# Gene Networks and Pathways Involved in _Escherichia coli_ Response to Multiple Stressors
## 4 Discussion
Our analysis indicated that _fidD_, _fidE_, _fidL_, and _fidR_ were downregulated under at least two stressors, suggesting that, during stress, _E. coli_ downregulates the uptake of exogenous fatty acids along with its metabolism and degradation which generates various reduced cofactors. As previously reported, LCFA degradation generates oxidative stress with high levels of reactive oxygen species [70; 71]. * _cvpA_ encodes colicin V production protein [72] and is located directly upstream of _purF_ and repressed by PurR, the main repressor of purine synthetic pathway [73]. Its deletion mutant in EHEC was highly sensitive to bile and was deemed important in cell envelope homeostasis in response to stressors, such as deoxycholate bile salt [74]. * _ybhC_ encodes an outer membrane lipoprotein [75]. Genome-wide screening of an ASKA library found that overexpression of _yhbC_ leads to an increase in the minimum inhibitory concentration (MIC) of hydrogen peroxide by more than three folds [76]. * _gtrB (yfdH)_ and _gtrS (yfdI)_ are part of the _yfdGHI_ operon. Our analysis indicated that _yfdG_ was downregulated under two stressors. _yfdG_, _yfdH_, and _yfdI_ are homologous to the type IV O antigen modification genes (_gtrAIV_, _gtrBIV_, and _gtrIV_) in the genome of _Shigella flexneri_ NCTC 8296 [77]. * _rnb_ encodes the ribonuclease II enzyme (RNase II), involved in the specific degradation of mRNA in the 3\({}^{\prime}\) to 5\({}^{\prime}\) direction [78]. Network analysis identified upregulated hub genes, which included seven genes involved in biofilm formation (_dosC_, _ydhN_, _yodD_, _dgcZ_, _mqR_, _elFA_, and _glgS_), suggesting that stress response can lead to biofilm formation. Hub genes also include genes involved in ferri-entrobactin transport (_fepB_, _fepC_, _fpD_, and _fepG_) and utilization (_fes_). _entF_ was upregulated under three stressors (antibiotics, heat, and oxidative stress). It is part of the entABCDEF_ operon. Our analysis indicated that _entA_, _entB_, _entC_, _entD_, and _entE_ were upregulated in antibiotic and oxidative stress. This operon is involved in enterobactin biosynthesis, which is a well-known siderophore. This highlights the importance of iron availability for _E. coli_ to cope with different stressors. Downregulated hub genes include seven genes of flagellar biogenesis and assembly (_f9H_, _f9G_, _f9H_K_, _f9H_, _f1H_, _f1H_, _f1H_, and _f1 hB_). A strong relation between motility suppression and high pH was previously reported [67]. Here, we believe that most of those genes are downregulated to preserve energy when _E. coli_ is exposed to cold, heat, oxidative stress, or antibiotic treatment. In general, the purpose of stress response to concentrate cellular resources on survival, as opposed to growth/multiplication. So, based on our analysis and several prior studies, we conclude that major stress responses involve maintaining or upregulating genes related to survival, biofilm formation, and stress response, while downregulating non-essential energy-requiring processes related to growth and replication. Overall, the globally up-regulated pathways we identified for stress responses fall into three major categories: (i) cellular stress response, (ii) DNA repair, and (iii) cell adhesion and biofilm. On the other hand, the main downregulated pathways we identified for stress responses are: (i) de novo purine and pyrimidine biosynthesis pathways, salvage, and uptake, (ii) oxidative phosphorylation/aerobic respiration, and (iii) motility. Of note, while this manuscript was in final preparation, a publication using a similar approach reported a set of genes and networks involved in a collection of stressors [8]. The studied stressors were nutrition limitations (rich M9 and poor M9), acidic stress (pH\({}_{5}\)), antibiotics (trimethoprim (TMP) and chloramphenicol (CAM)), and oxidative stress conferred by growth in low oxygen (LOX) environments, yet the main emphasis of the paper was on transcription factors and regulatory networks.