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New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences

Fungal genome sequencing data represent an enormous pool of information for enzyme discovery. Here, we report a new approach to identify and quantitatively compare biomass-degrading capacity and diversity of fungal genomes via integrated function-family annotation of carbohydrate-active enzymes (CAZ...

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Autores principales: Lange, Lene, Barrett, Kristian, Meyer, Anne S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8000046/
https://www.ncbi.nlm.nih.gov/pubmed/33799907
http://dx.doi.org/10.3390/jof7030207
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author Lange, Lene
Barrett, Kristian
Meyer, Anne S.
author_facet Lange, Lene
Barrett, Kristian
Meyer, Anne S.
author_sort Lange, Lene
collection PubMed
description Fungal genome sequencing data represent an enormous pool of information for enzyme discovery. Here, we report a new approach to identify and quantitatively compare biomass-degrading capacity and diversity of fungal genomes via integrated function-family annotation of carbohydrate-active enzymes (CAZymes) encoded by the genomes. Based on analyses of 1932 fungal genomes the most potent hotspots of fungal biomass processing CAZymes are identified and ranked according to substrate degradation capacity. The analysis is achieved by a new bioinformatics approach, Conserved Unique Peptide Patterns (CUPP), providing for CAZyme-family annotation and robust prediction of molecular function followed by conversion of the CUPP output to lists of integrated “Function;Family” (e.g., EC 3.2.1.4;GH5) enzyme observations. An EC-function found in several protein families counts as different observations. Summing up such observations allows for ranking of all analyzed genome sequenced fungal species according to richness in CAZyme function diversity and degrading capacity. Identifying fungal CAZyme hotspots provides for identification of fungal species richest in cellulolytic, xylanolytic, pectinolytic, and lignin modifying enzymes. The fungal enzyme hotspots are found in fungi having very different lifestyle, ecology, physiology and substrate/host affinity. Surprisingly, most CAZyme hotspots are found in enzymatically understudied and unexploited species. In contrast, the most well-known fungal enzyme producers, from where many industrially exploited enzymes are derived, are ranking unexpectedly low. The results contribute to elucidating the evolution of fungal substrate-digestive CAZyme profiles, ecophysiology, and habitat adaptations, and expand the knowledge base for novel and improved biomass resource utilization.
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spelling pubmed-80000462021-03-28 New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences Lange, Lene Barrett, Kristian Meyer, Anne S. J Fungi (Basel) Article Fungal genome sequencing data represent an enormous pool of information for enzyme discovery. Here, we report a new approach to identify and quantitatively compare biomass-degrading capacity and diversity of fungal genomes via integrated function-family annotation of carbohydrate-active enzymes (CAZymes) encoded by the genomes. Based on analyses of 1932 fungal genomes the most potent hotspots of fungal biomass processing CAZymes are identified and ranked according to substrate degradation capacity. The analysis is achieved by a new bioinformatics approach, Conserved Unique Peptide Patterns (CUPP), providing for CAZyme-family annotation and robust prediction of molecular function followed by conversion of the CUPP output to lists of integrated “Function;Family” (e.g., EC 3.2.1.4;GH5) enzyme observations. An EC-function found in several protein families counts as different observations. Summing up such observations allows for ranking of all analyzed genome sequenced fungal species according to richness in CAZyme function diversity and degrading capacity. Identifying fungal CAZyme hotspots provides for identification of fungal species richest in cellulolytic, xylanolytic, pectinolytic, and lignin modifying enzymes. The fungal enzyme hotspots are found in fungi having very different lifestyle, ecology, physiology and substrate/host affinity. Surprisingly, most CAZyme hotspots are found in enzymatically understudied and unexploited species. In contrast, the most well-known fungal enzyme producers, from where many industrially exploited enzymes are derived, are ranking unexpectedly low. The results contribute to elucidating the evolution of fungal substrate-digestive CAZyme profiles, ecophysiology, and habitat adaptations, and expand the knowledge base for novel and improved biomass resource utilization. MDPI 2021-03-11 /pmc/articles/PMC8000046/ /pubmed/33799907 http://dx.doi.org/10.3390/jof7030207 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ).
spellingShingle Article
Lange, Lene
Barrett, Kristian
Meyer, Anne S.
New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences
title New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences
title_full New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences
title_fullStr New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences
title_full_unstemmed New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences
title_short New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences
title_sort new method for identifying fungal kingdom enzyme hotspots from genome sequences
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8000046/
https://www.ncbi.nlm.nih.gov/pubmed/33799907
http://dx.doi.org/10.3390/jof7030207
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