Comparative Plant Genomics Resources at PlantGDB

Dong, Qunfeng; Lawrence, Carolyn J.; Schlueter, Shannon D.; Wilkerson, Matthew D.; Kurtz, Stefan; Lushbough, Carol; Brendel, Volker

doi:10.1104/pp.104.059212

Cited by 90 publications

(77 citation statements)

References 31 publications

(30 reference statements)

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“…Sequences similar to the target sites of ADH1 and TT4 ZFNs were identifed by using a web-based pattern search tool (44). Two sequences (one for each target site) most similar to the target sites were chosen for subsequent genotyping.…”

Section: Methodsmentioning

confidence: 99%

High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases

Zhang

Maeder

Unger-Wallace

et al. 2010

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

340

228

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We report here an efficient method for targeted mutagenesis of Arabidopsis genes through regulated expression of zinc finger nucleases (ZFNs)-enzymes engineered to create DNA doublestrand breaks at specific target loci. ZFNs recognizing the Arabidopsis ADH1 and TT4 genes were made by Oligomerized Pool ENgineering (OPEN)-a publicly available, selection-based platform that yields high quality zinc finger arrays. The ADH1 and TT4 ZFNs were placed under control of an estrogen-inducible promoter and introduced into Arabidopsis plants by floral-dip transformation. Primary transgenic Arabidopsis seedlings induced to express the ADH1 or TT4 ZFNs exhibited somatic mutation frequencies of 7% or 16%, respectively. The induced mutations were typically insertions or deletions (1-142 bp) that were localized at the ZFN cleavage site and likely derived from imprecise repair of chromosome breaks by nonhomologous end-joining. Mutations were transmitted to the next generation for 69% of primary transgenics expressing the ADH1 ZFNs and 33% of transgenics expressing the TT4 ZFNs. Furthermore, ≈20% of the mutant-producing plants were homozygous for mutations at ADH1 or TT4, indicating that both alleles were disrupted. ADH1 and TT4 were chosen as targets for this study because of their selectable or screenable phenotypes (adh1, allyl alcohol resistance; tt4, lack of anthocyanins in the seed coat). However, the high frequency of observed ZFNinduced mutagenesis suggests that targeted mutations can readily be recovered by simply screening progeny of primary transgenic plants by PCR and DNA sequencing. Taken together, our results suggest that it should now be possible to obtain mutations in any Arabidopsis target gene regardless of its mutant phenotype.nonhomologous end-joining | gene knockout | alcohol dehydrogenase | chalcone synthase

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Section: Methodsmentioning

confidence: 99%

High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases

Zhang

Maeder

Unger-Wallace

et al. 2010

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

340

228

View full text Add to dashboard Cite

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“…If the genome was sequenced, the automated predicted peptides were used; otherwise, the translated peptides in six frames from the assembled EST UniGenes in PlantGDB were used (Dong et al, 2005). The homologs found in the three searches under the E-value cutoff of < 0.01 were collected respectively and subjected to multiple sequence alignments using the MAFFT v6.717 program (Katoh et al, 2005) with the L-INS-I method.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

LACCASE Is Necessary and Nonredundant with PEROXIDASE for Lignin Polymerization during Vascular Development in Arabidopsis

et al. 2013

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The evolution of lignin biosynthesis was critical in the transition of plants from an aquatic to an upright terrestrial lifestyle. Lignin is assembled by oxidative polymerization of two major monomers, coniferyl alcohol and sinapyl alcohol. Although two recently discovered laccases, LAC4 and LAC17, have been shown to play a role in lignin polymerization in Arabidopsis thaliana, disruption of both genes only leads to a relatively small change in lignin content and only under continuous illumination. Simultaneous disruption of LAC11 along with LAC4 and LAC17 causes severe plant growth arrest, narrower root diameter, indehiscent anthers, and vascular development arrest with lack of lignification. Genome-wide transcript analysis revealed that all the putative lignin peroxidase genes are expressed at normal levels or even higher in the laccase triple mutant, suggesting that lignin laccase activity is necessary and nonredundant with peroxidase activity for monolignol polymerization during plant vascular development. Interestingly, even though lignin deposition in roots is almost completely abolished in the lac11 lac4 lac17 triple mutant, the Casparian strip, which is lignified through the activity of peroxidase, is still functional. Phylogenetic analysis revealed that lignin laccase genes have no orthologs in lower plant species, suggesting that the monolignol laccase genes diverged after the evolution of seed plants.

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“…The MS and MS/MS spectra were searched against the soybean EST assembly from PlantGDB (Dong et al, 2005; release October 2007, based on GenBank release 161) and soybean and Arabidopsis (Arabidopsis thaliana) proteins from the uniprot database (release 12.4, October 2007) using an inhouse installation of the program OMSSA (Geer et al, 2004; version 2.1). Search results were filtered and sorted using in-house-written software (F. Drepper, unpublished data).…”

Section: Protein Identification By Hplc-electrospray Mass Spectrometrymentioning

confidence: 99%

Naphthoquinone-Dependent Generation of Superoxide Radicals by Quinone Reductase Isolated from the Plasma Membrane of Soybean

et al. 2008

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Using a tetrazolium-based assay, a NAD(P)H oxidoreductase was purified from plasma membranes prepared from soybean (Glycine max) hypocotyls. The enzyme, a tetramer of 85 kD, produces O 2 Á2 by a reaction that depended on menadione or several other 1,4-naphthoquinones, in apparent agreement with a classification as a one-electron-transferring flavoenzyme producing semiquinone radicals. However, the enzyme displayed catalytic and molecular properties of obligatory two-electrontransferring quinone reductases of the DT-diaphorase type, including insensitivity to inhibition by diphenyleneiodonium. This apparent discrepancy was clarified by investigating the pH-dependent reactivity of menadionehydroquinone toward O 2 and identifying the protein by mass spectrometry and immunological techniques. The enzyme turned out to be a classical NAD(P)H:quinone-acceptor oxidoreductase (EC 1.6.5.2, formerly 1.6.99.2) that reduces menadione to menadionehydroquinone and subsequently undergoes autoxidation at pH $ 6.5. Autoxidation involves the production of the semiquinone as an intermediate, creating the conditions for one-electron reduction of O 2 . The possible function of this enzyme in the generation of O 2 Á2 and H 2 O 2 at the plasma membrane of plants in vivo is discussed.

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Comparative Plant Genomics Resources at PlantGDB

Cited by 90 publications

References 31 publications

High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases

High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases

LACCASE Is Necessary and Nonredundant with PEROXIDASE for Lignin Polymerization during Vascular Development in Arabidopsis

Naphthoquinone-Dependent Generation of Superoxide Radicals by Quinone Reductase Isolated from the Plasma Membrane of Soybean

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