In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi
Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
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Academic Editors: Dietmar Schlosser, Paul Olusegun Bankole and Cheng Gao
J. Fungi 2022, 8(1), 67; https://doi.org/10.3390/jof8010067
Received: 9 November 2021
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Revised: 6 January 2022
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Accepted: 7 January 2022
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Published: 9 January 2022
(This article belongs to the Special Issue Fungal Enzymes 2021)
Early-diverging fungi (EDF) are ubiquitous and versatile. Their diversity is reflected in their genome sizes and complexity. For instance, multiple protein families have been reported to expand or disappear either in particular genomes or even whole lineages. The most commonly mentioned are CAZymes (carbohydrate-active enzymes), peptidases and transporters that serve multiple biological roles connected to, e.g., metabolism and nutrients intake. In order to study the link between ecology and its genomic underpinnings in a more comprehensive manner, we carried out a systematic in silico survey of protein family expansions and losses among EDF with diverse lifestyles. We found that 86 protein families are represented differently according to EDF ecological features (assessed by median count differences). Among these there are 19 families of proteases, 43 CAZymes and 24 transporters. Some of these protein families have been recognized before as serine and metallopeptidases, cellulases and other nutrition-related enzymes. Other clearly pronounced differences refer to cell wall remodelling and glycosylation. We hypothesize that these protein families altogether define the preliminary fungal adaptasome. However, our findings need experimental validation. Many of the protein families have never been characterized in fungi and are discussed in the light of fungal ecology for the first time.
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Keywords:
protein family; peptidases; cazymes; earl diverging fungi; cell wall; adaptasome
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MDPI and ACS Style
Orłowska, M.; Muszewska, A. In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi. J. Fungi 2022, 8, 67. https://doi.org/10.3390/jof8010067
AMA Style
Orłowska M, Muszewska A. In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi. Journal of Fungi. 2022; 8(1):67. https://doi.org/10.3390/jof8010067
Chicago/Turabian StyleOrłowska, Małgorzata, and Anna Muszewska. 2022. "In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi" Journal of Fungi 8, no. 1: 67. https://doi.org/10.3390/jof8010067
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