Intracellular Carbon Fluxes in Riboflavin-Producing Bacillus subtilis during Growth on Two-Carbon Substrate Mixtures

Abstract

Metabolic responses to cofeeding of different carbon substrates in carbon-limited chemostat cultures were investigated with riboflavin-producing Bacillus subtilis. Relative to the carbon content (or energy content) of the substrates, the biomass yield was lower in all cofeeding experiments than with glucose alone. The riboflavin yield, in contrast, was significantly increased in the acetoin-and gluconate-cofed cultures. In these two scenarios, unusually high intracellular ATP-to-ADP ratios correlated with improved riboflavin yields. Nuclear magnetic resonance spectra recorded with amino acids obtained from biosynthetically directed fractional 13 C labeling experiments were used in an isotope isomer balancing framework to estimate intracellular carbon fluxes. The glycolysis-to-pentose phosphate (PP) pathway split ratio was almost invariant at about 80% in all experiments, a result that was particularly surprising for the cosubstrate gluconate, which feeds directly into the PP pathway. The in vivo activities of the tricarboxylic acid cycle, in contrast, varied more than twofold. The malic enzyme was active with acetate, gluconate, or acetoin cofeeding but not with citrate cofeeding or with glucose alone. The in vivo activity of the gluconeogenic phosphoenolpyruvate carboxykinase was found to be relatively high in all experiments, with the sole exception of the gluconate-cofed culture.During batch growth on mixtures of carbon substrates, bacteria frequently first consume almost exclusively their preferred substrate. Consumption of any other substrate(s) occurs only after depletion of the preferred one, leading to a diauxic pattern of growth. The primary molecular mechanisms that inhibit the simultaneous utilization of substrates are catabolite repression (9) and inducer exclusion (47). Under carbon-limited conditions in chemostat cultures, in contrast, mixtures of carbon sources are often utilized simultaneously at low and intermediate dilution rates (D) (18). Thus, for the most frequently used paradigm catabolite repression sugar, glucose, such coutilization occurs at concentrations below a critical repression level (29). Consequently, many catabolic enzymes are relieved from repression so that alternative substrates can be catabolized (32,34).While many biotechnological processes operate on a single carbon source, substrate mixtures may help to diagnose potential bottlenecks in the biosynthetic pathways to a desired product (10). For the production of riboflavin (vitamin B 2 ), which is a commercially important additive in the feed and food industries, such cofeeding experiments were used to identify potential limitations in building block supply (55) (Fig. 1). Generally, cofeeding experiments are evaluated on the basis of physiological analysis, with a primary focus on production. Much information on the underlying metabolic network response, however, is not accessible from extracellular physiological data but requires knowledge of intracellular carbon fluxes.The classical approach to analyzing intracellular car...

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“…The intracellular flux distribution estimated by metabolic flux analysis provides a holistic view of cellular metabolism. The result can be used for quantitative comparison of cells grown under different environmental conditions or for comparison of different mutant strains (9,21,37,47). Moreover, as these two methods are very different, flux ratio analysis may provide an independent verification of the flux estimates (14).…”

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“…For glucose-grown B. subtilis, such flux analyses have revealed highly variable fluxes through the oxidative PP pathway, ranging from an almost complete absence during slow growth under nitrogen limitation (12) or when glucose and intermediates of the tricarboxylic acid cycle are cometabolized (11) to PP pathway fluxes that may exceed the glycolytic flux under phosphate limitation (12) or in certain riboflavin-producing strains (42). Generally, the flux through the PP pathway does not appear to be regulated by the cellular demand for NADPH and/or pentoses in B. subtilis but rather is determined by the kinetic properties of the enzymes at the glucose-6-P branch point (11), as has been shown for Corynebacterium glutamicum (33,34). During standard batch growth in minimal medium, around 30 to 40% of the consumed glucose is catabolized through the oxidative PP pathway flux in B. subtilis (52), which is more than the amount catabolized in E. coli (16) or other bacilli (9).…”