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Panorama of ancient metazoan macromolecular complexes

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ABSTRACT

Macromolecular complexes are essential to conserved biological processes, but their prevalence across animals is unclear. By combining extensive biochemical fractionation with quantitative mass spectrometry, we directly examined the composition of soluble multiprotein complexes among diverse metazoan models. Using an integrative approach, we then generated a draft conservation map consisting of >1 million putative high-confidence co-complex interactions for species with fully sequenced genomes that encompasses functional modules present broadly across all extant animals. Clustering revealed a spectrum of conservation, ranging from ancient Eukaryal assemblies likely serving cellular housekeeping roles for at least 1 billion years, ancestral complexes that have accrued contemporary components, and rarer metazoan innovations linked to multicellularity. We validated these projections by independent co-fractionation experiments in evolutionarily distant species, by affinity-purification and by functional analyses. The comprehensiveness, centrality and modularity of these reconstructed interactomes reflect their fundamental mechanistic significance and adaptive value to animal cell systems.

No MeSH data available.


Agreement of derived complexes’ molecular weights with measurement by HPLC and density centrifugationa, CORUM reference complexes’ inferred molecular weights (MW) are consistent with their components’ average cumulative size exclusion chromatograms. The molecular weights of each complex was calculated as the sum of putative component molecular weights, assuming 1:1 stoichiometry. Data from ref. 43 were analyzed as in Fig. 4c and show a similar trend as for the derived complexes. b, Derived complexes’ inferred molecular weights (MW) are broadly consistent with their components’ average cumulative ultracentrifugation profiles on a sucrose density gradient. Average profiles are plotted for X. laevis orthologs, based on a preparation of hemoglobin-depleted heart and liver proteins separated on a 7 – 47% sucrose density gradient, as described in the Extended Methods.
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Figure 12: Agreement of derived complexes’ molecular weights with measurement by HPLC and density centrifugationa, CORUM reference complexes’ inferred molecular weights (MW) are consistent with their components’ average cumulative size exclusion chromatograms. The molecular weights of each complex was calculated as the sum of putative component molecular weights, assuming 1:1 stoichiometry. Data from ref. 43 were analyzed as in Fig. 4c and show a similar trend as for the derived complexes. b, Derived complexes’ inferred molecular weights (MW) are broadly consistent with their components’ average cumulative ultracentrifugation profiles on a sucrose density gradient. Average profiles are plotted for X. laevis orthologs, based on a preparation of hemoglobin-depleted heart and liver proteins separated on a 7 – 47% sucrose density gradient, as described in the Extended Methods.

Mentions: We also observed broad agreement between the derived complexes’ inferred molecular weights (assuming 1:1 stiochiometries) and migration by size exclusion chromatography (Fig. 4c; Extended Data Fig. 7a) and density gradient centrifugation (Extended Data Fig. 7b). A prime example is the coherent profiles of a large (~500 kDa) ‘mixed’ complex with several unannotated components (Fig. 4d; Extended Data Fig. 8), dubbed Commander because most subunits share COMM (copper metabolism MURR1) domains30 implicated in copper toxicosis31, among other roles30,32. Commander contains coiled-coil domain proteins CCDC22 and CCDC93 (Figs. 4a, d) in addition to ten COMM domain proteins, broadly supported by co-fractionation in human, fly and sea urchin (Extended Data Fig. 9a–c and Supporting Web Site).


Panorama of ancient metazoan macromolecular complexes
Agreement of derived complexes’ molecular weights with measurement by HPLC and density centrifugationa, CORUM reference complexes’ inferred molecular weights (MW) are consistent with their components’ average cumulative size exclusion chromatograms. The molecular weights of each complex was calculated as the sum of putative component molecular weights, assuming 1:1 stoichiometry. Data from ref. 43 were analyzed as in Fig. 4c and show a similar trend as for the derived complexes. b, Derived complexes’ inferred molecular weights (MW) are broadly consistent with their components’ average cumulative ultracentrifugation profiles on a sucrose density gradient. Average profiles are plotted for X. laevis orthologs, based on a preparation of hemoglobin-depleted heart and liver proteins separated on a 7 – 47% sucrose density gradient, as described in the Extended Methods.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC5036527&req=5

Figure 12: Agreement of derived complexes’ molecular weights with measurement by HPLC and density centrifugationa, CORUM reference complexes’ inferred molecular weights (MW) are consistent with their components’ average cumulative size exclusion chromatograms. The molecular weights of each complex was calculated as the sum of putative component molecular weights, assuming 1:1 stoichiometry. Data from ref. 43 were analyzed as in Fig. 4c and show a similar trend as for the derived complexes. b, Derived complexes’ inferred molecular weights (MW) are broadly consistent with their components’ average cumulative ultracentrifugation profiles on a sucrose density gradient. Average profiles are plotted for X. laevis orthologs, based on a preparation of hemoglobin-depleted heart and liver proteins separated on a 7 – 47% sucrose density gradient, as described in the Extended Methods.
Mentions: We also observed broad agreement between the derived complexes’ inferred molecular weights (assuming 1:1 stiochiometries) and migration by size exclusion chromatography (Fig. 4c; Extended Data Fig. 7a) and density gradient centrifugation (Extended Data Fig. 7b). A prime example is the coherent profiles of a large (~500 kDa) ‘mixed’ complex with several unannotated components (Fig. 4d; Extended Data Fig. 8), dubbed Commander because most subunits share COMM (copper metabolism MURR1) domains30 implicated in copper toxicosis31, among other roles30,32. Commander contains coiled-coil domain proteins CCDC22 and CCDC93 (Figs. 4a, d) in addition to ten COMM domain proteins, broadly supported by co-fractionation in human, fly and sea urchin (Extended Data Fig. 9a–c and Supporting Web Site).

View Article: PubMed Central - PubMed

ABSTRACT

Macromolecular complexes are essential to conserved biological processes, but their prevalence across animals is unclear. By combining extensive biochemical fractionation with quantitative mass spectrometry, we directly examined the composition of soluble multiprotein complexes among diverse metazoan models. Using an integrative approach, we then generated a draft conservation map consisting of >1 million putative high-confidence co-complex interactions for species with fully sequenced genomes that encompasses functional modules present broadly across all extant animals. Clustering revealed a spectrum of conservation, ranging from ancient Eukaryal assemblies likely serving cellular housekeeping roles for at least 1 billion years, ancestral complexes that have accrued contemporary components, and rarer metazoan innovations linked to multicellularity. We validated these projections by independent co-fractionation experiments in evolutionarily distant species, by affinity-purification and by functional analyses. The comprehensiveness, centrality and modularity of these reconstructed interactomes reflect their fundamental mechanistic significance and adaptive value to animal cell systems.

No MeSH data available.