Fig. 6. A diagram of the proposed reaction scheme. (A) Low oxygen acts as a trigger to lower pHi, which enhances protein degradation. As a result, weak acids and other related metabolites (X) increase, which further lowers pHi. At the same time, ammonia (Y) is produced as the final end product. Ammonia, being a small neutral molecule, could permeate the cell membrane easily compared to weak acids, resulting in a large difference in their diffusion coefficient, which is a required condition for the Turing instability (Nicolis and Prigogine, 1977). When the pH is low, ammonia levels will decrease by protonation. Y is consumed in an oxygen-dependent fashion for the production of X by transamination, thus realizing a substrate-depletion type reaction (Meinhardt, 1982). (B) Reaction and diffusion of X and Y creates a stationary gradient with each peak positioned off-phase from each other (Bi). Gradients of X and Y influence pHi and, furthermore, cell differentiation (Bii). The positions of D19, ecmA and ecmB gene expression are also indicated (see text for details).

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