## 4 Discussion
### The Respiratory Chain  
The respiratory chain of _E. coli_ is comprised of NADH dehydrogenase I (NADH-I) and fumarate reductase (FDR). NADH-I, encoded by the _nuo_ operon (_nuoABCDEFGHIJKL_), represents the primary dehydrogenase in the respiratory chain in _E. coli_, and appears to be the only H\({}^{+}\)-pumping dehydrogenase in the respiratory chain. This multienzyme complex catalyzes the transfer of two electrons from NADH to quinone, coupled with the translocation of four protons across the membrane, contributing to the proton-motive force (PMF) required for the synthesis of ATP [4; 33; 34]. Transcriptomic analysis of the genes _nuoABCEF_ and _nuoMN_ in PB12 showed a slightly increased transcriptomic level in this mutant and no changes in PB12 AGD\({}^{+}\) (Table 3, Figure 3). These genes comprise the soluble fragment (NouEFG) involved in the oxidation of NADH, and constitute the electron input component of the complex, the amphipathic connecting section including the NuoBCD and NuoI, and the membrane fragment composed of NouA, H, J, K, L, and NuoMN [4; 33]. UbiE (encoded by _ubiE_) is a C-methyltransferasease that catalyzes reactions in both ubiquinone (Q) and menaquinone (vitamin K\({}_{2}\) [MK]) biosynthesis. The isoprenoid quinone ubiquinone (coenzyme Q) is an essential component in the respiratory electron transport chain, whereas MK is an isoprenoid naphthoquinone functioning as a redox mediator in _E. coli_ electron transfer chains [35]. The transcriptomic analysis of this gene showed an upregulation of this gene in PB12 and a slight upregulation in the apt mutant (Table 3). The gene _napA_ encodes for the molybdenum subunit of the periplasmic nitrate reductase Nap, and is involved in energy conservation during anaerobic bacterial growth [36]. This protein was shown to be upregulated in the two PB12 mutants. Still, this result is intriguing because the expression of _napA_ is induced in anaerbiosis with Fnr, and lower nitrate concentrations are mediated by the transcriptional regulator NarP. Nap was reported to support anaerobic respiration in various carbon sources at the expense of lower nitrate concentrations [37]. The gen _narG_ was found also upregulated in both PB12 mutants. This gene encodes the \(\alpha\) subunit of the nitrate reductase A (NRA), involved in the anaerobic respiratory chain with the NADH dehydrogenase transferring electrons from NADH to nitrate coupled to the generation of a PMF across the cytoplasmic membrane in _E. coli_[4]. Expression of NRA was observed in response to high levels of nitrate in the environment [38]. _eno, fbaB, gapA, glk, pgk, pykF, tpiA, pckA, prpsA)_, PPP (_zuf, eda_), the TCA cycle, and glyoxylate shunt enzymes (_aceEF, acnB, lpd_) (_icdA_, positively regulated), acetate production and utilization (_poxB_, positively regulated), respiratory genes (_cyoBCDE_), and genes encoding the Entner-Doudoroff pathway [4]. The Glc regulator (GlcC-glycolate DNA-binding transcriptional dual regulator, encoded with _glcC_) is proposed to control the expression of genes involved in utilizing glycolate as the sole carbon source [39]. The transcriptional regulator Gycolate-GlcNAc positively controls the transcription of the operon _glcDEFGBA_, resulting in the expression of the glycolate dehydrogenase (GlcEFD) and the malate synthase G (GlcB) involved in the glyoxylate shunt [4]. The gen _ihfA_ encodes the integration host factor subunit \(\alpha\) (IHF\(\alpha\) or IFHA). _E. coli_ IHF is a complex conformed by the subunits IHF\(\alpha\) and IHF\(\beta\). IHF\(\alpha\) is the subunit responsible for DNA binding and is essential for the induction of resistance to extreme acidic pH in _E. coli_[40]. IHF was also involved in controlling the expression of several regulators and genes involved in cellular processes in _E. coli_.