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Footprints of optimal protein assembly strategies in the operonic structure of prokaryotes.

Ewald J, Kötzing M, Bartl M, Kaleta C - Metabolites (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Research Group Theoretical Systems Biology, Friedrich-Schiller-Universität Jena, Leutragraben 1, 07743 Jena, Germany. jan.ewald@uni-jena.de.

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.

No MeSH data available.


(a) Advantage of the optimal solution compared to a simultaneous synthesis of subunits; (b) Position in activation sequence compared to the individual synthesis capacity for the same parameter sets as in (a). In both figures colors represent the minimal individual synthesis capacity.
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f4-metabolites-05-00252: (a) Advantage of the optimal solution compared to a simultaneous synthesis of subunits; (b) Position in activation sequence compared to the individual synthesis capacity for the same parameter sets as in (a). In both figures colors represent the minimal individual synthesis capacity.

Mentions: Analogous to the analysis in the last section, we calculated the advantage of the optimal solution and observed that the lowest value of di has a strong correlation with this advantage (Spearman correlation r = 0.774 P = 0). For very low values of di the advantage is nearly zero (Figure 4) and approaches the similar advantage of nearly 3% for high values of di. This indicates, in accordance with our previous results, that for a very low synthesis capacity a simultaneous synthesis strategy is optimal.


Footprints of optimal protein assembly strategies in the operonic structure of prokaryotes.

Ewald J, Kötzing M, Bartl M, Kaleta C - Metabolites (2015)

(a) Advantage of the optimal solution compared to a simultaneous synthesis of subunits; (b) Position in activation sequence compared to the individual synthesis capacity for the same parameter sets as in (a). In both figures colors represent the minimal individual synthesis capacity.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4495372&req=5

f4-metabolites-05-00252: (a) Advantage of the optimal solution compared to a simultaneous synthesis of subunits; (b) Position in activation sequence compared to the individual synthesis capacity for the same parameter sets as in (a). In both figures colors represent the minimal individual synthesis capacity.
Mentions: Analogous to the analysis in the last section, we calculated the advantage of the optimal solution and observed that the lowest value of di has a strong correlation with this advantage (Spearman correlation r = 0.774 P = 0). For very low values of di the advantage is nearly zero (Figure 4) and approaches the similar advantage of nearly 3% for high values of di. This indicates, in accordance with our previous results, that for a very low synthesis capacity a simultaneous synthesis strategy is optimal.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Research Group Theoretical Systems Biology, Friedrich-Schiller-Universität Jena, Leutragraben 1, 07743 Jena, Germany. jan.ewald@uni-jena.de.

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.

No MeSH data available.