Abstract
In this work, we investigate optimality principles behind synthesis strategies for protein complexes using a dynamic optimization approach. We show that the cellular capacity of protein synthesis has a strong influence on optimal synthesis strategies reaching from a simultaneous to a sequential synthesis of the subunits of a protein complex. Sequential synthesis is preferred if protein synthesis is strongly limited, whereas a simultaneous synthesis is optimal in situations with a high protein synthesis capacity. We confirm the predictions of our optimization approach through the analysis of the operonic organization of protein complexes in several hundred prokaryotes. Thereby, we are able to show that cellular protein synthesis capacity is a driving force in the dissolution of operons comprising the subunits of a protein complex. Thus, we also provide a tested hypothesis explaining why the subunits of many prokaryotic protein complexes are distributed across several operons despite the presumably less precise co-regulation.
Highlights
Evolutionary derived optimality principles are an often used approach to understand and explain biological phenomena in metabolism [1,2], evolution of enzymes [3,4] or even in the arrangement of plant leaves [5]
Since the stepwise assembly of protein complexes is known on an experimental basis only for a small number of complexes, like the 26s proteasome [11] or the RNA polymerase [12], we focus on general optimality principles behind protein complex synthesis and their influence on specific genomic features
The assembly and the production of complex ABCD is controlled by the synthesis rate ui (t) of each subunit i which are determined by solving a dynamic optimization problem that maximize the amount of active protein complex over time (Figure 1b)
Summary
Evolutionary derived optimality principles are an often used approach to understand and explain biological phenomena in metabolism [1,2], evolution of enzymes [3,4] or even in the arrangement of plant leaves [5]. According to the EcoCyc database [9], 1393 genes of Escherichia coli encode subunits of protein complexes and around 53% of them are associated with protein complexes with at least two protein entities (heteromers). The assembly of those complexes follows ordered steps and is not random due to the formation of energetically favorable subcomplexes [10]. This recent study provides evidence that the order of assembly is conserved through evolution by linking gene fusion events with assembly steps
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