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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.


Summary of Validation results. The number of protein complexes confirming (green) or rejecting (red) our hypotheses are depicted as polar area diagrams where the size represents the count number. In (a) the results based on the protein complexes retrieved from the EcoCyc database and in (b) from the PDB database are displayed.
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f5-metabolites-05-00252: Summary of Validation results. The number of protein complexes confirming (green) or rejecting (red) our hypotheses are depicted as polar area diagrams where the size represents the count number. In (a) the results based on the protein complexes retrieved from the EcoCyc database and in (b) from the PDB database are displayed.

Mentions: We retrieved 159 protein complexes with at least three entities from the EcoCyc database. For 100 protein complexes we found homologs in at least 50 organisms and could calculate a partial Spearman correlation. Table 2 displays the results for selected protein complexes and Figure 5a. illustrates a summary of confirmed and rejected hypotheses across all tested protein complexes (a detailed list is given in Supplemental Table S1 and S2). The table excerpt shows that our hypotheses are particularly confirmed by protein complexes which are shared by most prokaryotes, e.g., RNA-polymerase, ATP-synthase or chaperone systems. In general for hypothesis 1, we observe 16 protein complexes confirming our prediction and 8 protein complexes rejecting our hypothesis (significant correlation in the opposite direction). Also for hypothesis 2 and 3 the majority of protein complexes (hypothesis 2: 18, hypothesis 3: 23) confirm and the minority (hypothesis 2: 3, hypothesis 3: 13) reject our predictions.


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

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

Summary of Validation results. The number of protein complexes confirming (green) or rejecting (red) our hypotheses are depicted as polar area diagrams where the size represents the count number. In (a) the results based on the protein complexes retrieved from the EcoCyc database and in (b) from the PDB database are displayed.
© Copyright Policy
Related In: Results  -  Collection

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

f5-metabolites-05-00252: Summary of Validation results. The number of protein complexes confirming (green) or rejecting (red) our hypotheses are depicted as polar area diagrams where the size represents the count number. In (a) the results based on the protein complexes retrieved from the EcoCyc database and in (b) from the PDB database are displayed.
Mentions: We retrieved 159 protein complexes with at least three entities from the EcoCyc database. For 100 protein complexes we found homologs in at least 50 organisms and could calculate a partial Spearman correlation. Table 2 displays the results for selected protein complexes and Figure 5a. illustrates a summary of confirmed and rejected hypotheses across all tested protein complexes (a detailed list is given in Supplemental Table S1 and S2). The table excerpt shows that our hypotheses are particularly confirmed by protein complexes which are shared by most prokaryotes, e.g., RNA-polymerase, ATP-synthase or chaperone systems. In general for hypothesis 1, we observe 16 protein complexes confirming our prediction and 8 protein complexes rejecting our hypothesis (significant correlation in the opposite direction). Also for hypothesis 2 and 3 the majority of protein complexes (hypothesis 2: 18, hypothesis 3: 23) confirm and the minority (hypothesis 2: 3, hypothesis 3: 13) reject our predictions.

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.