Genome-Wide Analysis of the Class III Peroxidase Gene Family in <i>Physcomitrium patens</i> and a Search for Clues to Ancient Class III Peroxidase Functions
Plant class III peroxidases (PRXs) catalyze generation of reactive oxygen species and oxidation of various compounds including lignin precursors. PRXs function in cell wall metabolism, defense, and stress responses. However, gene redundancy and catalytic versatility have impeded detailed functional...
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2024-11-01
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| author | Vincent P. M. Aparato Fazle Rabbi Taylor Madarash Wyllie A. Brisbourne Elizabeth I. Barker Dae-Yeon Suh |
| author_facet | Vincent P. M. Aparato Fazle Rabbi Taylor Madarash Wyllie A. Brisbourne Elizabeth I. Barker Dae-Yeon Suh |
| author_sort | Vincent P. M. Aparato |
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| description | Plant class III peroxidases (PRXs) catalyze generation of reactive oxygen species and oxidation of various compounds including lignin precursors. PRXs function in cell wall metabolism, defense, and stress responses. However, gene redundancy and catalytic versatility have impeded detailed functional characterization of <i>PRX</i> genes. The genome of the model moss <i>Physcomitrium patens</i> harbors a relatively small number (49) of <i>PRX</i> genes. Conserved architecture of four exons and three ‘001’ introns, found in some algal <i>PRX</i> genes and in the <i>PpPRX</i> family, suggests that this architecture predated divergence of the green algal and land plant lineages. The <i>PpPRX</i> family expanded mainly through whole-genome duplications. All duplicated pairs but one were under purifying selection and generally exhibited similar expression profiles. An expanded phylogenetic tree revealed a conserved land plant-wide clade that contained PRXs implicated in stress responses in non-lignifying cells, providing a clue to ancient functions of land plant PRXs. Functional clustering was not observed, suggesting convergent evolution of specific PRX functions (e.g., lignification) in different plant lineages. With its small complement of PRXs, <i>P. patens</i> may be useful for functional characterization of land plant PRXs. Several PpPRXs were proposed for further study, including <i>PpPRX34</i> and <i>PpPRX39</i> in the ancient land plant-wide clade. |
| format | Article |
| id | doaj-art-50da625a8c494a938d6b2951d19c9bf0 |
| institution | Kabale University |
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| language | English |
| publishDate | 2024-11-01 |
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| series | International Journal of Plant Biology |
| spelling | doaj-art-50da625a8c494a938d6b2951d19c9bf02024-12-27T14:30:19ZengMDPI AGInternational Journal of Plant Biology2037-01642024-11-011541141116110.3390/ijpb15040079Genome-Wide Analysis of the Class III Peroxidase Gene Family in <i>Physcomitrium patens</i> and a Search for Clues to Ancient Class III Peroxidase FunctionsVincent P. M. Aparato0Fazle Rabbi1Taylor Madarash2Wyllie A. Brisbourne3Elizabeth I. Barker4Dae-Yeon Suh5Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, CanadaDepartment of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, CanadaDepartment of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, CanadaDepartment of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, CanadaDepartment of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, CanadaDepartment of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, CanadaPlant class III peroxidases (PRXs) catalyze generation of reactive oxygen species and oxidation of various compounds including lignin precursors. PRXs function in cell wall metabolism, defense, and stress responses. However, gene redundancy and catalytic versatility have impeded detailed functional characterization of <i>PRX</i> genes. The genome of the model moss <i>Physcomitrium patens</i> harbors a relatively small number (49) of <i>PRX</i> genes. Conserved architecture of four exons and three ‘001’ introns, found in some algal <i>PRX</i> genes and in the <i>PpPRX</i> family, suggests that this architecture predated divergence of the green algal and land plant lineages. The <i>PpPRX</i> family expanded mainly through whole-genome duplications. All duplicated pairs but one were under purifying selection and generally exhibited similar expression profiles. An expanded phylogenetic tree revealed a conserved land plant-wide clade that contained PRXs implicated in stress responses in non-lignifying cells, providing a clue to ancient functions of land plant PRXs. Functional clustering was not observed, suggesting convergent evolution of specific PRX functions (e.g., lignification) in different plant lineages. With its small complement of PRXs, <i>P. patens</i> may be useful for functional characterization of land plant PRXs. Several PpPRXs were proposed for further study, including <i>PpPRX34</i> and <i>PpPRX39</i> in the ancient land plant-wide clade.https://www.mdpi.com/2037-0164/15/4/79class III peroxidases<i>Physcomitrium patens</i>multigene familygene duplicationexpression profileancient enzyme functions |
| spellingShingle | Vincent P. M. Aparato Fazle Rabbi Taylor Madarash Wyllie A. Brisbourne Elizabeth I. Barker Dae-Yeon Suh Genome-Wide Analysis of the Class III Peroxidase Gene Family in <i>Physcomitrium patens</i> and a Search for Clues to Ancient Class III Peroxidase Functions International Journal of Plant Biology class III peroxidases <i>Physcomitrium patens</i> multigene family gene duplication expression profile ancient enzyme functions |
| title | Genome-Wide Analysis of the Class III Peroxidase Gene Family in <i>Physcomitrium patens</i> and a Search for Clues to Ancient Class III Peroxidase Functions |
| title_full | Genome-Wide Analysis of the Class III Peroxidase Gene Family in <i>Physcomitrium patens</i> and a Search for Clues to Ancient Class III Peroxidase Functions |
| title_fullStr | Genome-Wide Analysis of the Class III Peroxidase Gene Family in <i>Physcomitrium patens</i> and a Search for Clues to Ancient Class III Peroxidase Functions |
| title_full_unstemmed | Genome-Wide Analysis of the Class III Peroxidase Gene Family in <i>Physcomitrium patens</i> and a Search for Clues to Ancient Class III Peroxidase Functions |
| title_short | Genome-Wide Analysis of the Class III Peroxidase Gene Family in <i>Physcomitrium patens</i> and a Search for Clues to Ancient Class III Peroxidase Functions |
| title_sort | genome wide analysis of the class iii peroxidase gene family in i physcomitrium patens i and a search for clues to ancient class iii peroxidase functions |
| topic | class III peroxidases <i>Physcomitrium patens</i> multigene family gene duplication expression profile ancient enzyme functions |
| url | https://www.mdpi.com/2037-0164/15/4/79 |
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