Abstract
Stoichiometric balance, or dosage balance, implies that proteins that are subunits of obligate complexes (e.g. the ribosome) should have copy numbers expressed to match their stoichiometry in that complex. Establishing balance (or imbalance) is an important tool for inferring subunit function and assembly bottlenecks. We show here that these correlations in protein copy numbers can extend beyond complex subunits to larger protein-protein interactions networks (PPIN) involving a range of reversible binding interactions. We develop a simple method for quantifying balance in any interface-resolved PPINs based on network structure and experimentally observed protein copy numbers. By analyzing such a network for the clathrin-mediated endocytosis (CME) system in yeast, we found that the real protein copy numbers were significantly more balanced in relation to their binding partners compared to randomly sampled sets of yeast copy numbers. The observed balance is not perfect, highlighting both under and overexpressed proteins. We evaluate the potential cost and benefits of imbalance using two criteria. First, a potential cost to imbalance is that ‘leftover’ proteins without remaining functional partners are free to misinteract. We systematically quantify how this misinteraction cost is most dangerous for strong-binding protein interactions and for network topologies observed in biological PPINs. Second, a more direct consequence of imbalance is that the formation of specific functional complexes depends on relative copy numbers. We therefore construct simple kinetic models of two sub-networks in the CME network to assess multi-protein assembly of the ARP2/3 complex and a minimal, nine-protein clathrin-coated vesicle forming module. We find that the observed, imperfectly balanced copy numbers are less effective than balanced copy numbers in producing fast and complete multi-protein assemblies. However, we speculate that strategic imbalance in the vesicle forming module allows cells to tune where endocytosis occurs, providing sensitive control over cargo uptake via clathrin-coated vesicles.
Highlights
Protein copy numbers in yeast vary from a few to well over a million[1, 2]
Protein copy numbers are often found to be stoichiometrically balanced for subunits of multi-protein complexes
Imbalance is believed to be deleterious because it lowers complex yield and increases the risk of misinteractions, but imbalance may provide unexplored functional benefits
Summary
Protein copy numbers in yeast vary from a few to well over a million[1, 2]. Expression levels, along with a protein’s binding partners and corresponding affinities, are critical determinants of a protein’s function within the cell. In the context of multiprotein complexes–especially obligate complexes such as the ribosome–it is thought that protein concentrations are balanced according to the stoichiometry of the complex This is referred to as the dosage balance hypothesis (DBH)[3,4,5]. We expand this hypothesis to a network wide level, where proteins participate in multiple distinct complexes as well as transient interactions. In these more complex networks (Fig 1A), balance can be defined as having just enough copies of each protein to construct a target vector of complex abundances, with no proteins (or protein binding sites) in significant deficiency or excess. This generalized definition of balance reproduces the expected result for obligate complexes, where, for example, the ARP2/3 obligate complex (Fig 1B) would be balanced if all subunits had equal copy numbers
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