Article
Extended Data Fig. 7 | Sequential f lux limitation model and trade-off
between growth and lag. a, Intuitively, in our model, lag phases emerge
because the gluconeogenic f lux, JGNG (blue arrow), limits the synthesis of
proteins, which include gluconeogenic enzymes (green arrow). Therefore, the
production rate of limiting gluconeogenesis is proportional to the
gluconeogenic f lux: dtdφJGNG,lower∝GNG, in which φGNG,lower denotes the
abundance of lower gluconeogenic enzymes. JGNG in turn depends on limiting
metabolite concentrations. b, To understand the dynamic scaling of these
metabolite concentrations, based on the biochemistry of the pathway, we
describe gluconeogenesis by a coarse-grained model comprising two
irreversible steps (upper and lower gluconeogenesis), connected by reversible
reactions. Upper gluconeogenesis does not appear to be limited by its enzyme
(Fbp), whose abundance changed only moderately throughout the lag phase
and across growth conditions (Extended Data Fig. 6 and proteomics data in ref.
(^3) ). We thus assume the f lux through upper gluconeogenesis (top blue arrows) to
be limited by the concentration of its substrate, FBP, thus JGNG∝[FBP]. The FBP
concentration is connected to the output of lower gluconeogenesis, PEP, by the
relation []FBPP∝[EP]^2 , owing to the stoichiometry of the reversible reactions
(grey arrows). The enzymes of lower gluconeogenesis do appear to be limiting,
given previous proteomics data^3 (Fig. 3a and Extended Data Fig. 6). We assume
that the lag phase is dominated by a quasistationary period, where
transcriptional regulation can be considered constant. The abundances of
gluconeogenic enzymes are assumed to change in proportion to each other,
characterized by φGNG,lower. The latter assumption is plausible, as the expression
of gluconeogenic enzymes is primarily controlled by a common transcription
factor Cra. Indeed we note that for different preshift (steady-state) conditions,
the abundances of different gluconeogenic enzymes are proportional to each
other, as they show the same linear growth-rate dependence (Fig. 3a). The f lux
through lower gluconeogenesis (bottom blue arrow), which is proportional to
[PEP], is then governed by φGNG,lower. Thus, [PEP]∝φGNG,lower, resulting in
JGNG∝φGN^2 G,lower. c, During fast glycolytic growth (top), glycolytic enzymes are
highly abundant (thick red arrows), whereas gluconeogenic enzymes are scarce
(thin green arrows). The enzyme composition therefore strongly favours
glycolysis, resulting in severe depletion of carbon-based metabolites (blue
circles) after a shift to gluconeogenic conditions, and hence a long lag phase.
For slow glycolytic growth (bottom), the ratio of glycolytic and gluconeogenic
enzymes is much more balanced (red and green arrows of similar thickness),
resulting in an improved carbon supply to gluconeogenesis after shift and
hence a shorter lag. The thick blue and pink arrows illustrate inf lux from uptake
of glycolytic and gluconeogenic substrates, respectively. The thin blue and
pink arrows illustrate f lux branching off from central carbon metabolism to
provide biomass building blocks.