Characterization of T-Circles and Their Formation Reveal Similarities to Agrobacterium T-DNA Integration Patterns
Agrobacterium transfers T-DNA to plants where it may integrate into the genome. Non-homologous end-joining (NHEJ) has been invoked as the mechanism of T-DNA integration, but the role of various NHEJ proteins remains controversial. Genetic evidence for the role of NHEJ in T-DNA integration has yielde...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-05-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.849930/full |
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| author | Kamy Singer Lan-Ying Lee Jing Yuan Stanton B. Gelvin |
| author_facet | Kamy Singer Lan-Ying Lee Jing Yuan Stanton B. Gelvin |
| author_sort | Kamy Singer |
| collection | DOAJ |
| description | Agrobacterium transfers T-DNA to plants where it may integrate into the genome. Non-homologous end-joining (NHEJ) has been invoked as the mechanism of T-DNA integration, but the role of various NHEJ proteins remains controversial. Genetic evidence for the role of NHEJ in T-DNA integration has yielded conflicting results. We propose to investigate the formation of T-circles as a proxy for understanding T-DNA integration. T-circles are circular double-strand T-DNA molecules, joined at their left (LB) and right (RB) border regions, formed in plants. We characterized LB-RB junction regions from hundreds of T-circles formed in Nicotiana benthamiana or Arabidopsis thaliana. These junctions resembled T-DNA/plant DNA junctions found in integrated T-DNA: Among complex T-circles composed of multiple T-DNA molecules, RB-RB/LB-LB junctions predominated over RB-LB junctions; deletions at the LB were more frequent and extensive than those at the RB; microhomology was frequently used at junction sites; and filler DNA, from the plant genome or various Agrobacterium replicons, was often present between the borders. Ku80 was not required for efficient T-circle formation, and a VirD2 ω mutation affected T-circle formation and T-DNA integration similarly. We suggest that investigating the formation of T-circles may serve as a surrogate for understanding T-DNA integration. |
| first_indexed | 2024-04-14T01:32:35Z |
| format | Article |
| id | doaj.art-28802fadd7014ce68fba53963b95cdc3 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-14T01:32:35Z |
| publishDate | 2022-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-28802fadd7014ce68fba53963b95cdc32022-12-22T02:20:06ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-05-011310.3389/fpls.2022.849930849930Characterization of T-Circles and Their Formation Reveal Similarities to Agrobacterium T-DNA Integration PatternsKamy SingerLan-Ying LeeJing YuanStanton B. GelvinAgrobacterium transfers T-DNA to plants where it may integrate into the genome. Non-homologous end-joining (NHEJ) has been invoked as the mechanism of T-DNA integration, but the role of various NHEJ proteins remains controversial. Genetic evidence for the role of NHEJ in T-DNA integration has yielded conflicting results. We propose to investigate the formation of T-circles as a proxy for understanding T-DNA integration. T-circles are circular double-strand T-DNA molecules, joined at their left (LB) and right (RB) border regions, formed in plants. We characterized LB-RB junction regions from hundreds of T-circles formed in Nicotiana benthamiana or Arabidopsis thaliana. These junctions resembled T-DNA/plant DNA junctions found in integrated T-DNA: Among complex T-circles composed of multiple T-DNA molecules, RB-RB/LB-LB junctions predominated over RB-LB junctions; deletions at the LB were more frequent and extensive than those at the RB; microhomology was frequently used at junction sites; and filler DNA, from the plant genome or various Agrobacterium replicons, was often present between the borders. Ku80 was not required for efficient T-circle formation, and a VirD2 ω mutation affected T-circle formation and T-DNA integration similarly. We suggest that investigating the formation of T-circles may serve as a surrogate for understanding T-DNA integration.https://www.frontiersin.org/articles/10.3389/fpls.2022.849930/fullAgrobacteriumArabidopsis thalianaKu80Nicotiana benthamianaT-circlesT-DNA integration |
| spellingShingle | Kamy Singer Lan-Ying Lee Jing Yuan Stanton B. Gelvin Characterization of T-Circles and Their Formation Reveal Similarities to Agrobacterium T-DNA Integration Patterns Frontiers in Plant Science Agrobacterium Arabidopsis thaliana Ku80 Nicotiana benthamiana T-circles T-DNA integration |
| title | Characterization of T-Circles and Their Formation Reveal Similarities to Agrobacterium T-DNA Integration Patterns |
| title_full | Characterization of T-Circles and Their Formation Reveal Similarities to Agrobacterium T-DNA Integration Patterns |
| title_fullStr | Characterization of T-Circles and Their Formation Reveal Similarities to Agrobacterium T-DNA Integration Patterns |
| title_full_unstemmed | Characterization of T-Circles and Their Formation Reveal Similarities to Agrobacterium T-DNA Integration Patterns |
| title_short | Characterization of T-Circles and Their Formation Reveal Similarities to Agrobacterium T-DNA Integration Patterns |
| title_sort | characterization of t circles and their formation reveal similarities to agrobacterium t dna integration patterns |
| topic | Agrobacterium Arabidopsis thaliana Ku80 Nicotiana benthamiana T-circles T-DNA integration |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.849930/full |
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