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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.


Workflowa, Phylogenetic relationships of organisms analyzed in this study. We fractionated soluble protein complexes from worm (C. elegans) larvae, fly (D. melanogaster) S2 cells, mouse (M. musculus) embryonic stem cells, sea urchin (S. purpuratus) eggs, and human (HEK293/HeLa) cell lines. Holdout species (‘T’, for test) likewise analyzed were frog (X. laevis), an amphibian; sea anemone (N. vectensis), a Cnidarian with primitive Eumetazoan tissue organization; slime mold (D. discoideum), an amoeba; and yeast (S. cerevisiae), a unicellular eukaryote. b, Protein fractions were digested and analysed by high performance liquid chromatography-tandem mass spectrometry (LC-MS/MS), measuring peptide spectral counts and precursor ion intensities. c. Integrative computational analysis: after ortholog mapping to human, correlation scores of co-eluting protein pairs detected in each ‘input’ species were subjected to machine learning together with additional external association evidence, using the CORUM complex database as a reference standard for training. High-confidence interactions were clustered to define co-complex membership.
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Figure 1: Workflowa, Phylogenetic relationships of organisms analyzed in this study. We fractionated soluble protein complexes from worm (C. elegans) larvae, fly (D. melanogaster) S2 cells, mouse (M. musculus) embryonic stem cells, sea urchin (S. purpuratus) eggs, and human (HEK293/HeLa) cell lines. Holdout species (‘T’, for test) likewise analyzed were frog (X. laevis), an amphibian; sea anemone (N. vectensis), a Cnidarian with primitive Eumetazoan tissue organization; slime mold (D. discoideum), an amoeba; and yeast (S. cerevisiae), a unicellular eukaryote. b, Protein fractions were digested and analysed by high performance liquid chromatography-tandem mass spectrometry (LC-MS/MS), measuring peptide spectral counts and precursor ion intensities. c. Integrative computational analysis: after ortholog mapping to human, correlation scores of co-eluting protein pairs detected in each ‘input’ species were subjected to machine learning together with additional external association evidence, using the CORUM complex database as a reference standard for training. High-confidence interactions were clustered to define co-complex membership.

Mentions: Since previous cross-species interactome comparisons, based on experimental data from different sources and methods, show limited overlap12,18, we sought to produce a more comprehensive and accurate map of protein complexes common to metazoa by applying a standardized approach to multiple species. We employed biochemical fractionation of native macromolecular assemblies followed by tandem mass spectrometry to elucidate protein complex membership (Fig. 1; see Extended Methods). Previous application of this co-fractionation strategy to human cell lines preferentially identified Vertebrate specific protein complexes6, so we selected eight additional species for study based on their relevance as model organisms, spanning roughly a billion years of evolutionary divergence (Fig. 1a). The resulting co-fractionation data (Fig. 1b) acquired for Caenorhabditis elegans (worm), Drosophila melanogaster (fly), Mus musculus (mouse), Strongylocentrotus purpuratus (sea urchin), and human was used to discover conserved interactions (Fig. 1c), while the data obtained for Xenopus laevis (frog), Nematostella vectensis (sea anemone), Dictyostelium discoideum (amoeba), and Saccharomyces cerevisiae (yeast) was used for independent validation. Details on the cell types, developmental stages, and fractionation procedures used are provided in Supplementary Table 1.


Panorama of ancient metazoan macromolecular complexes
Workflowa, Phylogenetic relationships of organisms analyzed in this study. We fractionated soluble protein complexes from worm (C. elegans) larvae, fly (D. melanogaster) S2 cells, mouse (M. musculus) embryonic stem cells, sea urchin (S. purpuratus) eggs, and human (HEK293/HeLa) cell lines. Holdout species (‘T’, for test) likewise analyzed were frog (X. laevis), an amphibian; sea anemone (N. vectensis), a Cnidarian with primitive Eumetazoan tissue organization; slime mold (D. discoideum), an amoeba; and yeast (S. cerevisiae), a unicellular eukaryote. b, Protein fractions were digested and analysed by high performance liquid chromatography-tandem mass spectrometry (LC-MS/MS), measuring peptide spectral counts and precursor ion intensities. c. Integrative computational analysis: after ortholog mapping to human, correlation scores of co-eluting protein pairs detected in each ‘input’ species were subjected to machine learning together with additional external association evidence, using the CORUM complex database as a reference standard for training. High-confidence interactions were clustered to define co-complex membership.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 1: Workflowa, Phylogenetic relationships of organisms analyzed in this study. We fractionated soluble protein complexes from worm (C. elegans) larvae, fly (D. melanogaster) S2 cells, mouse (M. musculus) embryonic stem cells, sea urchin (S. purpuratus) eggs, and human (HEK293/HeLa) cell lines. Holdout species (‘T’, for test) likewise analyzed were frog (X. laevis), an amphibian; sea anemone (N. vectensis), a Cnidarian with primitive Eumetazoan tissue organization; slime mold (D. discoideum), an amoeba; and yeast (S. cerevisiae), a unicellular eukaryote. b, Protein fractions were digested and analysed by high performance liquid chromatography-tandem mass spectrometry (LC-MS/MS), measuring peptide spectral counts and precursor ion intensities. c. Integrative computational analysis: after ortholog mapping to human, correlation scores of co-eluting protein pairs detected in each ‘input’ species were subjected to machine learning together with additional external association evidence, using the CORUM complex database as a reference standard for training. High-confidence interactions were clustered to define co-complex membership.
Mentions: Since previous cross-species interactome comparisons, based on experimental data from different sources and methods, show limited overlap12,18, we sought to produce a more comprehensive and accurate map of protein complexes common to metazoa by applying a standardized approach to multiple species. We employed biochemical fractionation of native macromolecular assemblies followed by tandem mass spectrometry to elucidate protein complex membership (Fig. 1; see Extended Methods). Previous application of this co-fractionation strategy to human cell lines preferentially identified Vertebrate specific protein complexes6, so we selected eight additional species for study based on their relevance as model organisms, spanning roughly a billion years of evolutionary divergence (Fig. 1a). The resulting co-fractionation data (Fig. 1b) acquired for Caenorhabditis elegans (worm), Drosophila melanogaster (fly), Mus musculus (mouse), Strongylocentrotus purpuratus (sea urchin), and human was used to discover conserved interactions (Fig. 1c), while the data obtained for Xenopus laevis (frog), Nematostella vectensis (sea anemone), Dictyostelium discoideum (amoeba), and Saccharomyces cerevisiae (yeast) was used for independent validation. Details on the cell types, developmental stages, and fractionation procedures used are provided in Supplementary Table 1.

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.