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Phylogenomic analysis of glycogen branching and debranching enzymatic duo

BACKGROUND: Branched polymers of glucose are universally used for energy storage in cells, taking the form of glycogen in animals, fungi, Bacteria, and Archaea, and of amylopectin in plants. Some enzymes involved in glycogen and amylopectin metabolism are similarly conserved in all forms of life, bu...

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Autores principales: Zmasek, Christian M, Godzik, Adam
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4236520/
https://www.ncbi.nlm.nih.gov/pubmed/25148856
http://dx.doi.org/10.1186/s12862-014-0183-2
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author Zmasek, Christian M
Godzik, Adam
author_facet Zmasek, Christian M
Godzik, Adam
author_sort Zmasek, Christian M
collection PubMed
description BACKGROUND: Branched polymers of glucose are universally used for energy storage in cells, taking the form of glycogen in animals, fungi, Bacteria, and Archaea, and of amylopectin in plants. Some enzymes involved in glycogen and amylopectin metabolism are similarly conserved in all forms of life, but some, interestingly, are not. In this paper we focus on the phylogeny of glycogen branching and debranching enzymes, respectively involved in introducing and removing of the α(1–6) bonds in glucose polymers, bonds that provide the unique branching structure to glucose polymers. RESULTS: We performed a large-scale phylogenomic analysis of branching and debranching enzymes in over 400 completely sequenced genomes, including more than 200 from eukaryotes. We show that branching and debranching enzymes can be found in all kingdoms of life, including all major groups of eukaryotes, and thus were likely to have been present in the last universal common ancestor (LUCA) but have been lost in seemingly random fashion in numerous single-celled eukaryotes. We also show how animal branching and debranching enzymes evolved from their LUCA ancestors by acquiring additional domains. Furthermore, we show that enzymes commonly perceived as orthologous, such as human branching enzyme GBE1 and E. coli branching enzyme GlgB, are in fact related by a gene duplication and consequently paralogous. CONCLUSIONS: Despite being usually associated with animal liver glycogen and plant starch, energy storage in the form of branched glucose polymers is clearly an ancient process and has probably been present in the last universal common ancestor of all present life. The evolution of the enzymes enabling this form of energy storage is more complex than previously thought and illustrates the need for explicit phylogenomic analysis in the study of even seemingly “simple” metabolic enzymes. Patterns of conservation in the evolution of the glycogen/starch branching and debranching enzymes hint at some as yet unknown mechanisms, as mutations disrupting these patterns lead to a variety of genetic diseases in humans and other mammals.
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spelling pubmed-42365202014-11-19 Phylogenomic analysis of glycogen branching and debranching enzymatic duo Zmasek, Christian M Godzik, Adam BMC Evol Biol Research Article BACKGROUND: Branched polymers of glucose are universally used for energy storage in cells, taking the form of glycogen in animals, fungi, Bacteria, and Archaea, and of amylopectin in plants. Some enzymes involved in glycogen and amylopectin metabolism are similarly conserved in all forms of life, but some, interestingly, are not. In this paper we focus on the phylogeny of glycogen branching and debranching enzymes, respectively involved in introducing and removing of the α(1–6) bonds in glucose polymers, bonds that provide the unique branching structure to glucose polymers. RESULTS: We performed a large-scale phylogenomic analysis of branching and debranching enzymes in over 400 completely sequenced genomes, including more than 200 from eukaryotes. We show that branching and debranching enzymes can be found in all kingdoms of life, including all major groups of eukaryotes, and thus were likely to have been present in the last universal common ancestor (LUCA) but have been lost in seemingly random fashion in numerous single-celled eukaryotes. We also show how animal branching and debranching enzymes evolved from their LUCA ancestors by acquiring additional domains. Furthermore, we show that enzymes commonly perceived as orthologous, such as human branching enzyme GBE1 and E. coli branching enzyme GlgB, are in fact related by a gene duplication and consequently paralogous. CONCLUSIONS: Despite being usually associated with animal liver glycogen and plant starch, energy storage in the form of branched glucose polymers is clearly an ancient process and has probably been present in the last universal common ancestor of all present life. The evolution of the enzymes enabling this form of energy storage is more complex than previously thought and illustrates the need for explicit phylogenomic analysis in the study of even seemingly “simple” metabolic enzymes. Patterns of conservation in the evolution of the glycogen/starch branching and debranching enzymes hint at some as yet unknown mechanisms, as mutations disrupting these patterns lead to a variety of genetic diseases in humans and other mammals. BioMed Central 2014-08-23 /pmc/articles/PMC4236520/ /pubmed/25148856 http://dx.doi.org/10.1186/s12862-014-0183-2 Text en Copyright © 2014 Zmasek and Godzik; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Zmasek, Christian M
Godzik, Adam
Phylogenomic analysis of glycogen branching and debranching enzymatic duo
title Phylogenomic analysis of glycogen branching and debranching enzymatic duo
title_full Phylogenomic analysis of glycogen branching and debranching enzymatic duo
title_fullStr Phylogenomic analysis of glycogen branching and debranching enzymatic duo
title_full_unstemmed Phylogenomic analysis of glycogen branching and debranching enzymatic duo
title_short Phylogenomic analysis of glycogen branching and debranching enzymatic duo
title_sort phylogenomic analysis of glycogen branching and debranching enzymatic duo
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4236520/
https://www.ncbi.nlm.nih.gov/pubmed/25148856
http://dx.doi.org/10.1186/s12862-014-0183-2
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