Journal article
Evolution and emergence: higher order information structure in protein interactomes across the tree of life
INTEGRATIVE BIOLOGY, v 13(12), pp 283-294
Dec 2021
PMID: 34933345
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
The internal workings of biological systems are notoriously difficult to understand. Due to the prevalence of noise and degeneracy in evolved systems, in many cases the workings of everything from gene regulatory networks to protein-protein interactome networks remain black boxes. One consequence of this black-box nature is that it is unclear at which scale to analyze biological systems to best understand their function. We analyzed the protein interactomes of over 1800 species, containing in total 8 782 166 protein-protein interactions, at different scales. We show the emergence of higher order `macroscales' in these interactomes and that these biological macroscales are associated with lower noise and degeneracy and therefore lower uncertainty. Moreover, the nodes in the interactomes that make up the macroscale are more resilient compared with nodes that do not participate in the macroscale. These effects are more pronounced in interactomes of eukaryota, as compared with prokaryota; these results hold even after sensitivity tests where we recalculate the emergent macroscales under network simulations where we add different edge weights to the interactomes. This points to plausible evolutionary adaptation for macroscales: biological networks evolve informative macroscales to gain benefits of both being uncertain at lower scales to boost their resilience, and also being 'certain' at higher scales to increase their effectiveness at information transmission. Our work explains some of the difficulty in understanding the workings of biological networks, since they are often most informative at a hidden higher scale, and demonstrates the tools to make these informative higher scales explicit.
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Details
- Title
- Evolution and emergence: higher order information structure in protein interactomes across the tree of life
- Publication Details
- INTEGRATIVE BIOLOGY, v 13(12), pp 283-294
- Publisher
- OXFORD UNIV PRESS; OXFORD
- Number of pages
- 11
- Grant note
- Allen Discovery Center Program through The Paul G. Allen Frontiers Group (12171 to M.L.);Templeton World Charity Foundation, Inc. (TWCFG0273); Army Research Office (proposal 77111 -PH -II); National Science Foundation (DGE-1632976 to A.S.). John Templeton Foundation (61780 to B.K. and 62212 to M.L.).
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Drexel University
- Web of Science ID
- WOS:000743976000001
- Scopus ID
- 2-s2.0-85124533287
- Other Identifier
- 991021860664304721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Cell Biology