Non-adaptive origins of interactome complexity

Journal name:
Nature
Volume:
474,
Pages:
502–505
Date published:
DOI:
doi:10.1038/nature09992
Received
Accepted
Published online

The boundaries between prokaryotes, unicellular eukaryotes and multicellular eukaryotes are accompanied by orders-of-magnitude reductions in effective population size, with concurrent amplifications of the effects of random genetic drift and mutation1. The resultant decline in the efficiency of selection seems to be sufficient to influence a wide range of attributes at the genomic level in a non-adaptive manner2. A key remaining question concerns the extent to which variation in the power of random genetic drift is capable of influencing phylogenetic diversity at the subcellular and cellular levels2, 3, 4. Should this be the case, population size would have to be considered as a potential determinant of the mechanistic pathways underlying long-term phenotypic evolution. Here we demonstrate a phylogenetically broad inverse relation between the power of drift and the structural integrity of protein subunits. This leads to the hypothesis that the accumulation of mildly deleterious mutations in populations of small size induces secondary selection for protein–protein interactions that stabilize key gene functions. By this means, the complex protein architectures and interactions essential to the genesis of phenotypic diversity may initially emerge by non-adaptive mechanisms.

At a glance

Figures

  1. Structural deficiencies in soluble proteins promote protein associations.
    Figure 1: Structural deficiencies in soluble proteins promote protein associations.

    a, Hydration of exposed polar backbone induces interfacial tension by causing water molecules near the defect to relinquish part of their coordination (g<4) relative to the level in surrounding bulk solvent (g = 4). White represents hydrogen atoms; red, oxygen; blue, nitrogen; black, carbon; the larger purple circles denote side chains for amino acids. Hydrogen bonds are denoted by dashed lines. Thick grey lines outline the external surface of the overall protein molecule, and the underlying structure represents two amino acids made adjacent by the protein architecture and bound by a hydrogen bond between the backbone amide (blue:white) of one amino acid and carbonyl (red:black) of the other. Water molecules are shown as angular red and white segments, with the coordination number g denoting the number of hydrogen bonds associated with a water molecule (g = 4 for bulk water; g<4 for confined interfacial water). In the centre, the structure of the protein causes local exposure and unfavourable hydration of the polar backbone, whereas the absence of such local interactions between water molecules and the well-wrapped proteins on the left and right reduces interfacial tension (interfacial water is bulk-like, retaining the maximum coordination g = 4). b, Comparison of orthologous proteins with different levels of homo-oligomerization reveals that the PWIT is an indicator of the propensity for cooperative improvement/refinement of protein function through complexation. The ratio of protein–protein interfaces (small to large) was determined for pairs of orthologous proteins with different levels of oligomerization in different species (Supplementary Table 2) and plotted against the ratio of PWITs for the respective free subunits. The tight correlation (r2 = 0.94) reveals that interspecific differences in PWIT accompany differences in levels of oligomerization, thus providing a measure of potential allosteric or cooperative improvement of basic protein function. Complexes with cyclic rotational symmetry (C2, C3, ) can further oligomerize into complexes with dihedral (D2, D3, ) symmetry, as shown in the idealized diagrams in the lower right. For example, C2 complexes can dimerize into D2 complexes, trimerize into D3 complexes, etc., whereas a D3 complex can also be obtained by dimerization of a C3 complex. For the protein–protein interface and PWIT ratios examined, the interface for the subunit in the complex with lower-order symmetry is compared with that in the complex with higher-order symmetry, yielding analyses based on protein pairs contrasted within three groupings: C2 versus D2, C2 versus D3, and C3 versus D3. c, The SABHB patterns from two haemoglobins with different oligomerization levels in their native states are compared. In the bottom panels, the protein backbone is represented by virtual bonds in blue joining α-carbons, with well-protected BHBs shown as light grey and SABHBs as green lines joining the α-carbons of the paired residues. The ribbon representations of the human complex and dissociated subunit (chain A in PDB.2DN2, left and centre, respectively) are included as aids to the eye, representing the structuring of the backbone in each subunit. The free subunit isolated from the tetramer in H. sapiens (PDB.2DN2, chain A, centre) has seven excess SABHBs (denoted by stars) when compared with the subunit within the tetrameric complex, where they are well-protected intermolecularly, alleviating interfacial tension. As a consequence of this better wrapping, the overall extent of structural deficiency (ν value) for the subunit within the human complex is identical to that of the natively monomeric haemoglobin from the trematode F. hepatica (PDB.2VYW). This raises the possibility that the accumulation of structural deficiencies in the mammalian haemoglobin subunit promoted the emergence of an oligomeric association as a means of reducing excess interfacial tension. The structural displays were obtained by uploading the PDB text files into the program YAPview, a displayer of local backbone desolvation of soluble proteins that can be downloaded from the link ‘Dehydron Calculator’ at http://www.owlnet.rice.edu/~arifer/.

  2. Structural degradation enhances PWIT and promotes protein interactivity in species with small population sizes.
    Figure 2: Structural degradation enhances PWIT and promotes protein interactivity in species with small population sizes.

    a, Potential for interactome complexity of 36 species with diverse population sizes (Supplementary Table 2), relative to E. coli. To highlight the relative power of random genetic drift, bars are colour-coded to reflect groupings of species in broad population-size categories. b, Overall structural deficiency of orthologues of the enzyme superoxide dismutase (Mn), revealing a progressive accumulation of SABHBs in the orthologues of the bacterium E. coli, the nematode Caenorhabditis elegans and H. sapiens. The upper ribbon representations illustrate the structural conservation across orthologues (respective PDB accession numbers 3ot7, 3dc6, 2adq). The conventional colour coding is red, blue, magenta and light blue for helix, β-strand, loop and turn, respectively. c, Average structural deficiency (ν value) of protein orthologues for intracellular and free-living bacterial species. Species identities, progressing from left to right are as follows: α-Proteobacteria—Rickettsia typhi, Orientia tsutsugamushi, Anaplasma centrale str. Israel, Wolbachia sp. wRi, Rhodospirillum centenum SW, Magnetospirillum magneticum, Silicibacter TM1040, Erythrobacter litoralis; γ-Proteobacteria—Buchnera aphidicola, Wigglesworthia brevipalpis, Candidatus Blochmannia pennsylvanicus, Marinomonas MWYL1, E. coli, Pseudomonas aeruginosa. Only proteins with orthologues across the full set of species within each group were considered for analysis (Supplementary Tables 6 and 7).

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Author information

Affiliations

  1. Department of Computer Science, The University of Chicago, Chicago, Illinois 60637, USA

    • Ariel Fernández
  2. Department of Bioengineering, Rice University, Houston, Texas 77005, USA

    • Ariel Fernández
  3. Department of Biology, Indiana University, Bloomington, Indiana 47405, USA

    • Michael Lynch

Contributions

A.F. and M.L. conceived the project and wrote the paper. A.F. collected the orthologue groups across 36 species with sufficient structural representation, performed the structural analysis and determined the interaction propensities across orthologues.

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The authors declare no competing financial interests.

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Supplementary information

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  1. Supplementary Information (1.8M)

    The file contains Supplementary Information Parts 1 and 2, which include Supplementary Text and Data, Supplementary Tables 1-7, Supplementary Figures 1-7 with legends and additional references.

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