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Under anaerobic conditions E. coli has two options to generate ATP: fermentation (substrate-level phosphorylation), and respiration (proton gradient, chemisomotic phosphorylation). Which is favored? What determines the choice? If availability of enzymes required for anaerobic respiration is decisive, what regulates them under anaerobic conditions?

I looked into the web but did not find the answer. Rather web is littered with confusion between fermentation and anaerobic respiration.

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Let me first clarify the difference between anaerobic respiration and fermentation. Literally respiration refers to breathing, but its definition has been extended to include cellular metabolism that leads to ATP generation.

Fermentation, as you said depends on substrate level phosphorylation. Anaerobic respiration on the other hand just means ATP synthesis in the absence of oxygen- in other words anoxic. This happens in several cases in which the terminal electron acceptor is not oxygen but some other chemical species such as $Fe^{3+}$ or fumarate.

E.coli can carry out ETC mediated ATP synthesis both in the presence and absence of oxygen. At high oxygen concentration it uses $O_2$ as electron acceptor, mediated by cytochrome-d. At low oxygen concentration other kinds of cytochromes accumulate and the cell uses fumarate or nitrate as the terminal electron acceptor with the help of fumarate reductase and nitrate reductase respectively. This is an old article but is still quite informative. Check it out. Fumarate and nitrate reductases are regulated as a part of what is known as FNR regulon. FNR is an oxygen-sensitive transcription regulator. In the presence of oxygen it is inactivated. In the absence of oxygen it activates the fumarate and nitrate reductase genes.

Perhaps in the absence of these alternate electron acceptors, the bacterium totally depends on SLP.

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