# Gene Networks and Pathways Involved in _Escherichia coli_ Response to Multiple Stressors
## 4 Discussion
Although different computational approaches were used, the work agrees with ours in the following: nutrition limitations in _E. coli_ indicated by the poor M9 medium were enriched in downregulation of the flagellar genes and upregulation of CsgD, a biofilm master regulator. TMP induced SOS response and cellular response to various stimuli. The SOS response inhibits cell division upon exposure to TMP by upregulating _sulA_. _sulA_ was also upregulated in all five stressors in our analysis. TMP also induced upregulation of genes _csgD_, _csgE_, and _csgF_ of the _csgDEFG_ operon as well as _csgB_ of the _csgBA_ operon. In our study _csgF_ and _csgB_ were upregulated in three stressors, _csgG_ was upregulated in two stressors, and heat stress upregulated _csgA_, _csgD_, and _csgE_. Those two operons involved in biofilm formation confer protection to bacteria against antibiotics and stressful conditions. Genes in the main five sub-networks generated in that study belonged to flagellar assembly, energy metabolism, SOS response and DNA repair, RNA binding proteins, and biosynthesis of amino acids and secondary metabolites. This is consistent with our finding as biofilm formation, DNA repair, and the bacterial response to stress and to various stimuli were enriched in upregulated genes. Functions such as energy-requiring metabolism, purine and pyrimidine biosynthesis, flagellar assembly, biogenesis, and export were enriched in downregulated genes. Individual genes in those main sub-networks were represented in our hub up or downregulated genes: nineteen genes of energy metabolism (_elaB_, _dps_, _fbuB_, _fic_, _msyB_, _osmY_, _sra_, _wrbA_, _ybaY_, _ybgS_, _ycaC_, _yccl_, _ycgB_, _yeaG_, _yeaH_, _yegP_, _yiaG_, _yodD_, and _yqjC_; Figure 6A), four genes of DNA repair (_lexA_, _recF_, _recN_, and _recQ_; Figure 6D) and four genes of amino acids and secondary metabolites biosynthesis (_entF_, _fepC_, _fepG_, and _feS_; Figure 6B) were in hub upregulated genes; six flagellar genes (_f9H_, _f9G_, _f9K_, _f1H_, _f1H_, _f1H_, and _f1 hB_; Figure 7B) and one gene of amino acids and secondary metabolites biosynthesis (_cyoB_; Figure 7C) were in hub downregulated genes. Intriguingly, PurR was identified as a major regulator that is related to several of the genes and pathways detected in our analysis. PurR is considered one of the general transcription factors (TFs) as it controls the expression of genes related to connecting reactions as well as genes with diverse functional categories [79]. PurR function and size are considered limited when compared to other general TFs in _E. coli_, such as Crp [80],Farr [81], and Lrp [82]. In _Bacillus_ subtilis, the nucleotide messengers ppGpp and pppGpp (collectively (p)ppGpp) were reported to bind to PurR, therefore increasing its DNA binding and enhancing the downregulation of PurR-regulated genes involved in purine biosynthesis during nutrient starvation. This suggests that purine biosynthesis is repressed by PurR to cope with unfavorable conditions during starvation [83]. PurR has not been previously reported to be related to stress in _E. coli_, yet in our analysis, most of the downregulated genes are known to be repressed by PurR, and the purine and pyrimidine biosynthesis, salvage, and uptake pathways were highly represented among downregulated data. Taken together, these findings suggest that PurR has a critical role in balancing the metabolism _E. coli_ under different types of stress.