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The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases
BACKGROUND: The glucose–methanol–choline (GMC) superfamily is a large and functionally diverse family of oxidoreductases that share a common structural fold. Fungal members of this superfamily that are characterised and relevant for lignocellulose degradation include aryl-alcohol oxidoreductase, alc...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6509819/ https://www.ncbi.nlm.nih.gov/pubmed/31168323 http://dx.doi.org/10.1186/s13068-019-1457-0 |
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author | Sützl, Leander Foley, Gabriel Gillam, Elizabeth M J Bodén, Mikael Haltrich, Dietmar |
author_facet | Sützl, Leander Foley, Gabriel Gillam, Elizabeth M J Bodén, Mikael Haltrich, Dietmar |
author_sort | Sützl, Leander |
collection | PubMed |
description | BACKGROUND: The glucose–methanol–choline (GMC) superfamily is a large and functionally diverse family of oxidoreductases that share a common structural fold. Fungal members of this superfamily that are characterised and relevant for lignocellulose degradation include aryl-alcohol oxidoreductase, alcohol oxidase, cellobiose dehydrogenase, glucose oxidase, glucose dehydrogenase, pyranose dehydrogenase, and pyranose oxidase, which together form family AA3 of the auxiliary activities in the CAZy database of carbohydrate-active enzymes. Overall, little is known about the extant sequence space of these GMC oxidoreductases and their phylogenetic relations. Although some individual forms are well characterised, it is still unclear how they compare in respect of the complete enzyme class and, therefore, also how generalizable are their characteristics. RESULTS: To improve the understanding of the GMC superfamily as a whole, we used sequence similarity networks to cluster large numbers of fungal GMC sequences and annotate them according to functionality. Subsequently, different members of the GMC superfamily were analysed in detail with regard to their sequences and phylogeny. This allowed us to define the currently characterised sequence space and show that complete clades of some enzymes have not been studied in any detail to date. Finally, we interpret our results from an evolutionary perspective, where we could show, for example, that pyranose dehydrogenase evolved from aryl-alcohol oxidoreductase after a change in substrate specificity and that the cytochrome domain of cellobiose dehydrogenase was regularly lost during evolution. CONCLUSIONS: This study offers new insights into the sequence variation and phylogenetic relationships of fungal GMC/AA3 sequences. Certain clades of these GMC enzymes identified in our phylogenetic analyses are completely uncharacterised to date, and might include enzyme activities of varying specificities and/or activities that are hitherto unstudied. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13068-019-1457-0) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6509819 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-65098192019-06-05 The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases Sützl, Leander Foley, Gabriel Gillam, Elizabeth M J Bodén, Mikael Haltrich, Dietmar Biotechnol Biofuels Research BACKGROUND: The glucose–methanol–choline (GMC) superfamily is a large and functionally diverse family of oxidoreductases that share a common structural fold. Fungal members of this superfamily that are characterised and relevant for lignocellulose degradation include aryl-alcohol oxidoreductase, alcohol oxidase, cellobiose dehydrogenase, glucose oxidase, glucose dehydrogenase, pyranose dehydrogenase, and pyranose oxidase, which together form family AA3 of the auxiliary activities in the CAZy database of carbohydrate-active enzymes. Overall, little is known about the extant sequence space of these GMC oxidoreductases and their phylogenetic relations. Although some individual forms are well characterised, it is still unclear how they compare in respect of the complete enzyme class and, therefore, also how generalizable are their characteristics. RESULTS: To improve the understanding of the GMC superfamily as a whole, we used sequence similarity networks to cluster large numbers of fungal GMC sequences and annotate them according to functionality. Subsequently, different members of the GMC superfamily were analysed in detail with regard to their sequences and phylogeny. This allowed us to define the currently characterised sequence space and show that complete clades of some enzymes have not been studied in any detail to date. Finally, we interpret our results from an evolutionary perspective, where we could show, for example, that pyranose dehydrogenase evolved from aryl-alcohol oxidoreductase after a change in substrate specificity and that the cytochrome domain of cellobiose dehydrogenase was regularly lost during evolution. CONCLUSIONS: This study offers new insights into the sequence variation and phylogenetic relationships of fungal GMC/AA3 sequences. Certain clades of these GMC enzymes identified in our phylogenetic analyses are completely uncharacterised to date, and might include enzyme activities of varying specificities and/or activities that are hitherto unstudied. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13068-019-1457-0) contains supplementary material, which is available to authorized users. BioMed Central 2019-05-10 /pmc/articles/PMC6509819/ /pubmed/31168323 http://dx.doi.org/10.1186/s13068-019-1457-0 Text en © The Author(s) 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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 Sützl, Leander Foley, Gabriel Gillam, Elizabeth M J Bodén, Mikael Haltrich, Dietmar The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases |
title | The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases |
title_full | The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases |
title_fullStr | The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases |
title_full_unstemmed | The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases |
title_short | The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases |
title_sort | gmc superfamily of oxidoreductases revisited: analysis and evolution of fungal gmc oxidoreductases |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6509819/ https://www.ncbi.nlm.nih.gov/pubmed/31168323 http://dx.doi.org/10.1186/s13068-019-1457-0 |
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