T‐DNA integration into the <i>Arabidopsis</i> genome depends on sequences of pre‐insertion sites

Brunaud, Véronique; Balzergue, Sandrine; Dubreucq, Bertrand; Aubourg, Santiago P.; Samson, Franck; Chauvin, Stéphanie; Bechtold, Nicole; Cruaud, Corinne; DeRose, Richard T.; Pelletier, Georges; Lepiniec, Loïc; Caboche, Michel; Lecharny, Alain

doi:10.1093/embo-reports/kvf237

Cited by 159 publications

(146 citation statements)

References 23 publications

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“…All transplastomic DNA sequences adjacent to junction sites terminated at different, apparently random, positions of the transplastome with no insertional preference for AT-or T-rich sequences as previously observed in biolistic-and͞or Agrobacterium-mediated DNA integration (22)(23)(24)(25)(26).…”

Section: New Nupts Are Generally Larger Than the Transcripts Of Selecsupporting

confidence: 59%

“…These include nonhomologous recombination between transferred ptDNA fragments (kr1, kr5, and kr10); scrambling of transplastomic DNA sequences in the nuclear genomic DNA (kr17-2); incorporation of filler DNA between disjunct regions of ptDNA (kr5-1), from neighboring ptDNA (kr18-2), or from an unknown source (kr5-2); formation of complex nuclear loci with multiple ptDNA integrants ( Table 2); and the presence of microhomology (2-5 bp) near the transplastomic junctions (J1b, J5-1b, J7a, and J10a). The junction sequences display many of the hallmarks of nonhomologous recombination, and their organization is reminiscent of nuclear integrants after biolistic and T-DNA delivery (27,(29)(30)(31)(32), although they show no sequence preference for the ATand T-rich sequences observed in both biolistic and T-DNA transformation (22)(23)(24)(25)(26). We have not been able to obtain a complete picture of any native integration sites before nupt insertion, although several nuclear junctions were obtained.…”

Section: New Nupts Are Generally Larger Than the Transcripts Of Selecmentioning

confidence: 90%

“…3). Such microhomology is a feature often associated with nonhomologous integration in experimental transformation of plant nuclear DNA (17,22). A 12-bp palindromic sequence is present at the transplastomic͞nuclear junction of J14a (Fig.…”

Section: New Nupts Are Generally Larger Than the Transcripts Of Selecmentioning

confidence: 99%

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Simple and complex nuclear loci created by newly transferred chloroplast DNA in tobacco

Huang

Ayliffe

Timmis

2004

Proc. Natl. Acad. Sci. U.S.A.

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Transfer of organelle DNA into the nuclear genome has been significant in eukaryotic evolution, because it appears to be the origin of many nuclear genes. Most studies on organelle DNA transfer have been restricted to evolutionary events but experimental systems recently became available to monitor the process in real time. We designed an experimental screen to detect plastid DNA (ptDNA) transfers to the nucleus in whole plants grown under natural conditions. The resultant genotypes facilitated investigation of the evolutionary mechanisms underlying ptDNA transfer and nuclear integration. Here we report the characterization of nuclear loci formed by integration of newly transferred ptDNA. Large, often multiple, fragments of ptDNA between 6.0 and 22.3 kb in size are incorporated into chromosomes at single Mendelian loci. The lack of chloroplast transcripts of comparable size to the ptDNA integrants suggests that DNA molecules are directly involved in the transfer process. Microhomology (2-5 bp) and rearrangements of ptDNA and nuclear DNA were frequently found near integration sites, suggesting that nonhomologous recombination plays a major role in integration. The mechanisms of ptDNA integration appear similar to those of biolistic transformation of plant cells, but no sequence preference was identified near junctions. This article provides substantial molecular analysis of real-time ptDNA transfer and integration that has resulted from natural processes with no involvement of cell injury, infection, and tissue culture. We highlight the impact of cytoplasmic organellar genome mobility on nuclear genome evolution.

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Section: New Nupts Are Generally Larger Than the Transcripts Of Selecsupporting

confidence: 59%

Section: New Nupts Are Generally Larger Than the Transcripts Of Selecmentioning

confidence: 90%

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Simple and complex nuclear loci created by newly transferred chloroplast DNA in tobacco

Huang

Ayliffe

Timmis

2004

Proc. Natl. Acad. Sci. U.S.A.

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“…We identified one transfer-DNA (T-DNA) insertion mutant in At3g21420; FLAG_119G09 from the Versailles Arabidopsis Stock Center (31). This line is in the Wassilewskija ecotype (Ws-4) and carries a T-DNA in the second exon of At3g21420 (lbo-1) (Fig.…”

Section: Resultsmentioning

confidence: 99%

LATERAL BRANCHING OXIDOREDUCTASEacts in the final stages of strigolactone biosynthesis inArabidopsis

Brewer

Yoneyama

Filardo

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

218

256

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Strigolactones are a group of plant compounds of diverse but related chemical structures. They have similar bioactivity across a broad range of plant species, act to optimize plant growth and development, and promote soil microbe interactions. Carlactone, a common precursor to strigolactones, is produced by conserved enzymes found in a number of diverse species. Versions of the MORE AXILLARY GROWTH1 (MAX1) cytochrome P450 from rice and Arabidopsis thaliana make specific subsets of strigolactones from carlactone. However, the diversity of natural strigolactones suggests that additional enzymes are involved and remain to be discovered. Here, we use an innovative method that has revealed a missing enzyme involved in strigolactone metabolism. By using a transcriptomics approach involving a range of treatments that modify strigolactone biosynthesis gene expression coupled with reverse genetics, we identified LATERAL BRANCHING OXIDOREDUCTASE (LBO), a gene encoding an oxidoreductase-like enzyme of the 2-oxoglutarate and Fe(II)-dependent dioxygenase superfamily. Arabidopsis lbo mutants exhibited increased shoot branching, but the lbo mutation did not enhance the max mutant phenotype. Grafting indicated that LBO is required for a graft-transmissible signal that, in turn, requires a product of MAX1. Mutant lbo backgrounds showed reduced responses to carlactone, the substrate of MAX1, and methyl carlactonoate (MeCLA), a product downstream of MAX1. Furthermore, lbo mutants contained increased amounts of these compounds, and the LBO protein specifically converts MeCLA to an unidentified strigolactone-like compound. Thus, LBO function may be important in the later steps of strigolactone biosynthesis to inhibit shoot branching in Arabidopsis and other seed plants.plant | branching | strigolactone | biosynthesis | Arabidopsis

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“…Several studies indicate that T-DNA is transferred to plants as a single-stranded molecule that is then made double-stranded in the nucleus prior to or during the process of integration into the plant genome (Tinland, 1996;Tzfira and Citovsky, 2000;Brunaud et al, 2002;Gelvin 2003a). Following transfer of T-DNA to the plant cytoplasm, it likely forms complexes with various transferred Agrobacterium virulence effector proteins, including VirE2, a single-stranded DNA binding protein (Gietl et al, 1987;Christie et al, 1988;Citovsky et al, 1988Citovsky et al, , 1992Das, 1988) and VirF, which may mediate proteolysis of VirE2 in the nucleus (Schrammeijer et al, 2001;Tzfira et al, 2004).…”

Section: Overexpression Of a Hta1 Cdna Can Increase Expression Of A Smentioning

confidence: 99%

Overexpression of SeveralArabidopsisHistone Genes IncreasesAgrobacterium-Mediated Transformation and Transgene Expression in Plants

et al. 2009

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The Arabidopsis thaliana histone H2A-1 is important for Agrobacterium tumefaciens-mediated plant transformation. Mutation of HTA1, the gene encoding histone H2A-1, results in decreased T-DNA integration into the genome of Arabidopsis roots, whereas overexpression of HTA1 increases transformation frequency. To understand the mechanism by which HTA1 enhances transformation, we investigated the effects of overexpression of numerous Arabidopsis histones on transformation and transgene expression. Transgenic Arabidopsis containing cDNAs encoding histone H2A (HTA), histone H4 (HFO), and histone H3-11 (HTR11) displayed increased transformation susceptibility, whereas histone H2B (HTB) and most histone H3 (HTR) cDNAs did not increase transformation. A parallel increase in transient gene expression was observed when histone HTA, HFO, or HTR11 overexpression constructs were cotransfected with double-or single-stranded forms of a gusA gene into tobacco (Nicotiana tabacum) protoplasts. However, these cDNAs did not increase expression of a previously integrated transgene. We identified the N-terminal 39 amino acids of H2A-1 as sufficient to increase transient transgene expression in plants. After transfection, transgene DNA accumulates more rapidly in the presence of HTA1 than with a control construction. Our results suggest that certain histones enhance transgene expression, protect incoming transgene DNA during the initial stages of transformation, and subsequently increase the efficiency of Agrobacterium-mediated transformation. INTRODUCTIONAgrobacterium tumefaciens-mediated plant genetic transformation is an important experimental tool for investigation of various aspects of plant biology and for agricultural biotechnology. Development of this transformation technology represents the culmination of many decades of effort to improve tissue culture and plant genetic engineering techniques. Agrobacteriummediated transformation is based on a conjugative transfer-like process, which eventually takes the T-DNA to the host cell nucleus (Gelvin, 2000(Gelvin, , 2003a(Gelvin, , 2009Tzfira and Citovsky, 2003;Citovsky et al., 2007). After attachment of the bacterium to plant cells and induction of Agrobacterium virulence (vir) genes, a single-stranded DNA (the T-strand) is processed from the resident tumor-inducing or root-inducing plasmid and transported from the bacterium to the plant cell. In addition, a number of Virulence effector proteins, including VirD2 (attached to the T-strand), the single-strand DNA binding protein VirE2, plus VirE3, VirD5, and VirF are also transferred to the plant (Otten et al., 1984;Stahl et al., 1998;Vergunst et al., 2000Vergunst et al., , 2003Vergunst et al., , 2005Schrammeijer et al., 2003). These proteins are likely involved in protecting T-DNA from nuclease digestion, directing T-DNA to the nucleus, stripping proteins from the T-strand prior to integration, and integrating T-DNA into the plant genome. T-DNA integration occurs randomly into genomic DNA by the process of illegitimate recombination (...

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T‐DNA integration into the Arabidopsis genome depends on sequences of pre‐insertion sites

Cited by 159 publications

References 23 publications

Simple and complex nuclear loci created by newly transferred chloroplast DNA in tobacco

Simple and complex nuclear loci created by newly transferred chloroplast DNA in tobacco

LATERAL BRANCHING OXIDOREDUCTASEacts in the final stages of strigolactone biosynthesis inArabidopsis

Overexpression of SeveralArabidopsisHistone Genes IncreasesAgrobacterium-Mediated Transformation and Transgene Expression in Plants

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