ROS Consumers or Producers? Interpreting Transcriptomic Data by AlphaFold Modeling Provides Insights into Class III Peroxidase Functions in Response to Biotic and Abiotic Stresses
Participating in both biotic and abiotic stress responses, plant-specific class III peroxidases (PERs) show promise as candidates for crop improvement. The multigenic PER family is known to take part in diverse functions, such as lignin formation and defense against pathogens. Traditionally linked t...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-05-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/9/8297 |
| _version_ | 1797602351669837824 |
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| author | James New Daniel Barsky Claudia Uhde-Stone |
| author_facet | James New Daniel Barsky Claudia Uhde-Stone |
| author_sort | James New |
| collection | DOAJ |
| description | Participating in both biotic and abiotic stress responses, plant-specific class III peroxidases (PERs) show promise as candidates for crop improvement. The multigenic PER family is known to take part in diverse functions, such as lignin formation and defense against pathogens. Traditionally linked to hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) consumption, PERs can also produce reactive oxygen species (ROS), essential in tissue development, pathogen defense and stress signaling. The amino acid sequences of both orthologues and paralogues of PERs are highly conserved, but discovering correlations between sequence differences and their functional diversity has proven difficult. By combining meta-analysis of transcriptomic data and sequence alignments, we discovered a correlation between three key amino acid positions and gene expression in response to biotic and abiotic stresses. Phylogenetic analysis revealed evolutionary pressure on these amino acids toward stress responsiveness. Using AlphaFold modeling, we found unique interdomain and protein–heme interactions involving those key amino acids in stress-induced PERs. Plausibly, these structural interactions may act as “gate keepers” by preventing larger substrates from accessing the heme and thereby shifting PER function from consumption to the production of ROS. |
| first_indexed | 2024-03-11T04:15:53Z |
| format | Article |
| id | doaj.art-20efc53e3b34421c85eaa96b7420a559 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T04:15:53Z |
| publishDate | 2023-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-20efc53e3b34421c85eaa96b7420a5592023-11-17T23:07:39ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-05-01249829710.3390/ijms24098297ROS Consumers or Producers? Interpreting Transcriptomic Data by AlphaFold Modeling Provides Insights into Class III Peroxidase Functions in Response to Biotic and Abiotic StressesJames New0Daniel Barsky1Claudia Uhde-Stone2Department of Biological Sciences, California State University, East Bay, Hayward, CA 94542, USADepartment of Physics, California State University, East Bay, Hayward, CA 94542, USADepartment of Biological Sciences, California State University, East Bay, Hayward, CA 94542, USAParticipating in both biotic and abiotic stress responses, plant-specific class III peroxidases (PERs) show promise as candidates for crop improvement. The multigenic PER family is known to take part in diverse functions, such as lignin formation and defense against pathogens. Traditionally linked to hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) consumption, PERs can also produce reactive oxygen species (ROS), essential in tissue development, pathogen defense and stress signaling. The amino acid sequences of both orthologues and paralogues of PERs are highly conserved, but discovering correlations between sequence differences and their functional diversity has proven difficult. By combining meta-analysis of transcriptomic data and sequence alignments, we discovered a correlation between three key amino acid positions and gene expression in response to biotic and abiotic stresses. Phylogenetic analysis revealed evolutionary pressure on these amino acids toward stress responsiveness. Using AlphaFold modeling, we found unique interdomain and protein–heme interactions involving those key amino acids in stress-induced PERs. Plausibly, these structural interactions may act as “gate keepers” by preventing larger substrates from accessing the heme and thereby shifting PER function from consumption to the production of ROS.https://www.mdpi.com/1422-0067/24/9/8297AlphaFoldArabidopsisclass III peroxidasesplant stress responsephosphate deficiencyROS signaling |
| spellingShingle | James New Daniel Barsky Claudia Uhde-Stone ROS Consumers or Producers? Interpreting Transcriptomic Data by AlphaFold Modeling Provides Insights into Class III Peroxidase Functions in Response to Biotic and Abiotic Stresses International Journal of Molecular Sciences AlphaFold Arabidopsis class III peroxidases plant stress response phosphate deficiency ROS signaling |
| title | ROS Consumers or Producers? Interpreting Transcriptomic Data by AlphaFold Modeling Provides Insights into Class III Peroxidase Functions in Response to Biotic and Abiotic Stresses |
| title_full | ROS Consumers or Producers? Interpreting Transcriptomic Data by AlphaFold Modeling Provides Insights into Class III Peroxidase Functions in Response to Biotic and Abiotic Stresses |
| title_fullStr | ROS Consumers or Producers? Interpreting Transcriptomic Data by AlphaFold Modeling Provides Insights into Class III Peroxidase Functions in Response to Biotic and Abiotic Stresses |
| title_full_unstemmed | ROS Consumers or Producers? Interpreting Transcriptomic Data by AlphaFold Modeling Provides Insights into Class III Peroxidase Functions in Response to Biotic and Abiotic Stresses |
| title_short | ROS Consumers or Producers? Interpreting Transcriptomic Data by AlphaFold Modeling Provides Insights into Class III Peroxidase Functions in Response to Biotic and Abiotic Stresses |
| title_sort | ros consumers or producers interpreting transcriptomic data by alphafold modeling provides insights into class iii peroxidase functions in response to biotic and abiotic stresses |
| topic | AlphaFold Arabidopsis class III peroxidases plant stress response phosphate deficiency ROS signaling |
| url | https://www.mdpi.com/1422-0067/24/9/8297 |
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