in the cAMP-negative strain indicating a coordinated global regulation. The results demonstrate that cAMP is crucial for catabolic flexibility during slow, carbon-limited growth, whereas RpoS is primarily involved in the regulation of stress response systems necessary for the survival of this bacterium under hunger conditions.

Highlights

As a rule, two major factors control heterotrophic bacterial growth in most ecosystems: On the one hand it is temperature, as it controls the rate of biochemical processes; on the other hand, availability of assimilable carbon and energy sources is severely restricted, as most of the potentially utilizable carbon compounds are present in polymeric forms and are not directly accessible [1,2]
We have provided a comprehensive analysis of role of the global regulators cAMP and RpoS in E. coli under well-defined carbon- and energy-limited growth conditions
The lack of rpoS resulted in an enhanced fitness both under glucose-excess and glucose-limited conditions, whereas the lack of cAMP had a drastic negative effect on growth performance (Tables 1 and 3)

Summary

Introduction

Two major factors control heterotrophic bacterial growth in most ecosystems: On the one hand it is temperature, as it controls the rate of biochemical processes (and in most ecosystems temperatures are low); on the other hand, availability of assimilable carbon and energy sources is severely restricted, as most of the potentially utilizable carbon compounds are present in polymeric forms and are not directly accessible [1,2] This latter situation, usually referred to as oligotrophy, starvation, or (technically) carbon and energy limited conditions, has been described physiologically as the “hunger status” [3]. Microbial cells are exposed very directly to potentially harmful changes in temperature, light and other physicochemical parameters They have to be prepared for such challenges, and when necessary, to be able to rapidly react to environmental stresses. Microbial cells are known to be able to adjust their cellular composition to environmental needs [4] and they possess fine-tuned global regulatory mechanisms that allow coordinated gene expression in complex regulatory networks resulting from the interaction of different global regulators [5,6,7]

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