Integrative Transcriptomics Data Mining to Explore the Functions of <i>TDP1α</i> and <i>TDP1β</i> Genes in the <i>Arabidopsis thaliana</i> Model Plant
The tyrosyl-DNA phosphodiesterase 1 (TDP1) enzyme hydrolyzes the phosphodiester bond between a tyrosine residue and the 3′-phosphate of DNA in the DNA–topoisomerase I (TopI) complex, being involved in different DNA repair pathways. A small <i>TDP1</i> gene subfamily is present in plants,...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-04-01
|
| Series: | Genes |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-4425/14/4/884 |
| _version_ | 1797605303429103616 |
|---|---|
| author | Paola Pagano Andrea Pagano Stefano Paternolli Alma Balestrazzi Anca Macovei |
| author_facet | Paola Pagano Andrea Pagano Stefano Paternolli Alma Balestrazzi Anca Macovei |
| author_sort | Paola Pagano |
| collection | DOAJ |
| description | The tyrosyl-DNA phosphodiesterase 1 (TDP1) enzyme hydrolyzes the phosphodiester bond between a tyrosine residue and the 3′-phosphate of DNA in the DNA–topoisomerase I (TopI) complex, being involved in different DNA repair pathways. A small <i>TDP1</i> gene subfamily is present in plants, where <i>TDP1α</i> has been linked to genome stability maintenance, while <i>TDP1β</i> has unknown functions. This work aimed to comparatively investigate the function of the <i>TDP1</i> genes by taking advantage of the rich transcriptomics databases available for the <i>Arabidopsis thaliana</i> model plant. A data mining approach was carried out to collect information regarding gene expression in different tissues, genetic backgrounds, and stress conditions, using platforms where RNA-seq and microarray data are deposited. The gathered data allowed us to distinguish between common and divergent functions of the two genes. Namely, <i>TDP1β</i> seems to be involved in root development and associated with gibberellin and brassinosteroid phytohormones, whereas <i>TDP1α</i> is more responsive to light and abscisic acid. During stress conditions, both genes are highly responsive to biotic and abiotic treatments in a time- and stress-dependent manner. Data validation using gamma-ray treatments applied to <i>Arabidopsis</i> seedlings indicated the accumulation of DNA damage and extensive cell death associated with the observed changes in the <i>TDP1</i> genes expression profiles. |
| first_indexed | 2024-03-11T04:59:09Z |
| format | Article |
| id | doaj.art-850bf3e10d6e47f48dc51ddf2c04a0ed |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T04:59:09Z |
| publishDate | 2023-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-850bf3e10d6e47f48dc51ddf2c04a0ed2023-11-17T19:23:55ZengMDPI AGGenes2073-44252023-04-0114488410.3390/genes14040884Integrative Transcriptomics Data Mining to Explore the Functions of <i>TDP1α</i> and <i>TDP1β</i> Genes in the <i>Arabidopsis thaliana</i> Model PlantPaola Pagano0Andrea Pagano1Stefano Paternolli2Alma Balestrazzi3Anca Macovei4Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, ItalyDepartment of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, ItalyDepartment of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, ItalyDepartment of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, ItalyDepartment of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, ItalyThe tyrosyl-DNA phosphodiesterase 1 (TDP1) enzyme hydrolyzes the phosphodiester bond between a tyrosine residue and the 3′-phosphate of DNA in the DNA–topoisomerase I (TopI) complex, being involved in different DNA repair pathways. A small <i>TDP1</i> gene subfamily is present in plants, where <i>TDP1α</i> has been linked to genome stability maintenance, while <i>TDP1β</i> has unknown functions. This work aimed to comparatively investigate the function of the <i>TDP1</i> genes by taking advantage of the rich transcriptomics databases available for the <i>Arabidopsis thaliana</i> model plant. A data mining approach was carried out to collect information regarding gene expression in different tissues, genetic backgrounds, and stress conditions, using platforms where RNA-seq and microarray data are deposited. The gathered data allowed us to distinguish between common and divergent functions of the two genes. Namely, <i>TDP1β</i> seems to be involved in root development and associated with gibberellin and brassinosteroid phytohormones, whereas <i>TDP1α</i> is more responsive to light and abscisic acid. During stress conditions, both genes are highly responsive to biotic and abiotic treatments in a time- and stress-dependent manner. Data validation using gamma-ray treatments applied to <i>Arabidopsis</i> seedlings indicated the accumulation of DNA damage and extensive cell death associated with the observed changes in the <i>TDP1</i> genes expression profiles.https://www.mdpi.com/2073-4425/14/4/884<i>Arabidopsis thaliana</i>DNA damageDNA repairgene expressiontyrosyl-DNA phosphodiesterase 1stress response |
| spellingShingle | Paola Pagano Andrea Pagano Stefano Paternolli Alma Balestrazzi Anca Macovei Integrative Transcriptomics Data Mining to Explore the Functions of <i>TDP1α</i> and <i>TDP1β</i> Genes in the <i>Arabidopsis thaliana</i> Model Plant Genes <i>Arabidopsis thaliana</i> DNA damage DNA repair gene expression tyrosyl-DNA phosphodiesterase 1 stress response |
| title | Integrative Transcriptomics Data Mining to Explore the Functions of <i>TDP1α</i> and <i>TDP1β</i> Genes in the <i>Arabidopsis thaliana</i> Model Plant |
| title_full | Integrative Transcriptomics Data Mining to Explore the Functions of <i>TDP1α</i> and <i>TDP1β</i> Genes in the <i>Arabidopsis thaliana</i> Model Plant |
| title_fullStr | Integrative Transcriptomics Data Mining to Explore the Functions of <i>TDP1α</i> and <i>TDP1β</i> Genes in the <i>Arabidopsis thaliana</i> Model Plant |
| title_full_unstemmed | Integrative Transcriptomics Data Mining to Explore the Functions of <i>TDP1α</i> and <i>TDP1β</i> Genes in the <i>Arabidopsis thaliana</i> Model Plant |
| title_short | Integrative Transcriptomics Data Mining to Explore the Functions of <i>TDP1α</i> and <i>TDP1β</i> Genes in the <i>Arabidopsis thaliana</i> Model Plant |
| title_sort | integrative transcriptomics data mining to explore the functions of i tdp1α i and i tdp1β i genes in the i arabidopsis thaliana i model plant |
| topic | <i>Arabidopsis thaliana</i> DNA damage DNA repair gene expression tyrosyl-DNA phosphodiesterase 1 stress response |
| url | https://www.mdpi.com/2073-4425/14/4/884 |
| work_keys_str_mv | AT paolapagano integrativetranscriptomicsdataminingtoexplorethefunctionsofitdp1aianditdp1bigenesintheiarabidopsisthalianaimodelplant AT andreapagano integrativetranscriptomicsdataminingtoexplorethefunctionsofitdp1aianditdp1bigenesintheiarabidopsisthalianaimodelplant AT stefanopaternolli integrativetranscriptomicsdataminingtoexplorethefunctionsofitdp1aianditdp1bigenesintheiarabidopsisthalianaimodelplant AT almabalestrazzi integrativetranscriptomicsdataminingtoexplorethefunctionsofitdp1aianditdp1bigenesintheiarabidopsisthalianaimodelplant AT ancamacovei integrativetranscriptomicsdataminingtoexplorethefunctionsofitdp1aianditdp1bigenesintheiarabidopsisthalianaimodelplant |