45S rDNA Diversity <i>In Natura</i> as One Step towards Ribosomal Heterogeneity in <i>Arabidopsis thaliana</i>
The keystone of ribosome biogenesis is the transcription of 45S rDNA. The <i>Arabidopsis thaliana</i> genome contains hundreds of 45S rDNA units; however, they are not all transcribed. Notably, 45S rDNA units contain insertions/deletions revealing the existence of heterogeneous rRNA gene...
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MDPI AG
2023-07-01
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| Online Access: | https://www.mdpi.com/2223-7747/12/14/2722 |
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| author | Valérie Delorme-Hinoux Assane Mbodj Sophie Brando Anne De Bures Christel Llauro Fabrice Covato Joseph Garrigue Claude Guisset Jacques Borrut Marie Mirouze Jean-Philippe Reichheld Julio Sáez-Vásquez |
| author_facet | Valérie Delorme-Hinoux Assane Mbodj Sophie Brando Anne De Bures Christel Llauro Fabrice Covato Joseph Garrigue Claude Guisset Jacques Borrut Marie Mirouze Jean-Philippe Reichheld Julio Sáez-Vásquez |
| author_sort | Valérie Delorme-Hinoux |
| collection | DOAJ |
| description | The keystone of ribosome biogenesis is the transcription of 45S rDNA. The <i>Arabidopsis thaliana</i> genome contains hundreds of 45S rDNA units; however, they are not all transcribed. Notably, 45S rDNA units contain insertions/deletions revealing the existence of heterogeneous rRNA genes and, likely, heterogeneous ribosomes for rRNAs. In order to obtain an overall picture of 45S rDNA diversity sustaining the synthesis of rRNAs and, subsequently, of ribosomes <i>in natura</i>, we took advantage of 320 new occurrences of <i>Arabidopsis thaliana</i> as a metapopulation named At66, sampled from 0 to 1900 m of altitude in the eastern Pyrenees in France. We found that the 45S rDNA copy number is very dynamic <i>in natura</i> and identified new genotypes for both 5′ and 3′ External Transcribed Spacers (ETS). Interestingly, the highest 5′ETS genotype diversity is found in altitude while the highest 3′ETS genotype diversity is found at sea level. Structural analysis of 45S rDNA also shows conservation <i>in natura</i> of specific 5′ETS and 3′ETS sequences/features required to control rDNA expression and the processing of rRNAs. In conclusion, At66 is a worthwhile natural laboratory, and unraveled 45S rDNA diversity represents an interesting starting material to select subsets for rDNA transcription and alter the rRNA composition of ribosomes both intra- and inter-site. |
| first_indexed | 2024-03-11T00:43:26Z |
| format | Article |
| id | doaj.art-e48831955f2d48a99b3e999cac4ae272 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-11T00:43:26Z |
| publishDate | 2023-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-e48831955f2d48a99b3e999cac4ae2722023-11-18T21:01:10ZengMDPI AGPlants2223-77472023-07-011214272210.3390/plants1214272245S rDNA Diversity <i>In Natura</i> as One Step towards Ribosomal Heterogeneity in <i>Arabidopsis thaliana</i>Valérie Delorme-Hinoux0Assane Mbodj1Sophie Brando2Anne De Bures3Christel Llauro4Fabrice Covato5Joseph Garrigue6Claude Guisset7Jacques Borrut8Marie Mirouze9Jean-Philippe Reichheld10Julio Sáez-Vásquez11Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, FranceUniversité de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, FranceUniversité de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, FranceUniversité de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, FranceUniversité de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, FranceFRNC, Fédération des Réserves Naturelles Catalanes, 66500 Prades, FranceFRNC, Fédération des Réserves Naturelles Catalanes, 66500 Prades, FranceAssociation Charles Flahault, 66350 Toulouges, FranceAssociation Charles Flahault, 66350 Toulouges, FranceUniversité de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, FranceUniversité de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, FranceUniversité de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, FranceThe keystone of ribosome biogenesis is the transcription of 45S rDNA. The <i>Arabidopsis thaliana</i> genome contains hundreds of 45S rDNA units; however, they are not all transcribed. Notably, 45S rDNA units contain insertions/deletions revealing the existence of heterogeneous rRNA genes and, likely, heterogeneous ribosomes for rRNAs. In order to obtain an overall picture of 45S rDNA diversity sustaining the synthesis of rRNAs and, subsequently, of ribosomes <i>in natura</i>, we took advantage of 320 new occurrences of <i>Arabidopsis thaliana</i> as a metapopulation named At66, sampled from 0 to 1900 m of altitude in the eastern Pyrenees in France. We found that the 45S rDNA copy number is very dynamic <i>in natura</i> and identified new genotypes for both 5′ and 3′ External Transcribed Spacers (ETS). Interestingly, the highest 5′ETS genotype diversity is found in altitude while the highest 3′ETS genotype diversity is found at sea level. Structural analysis of 45S rDNA also shows conservation <i>in natura</i> of specific 5′ETS and 3′ETS sequences/features required to control rDNA expression and the processing of rRNAs. In conclusion, At66 is a worthwhile natural laboratory, and unraveled 45S rDNA diversity represents an interesting starting material to select subsets for rDNA transcription and alter the rRNA composition of ribosomes both intra- and inter-site.https://www.mdpi.com/2223-7747/12/14/2722rDNA<i>Arabidopsis thaliana</i>brassicaceaeribosomal heterogeneitynatural variation |
| spellingShingle | Valérie Delorme-Hinoux Assane Mbodj Sophie Brando Anne De Bures Christel Llauro Fabrice Covato Joseph Garrigue Claude Guisset Jacques Borrut Marie Mirouze Jean-Philippe Reichheld Julio Sáez-Vásquez 45S rDNA Diversity <i>In Natura</i> as One Step towards Ribosomal Heterogeneity in <i>Arabidopsis thaliana</i> Plants rDNA <i>Arabidopsis thaliana</i> brassicaceae ribosomal heterogeneity natural variation |
| title | 45S rDNA Diversity <i>In Natura</i> as One Step towards Ribosomal Heterogeneity in <i>Arabidopsis thaliana</i> |
| title_full | 45S rDNA Diversity <i>In Natura</i> as One Step towards Ribosomal Heterogeneity in <i>Arabidopsis thaliana</i> |
| title_fullStr | 45S rDNA Diversity <i>In Natura</i> as One Step towards Ribosomal Heterogeneity in <i>Arabidopsis thaliana</i> |
| title_full_unstemmed | 45S rDNA Diversity <i>In Natura</i> as One Step towards Ribosomal Heterogeneity in <i>Arabidopsis thaliana</i> |
| title_short | 45S rDNA Diversity <i>In Natura</i> as One Step towards Ribosomal Heterogeneity in <i>Arabidopsis thaliana</i> |
| title_sort | 45s rdna diversity i in natura i as one step towards ribosomal heterogeneity in i arabidopsis thaliana i |
| topic | rDNA <i>Arabidopsis thaliana</i> brassicaceae ribosomal heterogeneity natural variation |
| url | https://www.mdpi.com/2223-7747/12/14/2722 |
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