Deep evolutionary analysis reveals the design principles of fold A glycosyltransferases
- University of Georgia, United States
Abstract
Glycosyltransferases (GTs) are prevalent across the tree of life and regulate nearly all aspects of cellular functions. The evolutionary basis for their complex and diverse modes of catalytic functions remain enigmatic. Here, based on deep mining of over half million GT-A fold sequences, we define a minimal core component shared among functionally diverse enzymes. We find that variations in the common core and emergence of hypervariable loops extending from the core contributed to GT-A diversity. We provide a phylogenetic framework relating diverse GT-A fold families for the first time and show that inverting and retaining mechanisms emerged multiple times independently during evolution. Using evolutionary information encoded in primary sequences, we trained a machine learning classifier to predict donor specificity with nearly 90% accuracy and deployed it for the annotation of understudied GTs. Our studies provide an evolutionary framework for investigating complex relationships connecting GT-A fold sequence, structure, function and regulation.
Data availability
All the data generated during the study are summarized and provided in the manuscript and supporting files. Source files have been provided for Figures 1, 3, 6 and 7. Additionally, all the sequences curated during this study have been deposited to Dryad (doi:10.5061/dryad.v15dv41sh).
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Deep evolutionary analysis reveals the design principles of fold A glycosyltransferasesDryad Digital Repository, doi:10.5061/dryad.v15dv41sh.
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NCBI reference sequences (RefSeq): a curated non redundant sequence database of genomes, transcripts and proteinsNCBI RefSeq, doi:10.1093/nar/gkl842.
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UniProt: a worldwide hub of protein knowledgeUniProt, doi:10.1093/nar/gky1049.
Article and author information
Author details
Funding
National Institutes of Health (R01 GM130915)
- Kelley W Moremen
- Natarajan Kannan
National Institutes of Health (T32 GM107004)
- Rahil Taujale
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Monica Palcic, University of Victoria
Version history
- Received: December 17, 2019
- Accepted: March 31, 2020
- Accepted Manuscript published: April 1, 2020 (version 1)
- Version of Record published: April 27, 2020 (version 2)
Copyright
© 2020, Taujale et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Deep evolutionary analysis reveals the design principles of fold A glycosyltransferases
eLife 9:e54532.
https://doi.org/10.7554/eLife.54532
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