ROS Consumers or Producers? Interpreting Transcriptomic Data by AlphaFold Modeling Provides Insights into Class III Peroxidase Functions in Response to Biotic and Abiotic Stresses

New, James S.; Barsky, Daniel; Uhde‐Stone, Claudia

doi:10.3390/ijms24098297

Cited by 2 publications

(1 citation statement)

References 49 publications

(83 reference statements)

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“…Nonetheless, recent studies have pointed out that sets of amino acid residues, mostly at or close to the enzyme active site, have been positively selected for and thus might be useful in function prediction (Ren et al 2014; Kupriyanova et al 2015; New et al 2023). The present study also showed phylogenetic clustering of PRX genes from different taxa, and this could be used to predict functional similarity among the genes.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of the class III peroxidase gene family inPhyscomitrium patensand a search for clues to ancient class III peroxidase functions

Aparato,

Rabbi,

Madarash

et al. 2024

Preprint

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Plant class III peroxidases (PRX) 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 ofPRXgenes. The genome of the model mossPhyscomitrium patensharbors a relatively small number (49) ofPRXgenes. Conserved architecture of four exons and three '001' introns, found in some algalPRXgenes and in thePpPRXfamily, suggests that this architecture predated divergence of the green algal and land plant lineages. ThePpPRXfamily 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,P. patensmay be useful for functional characterization of land plant PRXs. Several PpPRXs were proposed for further study, includingPpPRX34andPpPRX39in the ancient land plant-wide clade.

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Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of the class III peroxidase gene family inPhyscomitrium patensand a search for clues to ancient class III peroxidase functions

Aparato,

Rabbi,

Madarash

et al. 2024

Preprint

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Peroxidase gene TaPrx109‐B1 enhances wheat tolerance to water deficit via modulating stomatal density

Jiao,

Lv,

Teng

et al. 2024

Plant Cell & Environment

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Increasing the tolerance of crops to water deficit is crucial for the improvement of crop production in water‐restricted regions. Here, a wheat peroxidase gene (TaPrx109‐B1) belonging to the class III peroxidase gene family was identified and its function in water deficit tolerance was revealed. We demonstrated that overexpression of TaPrx109‐B1 reduced leaf H2O2 level and stomatal density, increased leaf relative water content, water use efficiency, and tolerance to water deficit. The expression of TaEPF1 and TaEPF2, two key negative regulators of stomatal development, were significantly upregulated in TaPrx109‐B1 overexpression lines. Furthermore, exogenous H2O2 downregulated the expression of TaEPF1 and TaEPF2 and increased stomatal density, while exogenous application of diphenyleneiodonium chloride, a potent NADPH oxidase inhibitor that repressed the synthesis of H2O2, upregulated the expression of TaEPF1 and TaEPF2, decreased stomatal density, and enhanced wheat tolerance to water deficit. These findings suggest that TaPrx109‐B1 influences leaf stomatal density by modulation of H2O2 level, and consequently affecting the expression of TaEPF1 and TaEPF2. The results of the field trial showed that overexpressing TaPrx109‐B1 increased grain number per spike, which reduced the yield loss caused by water deficiency. Therefore, TaPrx109‐B1 has great potential in breeding wheat varieties with improved water deficit tolerance.

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ROS Consumers or Producers? Interpreting Transcriptomic Data by AlphaFold Modeling Provides Insights into Class III Peroxidase Functions in Response to Biotic and Abiotic Stresses

Cited by 2 publications

References 49 publications

Genome-wide analysis of the class III peroxidase gene family inPhyscomitrium patensand a search for clues to ancient class III peroxidase functions

Genome-wide analysis of the class III peroxidase gene family inPhyscomitrium patensand a search for clues to ancient class III peroxidase functions

Peroxidase gene TaPrx109‐B1 enhances wheat tolerance to water deficit via modulating stomatal density

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