Stress induces biphasic-rewiring and modularization patterns in the metabolomic networks of Escherichia coli

2020

Preprint

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Domains are the structural, functional and evolutionary units of proteins. They combine to form multidomain proteins. The evolutionary history of this molecular combinatorics has been studied with phylogenomic methods. Here, we construct networks of domain organization and explore their evolution. These networks revealed two ancient waves of structural novelty arising from ancient ‘p-loop’ and ‘winged helix’ domains and a massive ‘big bang’ of domain organization. The evolutionary recruitment of domains was highly modular, hierarchical and ongoing. Domain rearrangements elicited non-random and scale-free network structure. Comparative analyses of preferential attachment, randomness and modularity of networks showed yin-and-yang complementary transition patterns along the evolutionary timeline. Remarkably, evolving networks highlighted a central evolutionary role of cofactor-supporting structures of non-ribosomal peptide synthesis (NRPS) pathways, likely crucial to the early development of the genetic code. Some highly modular domains featured dual response regulation in two-component signal transduction systems with DNA-binding activity linked to transcriptional regulation of responses to environmental change. Interestingly, hub domains across the evolving networks shared the historical role of DNA binding and editing, an ancient protein function in molecular evolution. Our investigation unfolds historical source-sink patterns of evolutionary recruitment that further our understanding of protein architectures and functions.

Section: Emergence Of Preferential Attachment In Network Evolutionmentioning

confidence: 97%

Section: (Ii) Degree Distributionsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Evolution of Networks of Protein Domain Organization

2020

Preprint

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“…average relative distance of amino acid contacts in the tertiary structure of proteins), which is correlated to flexibility, showed that folding speed is optimized and increases in protein evolution 8 . In dynamic metabolomics networks of Escherichia coli , subjection to stress stochastically induces biphasic-rewiring and modularity at regular time intervals of few minutes 9 .…”

mentioning

confidence: 99%

The early history and emergence of molecular functions and modular scale-free network behavior

Caetano-Anollés

2016

Sci Rep

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The formation of protein structural domains requires that biochemical functions, defined by conserved amino acid sequence motifs, be embedded into a structural scaffold. Here we trace domain history onto a bipartite network of elementary functional loop sequences and domain structures defined at the fold superfamily level of SCOP classification. The resulting ‘elementary functionome’ network and its loop motif and structural domain graph projections create evolutionary ‘waterfalls’ describing the emergence of primordial functions. Waterfalls reveal how ancient loops are shared by domain structures in two initial waves of functional innovation that involve founder ‘p-loop’ and ‘winged helix’ domain structures. They also uncover a dynamics of modular motif embedding in domain structures that is ongoing, which transfers ‘preferential’ cooption properties of ancient loops to emerging domains. Remarkably, we find that the emergence of molecular functions induces hierarchical modularity and power law behavior in network evolution as the network of motifs and structures expand metabolic pathways and translation.

“…Multiple interactions of nodes along the timeline diversified connectivity, a feature captured and quantified by weighted degree. Interestingly, box-and-whisker’s plots of weighted outdegree and indegree demonstrate bimodal degree distributions typical of biological systems 49 , 50 (Supplementary Fig. S4 ).…”

Section: Resultsmentioning

confidence: 99%

Evolution of networks of protein domain organization

2021

Sci Rep

Self Cite

Domains are the structural, functional and evolutionary units of proteins. They combine to form multidomain proteins. The evolutionary history of this molecular combinatorics has been studied with phylogenomic methods. Here, we construct networks of domain organization and explore their evolution. A time series of networks revealed two ancient waves of structural novelty arising from ancient ‘p-loop’ and ‘winged helix’ domains and a massive ‘big bang’ of domain organization. The evolutionary recruitment of domains was highly modular, hierarchical and ongoing. Domain rearrangements elicited non-random and scale-free network structure. Comparative analyses of preferential attachment, randomness and modularity showed yin-and-yang complementary transition and biphasic patterns along the structural chronology. Remarkably, the evolving networks highlighted a central evolutionary role of cofactor-supporting structures of non-ribosomal peptide synthesis pathways, likely crucial to the early development of the genetic code. Some highly modular domains featured dual response regulation in two-component signal transduction systems with DNA-binding activity linked to transcriptional regulation of responses to environmental change. Interestingly, hub domains across the evolving networks shared the historical role of DNA binding and editing, an ancient protein function in molecular evolution. Our investigation unfolds historical source-sink patterns of evolutionary recruitment that further our understanding of protein architectures and functions.