Mechanistic model of nutrient uptake explains dichotomy between marine oligotrophic and copiotrophic bacteria
Fig 3
A simple metabolic model tracks the utilization of a generic nutrient by the cell.
The nutrient diffuses into the periplasm via a porous outer membrane and is then transported into the cytoplasm by membrane-bound transport units. The cell uses either transport by PTS, in which the substrate directly binds to the transport unit, or ABC transport, in which the substrate must first bind to a binding protein and then this complex binds to the transport unit. The intracellular substrate is next metabolized by a protein group that transforms the substrate into a precursor (a generic amino acid) that is needed to build the cell. The precursors are used (i) by a membrane biosynthesis protein group to build both the outer and inner membranes and (ii) by ribosomes to make proteins comprising the six protein groups. This model is subject to a number of constraints to determine the proteome allocation that maximizes the steady-state exponential growth rate. While this model does not consider the utilization of carbon for energy, we expanded the model to consider energy to show that differences in the energetic requirements of PTS and ABC transport do not change our results (Section E in S1 Appendix).