Identification of Heme Oxygenase-1 as a Putative DNA-Binding Protein
Heme oxygenase-1 (HO-1) is a rate-limiting enzyme in degrading heme into biliverdin and iron. HO-1 can also enter the nucleus and regulate gene transcription independent of its enzymatic activity. Whether HO-1 can alter gene expression through direct binding to target DNA remains unclear. Here, we p...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-10-01
|
| Series: | Antioxidants |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-3921/11/11/2135 |
| _version_ | 1797469257416572928 |
|---|---|
| author | Alejandro Scaffa George A. Tollefson Hongwei Yao Salu Rizal Joselynn Wallace Nathalie Oulhen Jennifer F. Carr Katy Hegarty Alper Uzun Phyllis A. Dennery |
| author_facet | Alejandro Scaffa George A. Tollefson Hongwei Yao Salu Rizal Joselynn Wallace Nathalie Oulhen Jennifer F. Carr Katy Hegarty Alper Uzun Phyllis A. Dennery |
| author_sort | Alejandro Scaffa |
| collection | DOAJ |
| description | Heme oxygenase-1 (HO-1) is a rate-limiting enzyme in degrading heme into biliverdin and iron. HO-1 can also enter the nucleus and regulate gene transcription independent of its enzymatic activity. Whether HO-1 can alter gene expression through direct binding to target DNA remains unclear. Here, we performed HO-1 CHIP-seq and then employed 3D structural modeling to reveal putative HO-1 DNA binding domains. We identified three probable DNA binding domains on HO-1. Using the Proteinarium, we identified several genes as the most highly connected nodes in the interactome among the HO-1 gene binding targets. We further demonstrated that HO-1 modulates the expression of these key genes using <i>Hmox1</i> deficient cells. Finally, mutation of four conserved amino acids (E215, I211, E201, and Q27) within HO-1 DNA binding domain 1 significantly increased expression of Gtpbp3 and Eif1 genes that were identified within the top 10 binding hits normalized by gene length predicted to bind this domain. Based on these data, we conclude that HO-1 protein is a putative DNA binding protein, and regulates targeted gene expression. This provides the foundation for developing specific inhibitors or activators targeting HO-1 DNA binding domains to modulate targeted gene expression and corresponding cellular function. |
| first_indexed | 2024-03-09T19:18:49Z |
| format | Article |
| id | doaj.art-2048e9a14bad48f2bf5f2c6170590d39 |
| institution | Directory Open Access Journal |
| issn | 2076-3921 |
| language | English |
| last_indexed | 2024-03-09T19:18:49Z |
| publishDate | 2022-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Antioxidants |
| spelling | doaj.art-2048e9a14bad48f2bf5f2c6170590d392023-11-24T03:29:47ZengMDPI AGAntioxidants2076-39212022-10-011111213510.3390/antiox11112135Identification of Heme Oxygenase-1 as a Putative DNA-Binding ProteinAlejandro Scaffa0George A. Tollefson1Hongwei Yao2Salu Rizal3Joselynn Wallace4Nathalie Oulhen5Jennifer F. Carr6Katy Hegarty7Alper Uzun8Phyllis A. Dennery9Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02912, USADepartment of Pathology and Laboratory Medicine, Rhode Island Hospital, Providence, RI 02903, USADepartment of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02912, USADepartment of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02912, USACenter for Computational Biology of Human Disease, and Center for Computation and Visualization, Brown University, Providence, RI 02906, USADepartment of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02912, USADepartment of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02912, USADepartment of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02912, USADepartment of Pediatrics, Warren Alpert Medical School of Brown University, Providence, RI 02903, USADepartment of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02912, USAHeme oxygenase-1 (HO-1) is a rate-limiting enzyme in degrading heme into biliverdin and iron. HO-1 can also enter the nucleus and regulate gene transcription independent of its enzymatic activity. Whether HO-1 can alter gene expression through direct binding to target DNA remains unclear. Here, we performed HO-1 CHIP-seq and then employed 3D structural modeling to reveal putative HO-1 DNA binding domains. We identified three probable DNA binding domains on HO-1. Using the Proteinarium, we identified several genes as the most highly connected nodes in the interactome among the HO-1 gene binding targets. We further demonstrated that HO-1 modulates the expression of these key genes using <i>Hmox1</i> deficient cells. Finally, mutation of four conserved amino acids (E215, I211, E201, and Q27) within HO-1 DNA binding domain 1 significantly increased expression of Gtpbp3 and Eif1 genes that were identified within the top 10 binding hits normalized by gene length predicted to bind this domain. Based on these data, we conclude that HO-1 protein is a putative DNA binding protein, and regulates targeted gene expression. This provides the foundation for developing specific inhibitors or activators targeting HO-1 DNA binding domains to modulate targeted gene expression and corresponding cellular function.https://www.mdpi.com/2076-3921/11/11/2135heme oxygenase-1DNA bindingproteinarium3D structural modeling |
| spellingShingle | Alejandro Scaffa George A. Tollefson Hongwei Yao Salu Rizal Joselynn Wallace Nathalie Oulhen Jennifer F. Carr Katy Hegarty Alper Uzun Phyllis A. Dennery Identification of Heme Oxygenase-1 as a Putative DNA-Binding Protein Antioxidants heme oxygenase-1 DNA binding proteinarium 3D structural modeling |
| title | Identification of Heme Oxygenase-1 as a Putative DNA-Binding Protein |
| title_full | Identification of Heme Oxygenase-1 as a Putative DNA-Binding Protein |
| title_fullStr | Identification of Heme Oxygenase-1 as a Putative DNA-Binding Protein |
| title_full_unstemmed | Identification of Heme Oxygenase-1 as a Putative DNA-Binding Protein |
| title_short | Identification of Heme Oxygenase-1 as a Putative DNA-Binding Protein |
| title_sort | identification of heme oxygenase 1 as a putative dna binding protein |
| topic | heme oxygenase-1 DNA binding proteinarium 3D structural modeling |
| url | https://www.mdpi.com/2076-3921/11/11/2135 |
| work_keys_str_mv | AT alejandroscaffa identificationofhemeoxygenase1asaputativednabindingprotein AT georgeatollefson identificationofhemeoxygenase1asaputativednabindingprotein AT hongweiyao identificationofhemeoxygenase1asaputativednabindingprotein AT salurizal identificationofhemeoxygenase1asaputativednabindingprotein AT joselynnwallace identificationofhemeoxygenase1asaputativednabindingprotein AT nathalieoulhen identificationofhemeoxygenase1asaputativednabindingprotein AT jenniferfcarr identificationofhemeoxygenase1asaputativednabindingprotein AT katyhegarty identificationofhemeoxygenase1asaputativednabindingprotein AT alperuzun identificationofhemeoxygenase1asaputativednabindingprotein AT phyllisadennery identificationofhemeoxygenase1asaputativednabindingprotein |