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Panorama of ancient metazoan macromolecular complexes

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.


Derivation and projection of protein co-complex associations across taxaa, Expanded coverage via experimental scale-up relative to our previous human study6. Chart shows number of proteins detected, most (63%) in two or more species. b, Performance benchmarks, measuring precision and recall of our method and data in identifying known co-complex interactions (annotated human complexes from CORUM39). Complexes were split into training and withheld test sets; 5-fold cross-validation against 4,528 interactions derived from the withheld test set shows strong performance gains, beyond baselines achieved using only co-fractionation or external evidence alone. c, Plots showing high enrichment (probability ratio of interacting) of predicted interacting orthologous protein pairs (relative to non-interacting pairs) among highly correlated fractionation profiles, in both the holdout validation (test, ‘T’) and input species (colors reflect clade memberships). d, (left) Representative co-fractionation data (normalized spectral counts shown for portions of 3 of 42 experimental profiles) from human, fly, and sea urchin showing characteristic profiles of proteasome core, base and lid subcomplexes. Hierarchical clustering (right) of pan-species pairwise Pearson correlation scores (centre) is consistent with accepted structural models (PDB id: 4CR2; core, red; base, blue; lid, green; out-clusters, white). e, Projection of conserved co-complex interactions across 122 eukaryotic species, indicating overlap with leading public PPI reference databases39–41. STRING bars indicate excess over CORUM; GeneMania bars indicate excess over both; component and interaction occurences across Clades indicated at bottom.
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Figure 2: Derivation and projection of protein co-complex associations across taxaa, Expanded coverage via experimental scale-up relative to our previous human study6. Chart shows number of proteins detected, most (63%) in two or more species. b, Performance benchmarks, measuring precision and recall of our method and data in identifying known co-complex interactions (annotated human complexes from CORUM39). Complexes were split into training and withheld test sets; 5-fold cross-validation against 4,528 interactions derived from the withheld test set shows strong performance gains, beyond baselines achieved using only co-fractionation or external evidence alone. c, Plots showing high enrichment (probability ratio of interacting) of predicted interacting orthologous protein pairs (relative to non-interacting pairs) among highly correlated fractionation profiles, in both the holdout validation (test, ‘T’) and input species (colors reflect clade memberships). d, (left) Representative co-fractionation data (normalized spectral counts shown for portions of 3 of 42 experimental profiles) from human, fly, and sea urchin showing characteristic profiles of proteasome core, base and lid subcomplexes. Hierarchical clustering (right) of pan-species pairwise Pearson correlation scores (centre) is consistent with accepted structural models (PDB id: 4CR2; core, red; base, blue; lid, green; out-clusters, white). e, Projection of conserved co-complex interactions across 122 eukaryotic species, indicating overlap with leading public PPI reference databases39–41. STRING bars indicate excess over CORUM; GeneMania bars indicate excess over both; component and interaction occurences across Clades indicated at bottom.

Mentions: We identified and quantified (see Extended Methods) 13,386 protein orthologs across 6,387 fractions obtained from 69 different experiments (Fig. 2a), an order of magnitude expansion in data coverage relative to our original (H. sapiens only) study6. Individual pair-wise protein associations were scored based on the fractionation profile similarity measured in each species. Next, we used an integrative computational scoring procedure (Fig. 1c; see Extended Methods) to derive conserved interactions for human proteins and their orthologs in worm, fly, mouse and sea urchin, defined as high pair-wise protein co-fractionation in at least two of the five input species. The support vector machine learning classifier used was trained (using 5-fold cross validation) on correlation scores obtained for conserved reference annotated protein complexes (see Extended Methods), and combined all of the input species co-fractionation data together with previously published human6,19 and fly interactions5 and additional supporting functional association evidence20 (HumanNet). Notably, measurements of overall performance showed high precision with reasonable recall by the co-fractionation data alone (Fig. 2b), with external datasets serving only to increase precision and recall as we required all derived interactions to have significant biochemical support (see Extended Methods). Co-fractionation data of each input species impacted overall performance, in each case increasing precision and recall (Extended Data Fig. 1a).


Panorama of ancient metazoan macromolecular complexes
Derivation and projection of protein co-complex associations across taxaa, Expanded coverage via experimental scale-up relative to our previous human study6. Chart shows number of proteins detected, most (63%) in two or more species. b, Performance benchmarks, measuring precision and recall of our method and data in identifying known co-complex interactions (annotated human complexes from CORUM39). Complexes were split into training and withheld test sets; 5-fold cross-validation against 4,528 interactions derived from the withheld test set shows strong performance gains, beyond baselines achieved using only co-fractionation or external evidence alone. c, Plots showing high enrichment (probability ratio of interacting) of predicted interacting orthologous protein pairs (relative to non-interacting pairs) among highly correlated fractionation profiles, in both the holdout validation (test, ‘T’) and input species (colors reflect clade memberships). d, (left) Representative co-fractionation data (normalized spectral counts shown for portions of 3 of 42 experimental profiles) from human, fly, and sea urchin showing characteristic profiles of proteasome core, base and lid subcomplexes. Hierarchical clustering (right) of pan-species pairwise Pearson correlation scores (centre) is consistent with accepted structural models (PDB id: 4CR2; core, red; base, blue; lid, green; out-clusters, white). e, Projection of conserved co-complex interactions across 122 eukaryotic species, indicating overlap with leading public PPI reference databases39–41. STRING bars indicate excess over CORUM; GeneMania bars indicate excess over both; component and interaction occurences across Clades indicated at bottom.
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Figure 2: Derivation and projection of protein co-complex associations across taxaa, Expanded coverage via experimental scale-up relative to our previous human study6. Chart shows number of proteins detected, most (63%) in two or more species. b, Performance benchmarks, measuring precision and recall of our method and data in identifying known co-complex interactions (annotated human complexes from CORUM39). Complexes were split into training and withheld test sets; 5-fold cross-validation against 4,528 interactions derived from the withheld test set shows strong performance gains, beyond baselines achieved using only co-fractionation or external evidence alone. c, Plots showing high enrichment (probability ratio of interacting) of predicted interacting orthologous protein pairs (relative to non-interacting pairs) among highly correlated fractionation profiles, in both the holdout validation (test, ‘T’) and input species (colors reflect clade memberships). d, (left) Representative co-fractionation data (normalized spectral counts shown for portions of 3 of 42 experimental profiles) from human, fly, and sea urchin showing characteristic profiles of proteasome core, base and lid subcomplexes. Hierarchical clustering (right) of pan-species pairwise Pearson correlation scores (centre) is consistent with accepted structural models (PDB id: 4CR2; core, red; base, blue; lid, green; out-clusters, white). e, Projection of conserved co-complex interactions across 122 eukaryotic species, indicating overlap with leading public PPI reference databases39–41. STRING bars indicate excess over CORUM; GeneMania bars indicate excess over both; component and interaction occurences across Clades indicated at bottom.
Mentions: We identified and quantified (see Extended Methods) 13,386 protein orthologs across 6,387 fractions obtained from 69 different experiments (Fig. 2a), an order of magnitude expansion in data coverage relative to our original (H. sapiens only) study6. Individual pair-wise protein associations were scored based on the fractionation profile similarity measured in each species. Next, we used an integrative computational scoring procedure (Fig. 1c; see Extended Methods) to derive conserved interactions for human proteins and their orthologs in worm, fly, mouse and sea urchin, defined as high pair-wise protein co-fractionation in at least two of the five input species. The support vector machine learning classifier used was trained (using 5-fold cross validation) on correlation scores obtained for conserved reference annotated protein complexes (see Extended Methods), and combined all of the input species co-fractionation data together with previously published human6,19 and fly interactions5 and additional supporting functional association evidence20 (HumanNet). Notably, measurements of overall performance showed high precision with reasonable recall by the co-fractionation data alone (Fig. 2b), with external datasets serving only to increase precision and recall as we required all derived interactions to have significant biochemical support (see Extended Methods). Co-fractionation data of each input species impacted overall performance, in each case increasing precision and recall (Extended Data Fig. 1a).

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.