In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi
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...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-01-01
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| Series: | Journal of Fungi |
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| Online Access: | https://www.mdpi.com/2309-608X/8/1/67 |
| _version_ | 1797492858974896128 |
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| author | Małgorzata Orłowska Anna Muszewska |
| author_facet | Małgorzata Orłowska Anna Muszewska |
| author_sort | Małgorzata Orłowska |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T01:10:44Z |
| format | Article |
| id | doaj.art-d73a78d303154bf7b882f8a6cb3cac6e |
| institution | Directory Open Access Journal |
| issn | 2309-608X |
| language | English |
| last_indexed | 2024-03-10T01:10:44Z |
| publishDate | 2022-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Fungi |
| spelling | doaj.art-d73a78d303154bf7b882f8a6cb3cac6e2023-11-23T14:18:30ZengMDPI AGJournal of Fungi2309-608X2022-01-01816710.3390/jof8010067In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging FungiMałgorzata Orłowska0Anna Muszewska1Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, PolandInstitute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, PolandEarly-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.https://www.mdpi.com/2309-608X/8/1/67protein familypeptidasescazymesearl diverging fungicell walladaptasome |
| spellingShingle | Małgorzata Orłowska Anna Muszewska In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi Journal of Fungi protein family peptidases cazymes earl diverging fungi cell wall adaptasome |
| title | In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi |
| title_full | In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi |
| title_fullStr | In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi |
| title_full_unstemmed | In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi |
| title_short | In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi |
| title_sort | in silico predictions of ecological plasticity mediated by protein family expansions in early diverging fungi |
| topic | protein family peptidases cazymes earl diverging fungi cell wall adaptasome |
| url | https://www.mdpi.com/2309-608X/8/1/67 |
| work_keys_str_mv | AT małgorzataorłowska insilicopredictionsofecologicalplasticitymediatedbyproteinfamilyexpansionsinearlydivergingfungi AT annamuszewska insilicopredictionsofecologicalplasticitymediatedbyproteinfamilyexpansionsinearlydivergingfungi |