The genetic and transcriptional basis of short and long term adaptation across multiple stresses in Escherichia coli

Abstract

Microbes exhibit short and long term responses when exposed to challenging environmental conditions. To what extent these responses are correlated, what their evolutionary potential is and how they translate to cross-stress fitness is still unclear. In this study, we comprehensively characterized the response of Escherichia coli populations to four abiotic stresses (n-butanol, osmotic, acidic, and oxidative) and their combinations by performing genome-scale transcriptional analysis and growth profiling. We performed an analysis of their cross-stress behavior which identified 15 cases of cross- protection and one case of cross vulnerability. To elucidate the evolutionary potential of stress responses to individual stresses and stress combinations, we re-sequenced E. coli populations evolved in those four environments for 500 generations. We developed and applied a network-driven method that integrates mutations and differential expression to identify core and stress-specific gene communities that are likely to have a phenotypic impact. Our results suggest that beyond what is expected from the general stress response mechanisms, cross-stress behavior arises both from common pathways, several including metal ion binding and glycolysis/gluconeogenesis, and stress-specific expression programs. The stress-specific dependences uncovered, argue that cross-stress behavior is ubiquitous and central to understanding microbial physiology under stressful conditions.

Population collapse and adaptive rescue during long‐term chemostat fermentation

“…Alternatively, several bacteria, under sublethal antibiotic concentration, induce the cellular machinery responsible for the formation of thicker biofilm, making them more tolerant (Fux, Costerton, Stewart, & Stoodley, ). If the environmental stress persists for longer duration, bacteria make permanent genetic changes to rescue themselves (Zorraquino et al, ).…”

“…environmental stress persists for longer duration, bacteria make permanent genetic changes to rescue themselves (Zorraquino et al, 2017).…”

“…The batch and fed-batch environments can be particularly dynamic and difficult to model due to the large number of parameters involved. In addition to serial dilutions as a method used to study the adaptation and evolution of bacterial cultures (Blount et al, 2012;Zorraquino et al, 2017), chemostats have been used for evolutionary studies when controllability, reproducibility, and continuous growth in a well-controlled static or dynamic conditions is critical (Gresham & Hong, 2015;Hoskisson & Hobbs, 2005). Industrial applications of bacterial biofermentation in batch, fed-batch, and chemostat cultures are many and their value in the billions of dollars per year (Rossouw & Bauer, 2009;Selvamani, Friehs, & Flaschel, 2014;Vaiphei, Pandey, & Mukherjee, 2009).…”

Morphological peculiarities of DNA-protein complexes in dormantEscherichia colicells, subjected to prolonged starvation Condensation of DNA in dormant cells ofEscherichia coli

“…Adaptive molecular strategies ensure the ability of microorganisms to survive in environments significantly different from those, optimal for their growth, and have been the subject of active research over the past years [2][3][4][5][6][7][8]. Such adaptive strategy often launch the increasing synthesis (up to 150-200 thousand copies) of a ferritin-like protein Dps (DNA-binding protein of starved cells) [9][10][11][12].…”

“…[9,15,[19][20][21]. The protective functions of Dps are carried out through condensation of DNA into "biocrystalline" or "in cellulo nanocrystalline" structures [2][3][4][5][6][7]19,[22][23][24] It is considered that the bacterial nucleoid represents an intermediate engineering solution between the protein-free DNA packaging in viruses and protein-defined DNA packaging in eukaryotes [25]. In diluted solutions, the diameter of a DNA double-helix is about 2 nm, while its length may reach up to several centimeters.…”