Stochastic ordering of complexoform protein assembly by genetic circuits

Mikkel Herholdt Jensen,Michael A Nash,Cheemeng Tan,Hai Tran,Eliza J Morris

doi:10.1371/journal.pcbi.1007997

Abstract

Top-down proteomics has enabled the elucidation of heterogeneous protein complexes with different cofactors, post-translational modifications, and protein membership. This heterogeneity is believed to play a previously unknown role in cellular processes. The different molecular forms of a protein complex have come to be called "complex isoform" or "complexoform". Despite the elucidation of the complexoform, it remains unclear how and whether cellular circuits control the distribution of a complexoform. To help address this issue, we first simulate a generic three-protein complexoform to reveal the control of its distribution by the timing of gene transcription, mRNA translation, and protein transport. Overall, we ran 265 computational experiments: each averaged over 1,000 stochastic simulations. Based on the experiments, we show that genes arranged in a single operon, a cascade, or as two operons all give rise to the different protein composition of complexoform because of timing differences in protein-synthesis order. We also show that changes in the kinetics of expression, protein transport, or protein binding dramatically alter the distribution of the complexoform. Furthermore, both stochastic and transient kinetics control the assembly of the complexoform when the expression and assembly occur concurrently. We test our model against the biological cellulosome system. With biologically relevant rates, we find that the genetic circuitry controls the average final complexoform assembly and the variation in the assembly structure. Our results highlight the importance of both the genetic circuit architecture and kinetics in determining the distribution of a complexoform. Our work has a broad impact on our understanding of non-equilibrium processes in both living and synthetic biological systems.

Highlights

Proteins are synthesized in specific orders to assemble large protein complexes, such as microtubule, proteasome, ribosomes, and cellulosome
Recent top-down proteomics shows that protein complexes can compose of different cofactors, post-translational modifications, and protein membership [1,2,3]
The proteins are exported to a sub-cellular location and bind to scaffold proteins, each consisting of two docking sites. This model system allows us to investigate the role of timing and genetic circuit architecture in modulating the protein assembly, irrespective of the exact number of types of proteins and binding sites

Summary

Introduction

Proteins are synthesized in specific orders to assemble large protein complexes, such as microtubule, proteasome, ribosomes, and cellulosome. These protein complexes are assembled both inside and outside cells through the coordination of gene expression, protein transport, and binding processes. A recent computational study [12] has investigated the formation of protein complexes using existing data on protein-protein interaction networks. This prior work shows that the composition of a protein complex can drift over time even when the simulation starts from the same initial condition. The work suggests that other cellular mechanisms must exist to prevent the compositional drift of some protein complexes

Methods

Results

Discussion

Conclusion