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The evolutionary traceability of proteins

Arpit Jain, Arndt von Haeseler, Ingo Ebersberger
doi: https://doi.org/10.1101/302109
Arpit Jain
Goethe University Frankfurt, Frankfurt am Main, Germany;
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Arndt von Haeseler
Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, Vienna, Austria;
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Ingo Ebersberger
Goethe University Frankfurt
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  • For correspondence: ebersberger@bio.uni-frankfurt.de
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Abstract

Orthologs document the evolution of genes and metabolic capacities encoded in extant and ancient genomes. Orthologous genes that are detected across the full diversity of contemporary life allow reconstructing the gene set of LUCA, the last universal common ancestor. These genes presumably represent the functional repertoire common to and necessary for all living organisms. Design of artificial life has the potential to test this. Recently, a minimal gene (MG) set for a self-replicating cell was determined experimentally, and a surprisingly high number of genes have unknown functions and are not represented in LUCA. However, as similarity between orthologs decays with time, it becomes insufficient to infer common ancestry, leaving ancient gene set reconstructions incomplete and distorted to an unknown extent. Here we introduce the evolutionary traceability, together with the software protTrace, that quantifies, for each protein, the evolutionary distance beyond which the sensitivity of the ortholog search becomes limiting. We show that the LUCA set comprises only high-traceable proteins most of which have catalytic functions. We further show that proteins in the MG set lacking orthologs outside bacteria mostly have low traceability, leaving open whether their eukaryotic orthologs have just been overlooked. On the example of REC8, a protein essential for chromosome cohesion, we demonstrate how a traceability-informed adjustment of the search sensitivity identifies hitherto missed orthologs in the fast-evolving microsporidia. Taken together, the evolutionary traceability helps to differentiate between true absence and non-detection of orthologs, and thus improves our understanding about the evolutionary conservation of functional protein networks.

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The copyright holder for this preprint is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
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  • Posted April 16, 2018.

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The evolutionary traceability of proteins
Arpit Jain, Arndt von Haeseler, Ingo Ebersberger
bioRxiv 302109; doi: https://doi.org/10.1101/302109
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The evolutionary traceability of proteins
Arpit Jain, Arndt von Haeseler, Ingo Ebersberger
bioRxiv 302109; doi: https://doi.org/10.1101/302109

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