Global responses ofEscherichia colito adverse conditions determined by microarrays and FT-IR spectroscopy

Abstract

The global gene expression and biomolecular composition in an Escherichia coli model strain exposed to 10 adverse conditions (sodium chloride, ethanol, glycerol, hydrochloric and acetic acid, sodium hydroxide, heat (46 degrees C), and cold (15 degrees C), as well as ethidium bromide and the disinfectant benzalkonium chloride) were determined using DNA microarrays and Fourier transform infrared (FT-IR) spectroscopy. In total, approximately 40% of all investigated genes (1682/4279 genes) significantly changed expression, compared with a nonstressed control. There were, however, only 3 genes (ygaW (unknown function), rmf (encoding a ribosomal modification factor), and ghrA (encoding a glyoxylate/hydroxypyruvate reductase)) that significantly changed expression under all conditions (not including benzalkonium chloride). The FT-IR analysis showed an increase in unsaturated fatty acids during ethanol and cold exposure, and a decrease during acid and heat exposure. Cold conditions induced changes in the carbohydrate composition of the cell, possibly related to the upregulation of outer membrane genes (glgAP and rcsA). Although some covariance was observed between the 2 data sets, principle component analysis and regression analyses revealed that the gene expression and the biomolecular responses are not well correlated in stressed populations of E. coli, underlining the importance of multiple strategies to begin to understand the effect on the whole cell.

Integrated Transcriptomic and Proteomic Analysis of the Physiological Response of Escherichia coli O157:H7 Sakai to Steady-state Conditions of Cold and Water Activity Stress

“…Among these genes, transaldolase A (talA) and transketolase B (tktB), encoding the enzymes in the nonoxidative branch of the pentose phosphate pathway, were commonly found to be significantly up-regulated. Both talA and tktB are positively regulated by RpoS at their transcriptional level (34), and up-regulation of these genes has also been described in previous studies of low temperature (15°C) (54) and high osmolarity (4.5% and 0.4 M NaCl) stress (54,56). Taken together, our findings suggest that the pentose phosphate pathway serves as a more general response to the stress conditions.…”

“…A decrease in cell growth was probably related to down-regulation of the cell division protein FtsZ at 14°C a w 0.985, implying delayed cell division (53). Finally, abundance of the housekeeping sigma factor (RpoD) was reduced under high osmolarity conditions (25°C a w 0.967 and 14°C a w 0.967), which was most likely because of the decreased growth rate (54). Carbohydrate Metabolism and Energy Generation-The alteration in metabolic pathways caused by stress typically disturbs the balance of metabolic flux, which leads to metabolic burden during cellular growth.…”

Dimethyl Sulfoxide and Ethanol Elicit Increased Amyloid Biogenesis and Amyloid-Integrated Biofilm Formation in Escherichia coli

“…Many thorough and well-examined transcriptional analyses of biofilm formation, though powerful in their comparisons and conclusions, were not focused on curli. Some were performed under conditions characterized by very low curli expression levels, e.g., in human urine (26,71), or under conditions in which curli expression and protein levels were not examined (53). The latter study, in particular, examined the complex response of E. coli to ethanol (53).…”

“…Although unanticipated, the selective upregulation of csgA and csgB gene expression was the most remarkable gene transcription response to each solvent identified by microarray analysis. The microarray data for DMSO-treated bacteria, which were more straightforward to consider, as growth in DMSO did not activate the global stress pathways associated with ethanol stress and tolerance (36,37,53), revealed no obvious influence on other genes canonically ascribed to curli or to biofilm regulation as described above. More-rigorous temporal studies may reveal time-dependent transcriptional changes that occurred earlier than those we examined.…”

“…A summary of results for all genes whose transcription changed by more than 2-fold in the case of DMSO and 3-fold in the case of ethanol is provided in Tables S2 and S3 in the supplemental material. Treatment with ethanol was associated with anticipated changes to many additional genes that are appreciated to be involved in the complex physiology of ethanol stress and tolerance (9,40,53). Yet even for ethanol-treated cells, csgB and csgA are the two genes whose transcription was identified as being the most highly altered in the microarray.…”