The FOX hunting system: an alternative gain‐of‐function gene hunting technique

Ichikawa, Takanari; Nakazawa, Miki; Kawashima, Mika; Iizumi, Haruko; Kawakubo, Hirofumi; Kondou, Youichi; Tsuhara, Yumi; Suzuki, Kumiko; Ishikawa, Akie; Seki, Motoaki; Fujita, Miki; Motohashi, Reiko; Nagata, Noriko; Такаги, Таичиро; Shinozaki, Kazuo; Matsui, Minami

doi:10.1111/j.1365-313x.2006.02924.x

Cited by 219 publications

(239 citation statements)

References 45 publications

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“…2E). Aberrant plastids containing plastoglobules were found in transgenic plants overexpressing ISE2 (20). Thus, ISE2 has a critical role in plastid development and function.…”

Section: Ise2 Is Found In Chloroplastsmentioning

confidence: 90%

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Organelle–nucleus cross-talk regulates plant intercellular communication via plasmodesmata

Burch‐Smith¹,

Brunkard²,

Choi

et al. 2011

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

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We use Arabidopsis thaliana embryogenesis as a model system for studying intercellular transport via plasmodesmata (PD). A forward genetic screen for altered PD transport identified increased size exclusion limit (ise) 1 and ise2 mutants with increased intercellular transport of fluorescent 10-kDa tracers. Both ise1 and ise2 exhibit increased formation of twinned and branched PD. ISE1 encodes a mitochondrial DEAD-box RNA helicase, whereas ISE2 encodes a DEVH-type RNA helicase. Here, we show that ISE2 foci are localized to the chloroplast stroma. Surprisingly, plastid development is defective in both ise1 and ise2 mutant embryos. In an effort to understand how RNA helicases that localize to different organelles have similar impacts on plastid and PD development/function, we performed whole-genome expression analyses. The most significantly affected class of transcripts in both mutants encode products that target to and enable plastid function. These results reinforce the importance of plastid-mitochondria-nucleus cross-talk, add PD as a critical player in the plant cell communication network, and thereby illuminate a previously undescribed signaling pathway dubbed organelle-nucleus-plasmodesmata signaling. Several genes with roles in cell wall synthesis and modification are also differentially expressed in both mutants, providing new targets for investigating PD development and function.

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“…2E). Aberrant plastids containing plastoglobules were found in transgenic plants overexpressing ISE2 (20). Thus, ISE2 has a critical role in plastid development and function.…”

Section: Ise2 Is Found In Chloroplastsmentioning

confidence: 90%

“…ii) A fusion of GFP to the first 100 N-terminal amino acids of ISE2 that contains the predicted chloroplast transit peptide localizes to chloroplasts (20). iii) Proteomic analyses consistently identified ISE2 in chloroplast extracts (21,22).…”

mentioning

confidence: 99%

Organelle–nucleus cross-talk regulates plant intercellular communication via plasmodesmata

Burch‐Smith¹,

Brunkard²,

Choi

et al. 2011

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

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“…The DCAR_032551 gene product represents a plant-specific protein of unknown function, and mutants of the A. thaliana homolog PSEUDO-ETIOLATION IN LIGHT (PEL) have an etiolated phenotype, a phenotype associated with defective responses to light 56 (Supplementary Table 44). In many ways, the physiology and genetics of carotenoid accumulation in dark orange and yellow (yy) carrots are similar to the phenotypes of the A. thaliana det, cop, and fus de-etiolated mutants.…”

Section: A Model For Carotenoid Accumulation In Carrot Rootsmentioning

confidence: 99%

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

et al. 2016

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5 7Carrot (Daucus carota subsp. carota L.; 2n = 2x = 18) is a globally important root crop whose production has quadrupled between 1976 and 2013 (FAO Statistics; see URLs), outpacing the overall rate of increase in vegetable production and world population growth (FAO Statistics; see URLs) through development of high-value products for fresh consumption, juices, and natural pigments and cultivars adapted to warmer production regions 1 .The first documented colors for domesticated carrot root were yellow and purple in Central Asia approximately 1,100 years ago 2,3 , with orange carrots not reliably reported until the sixteenth century in Europe 4,5 . The popularity of orange carrots is fortuitous for modern consumers because the orange pigmentation results from high quantities of alpha-and beta-carotene, making carrots the richest source of provitamin A in the US diet 6 . Carrot breeding has substantially increased nutritional value, with a 50% average increase in carotene content in the United States as compared to 40 years ago 6 . Lycopene and lutein in red and yellow carrots, respectively, are also nutritionally important carotenoids, making carrot a model system to study storage root development and carotenoid accumulation.Carrot is the most important crop in the Apiaceae family, which includes numerous other vegetables, herbs, spices, and medicinal plants that enhance the epicurean experience 7 , including celery, parsnip, arracacha, parsley, fennel, coriander, and cumin. The Apiaceae family belongs to the euasterid II clade, which includes important crops such as lettuce and sunflower 8 . Genome sequences of euasterid I species have been reported, but only two genomes 9,10 have been published among the other euasterid II species.Here we report a high-quality genome assembly of a doubledhaploid orange carrot, characterization of the mechanism controlling carotenoid accumulation in storage roots, and the resequencing of 35 accessions spanning the genetic diversity of the Daucus genus. Our comprehensive genomic analyses provide insights into the evolution of the asterids and several gene families. These results will facilitate biological discovery and crop improvement in carrot and other crops.A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution We report a high-quality chromosome-scale assembly and analysis of the carrot (Daucus carota) genome, the first sequenced genome to include a comparative evolutionary analysis among members of the euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carrot from members of the Asterales order, clarifying the evolutionary scenario before and after radiation of the two main asterid clades. Large- and small-scale lineage-specific duplications have contributed to the expansion of gene families, including those with roles in flowering time, defense response, flavor, and pigment accumulation. We identified a candidate gene, DCAR_032551, that conditions caro...

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“…Yeast Screening. cDNA libraries constructed from RNA extracted from 2-wkold Arabidopsis seedlings or a full-length cDNA library (36) were introduced into the yeast strain PJ69-4A containing AD-ABI1 and BD-PYR1, or AD-HAB1 and BD-PYR1, and colonies surviving on selection medium (synthetic dextrose; -Leu, -Trp, -Ura, -His) in the presence of 0.1 μM ABA were selected. Screening was performed according to standard protocols.…”

Section: Methodsmentioning

confidence: 99%

Identification of an abscisic acid transporter by functional screening using the receptor complex as a sensor

Kanno

Hanada

Chiba

et al. 2012

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

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429

378

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Movement of the plant hormone abscisic acid (ABA) within plants has been documented; however, the molecular mechanisms that regulate ABA transport are not fully understood. By using a modified yeast two-hybrid system, we screened Arabidopsis cDNAs capable of inducing interactions between the ABA receptor PYR/PYL/ RCAR and PP2C protein phosphatase under low ABA concentrations. By using this approach, we identified four members of the NRT1/PTR family as candidates for ABA importers. Transport assays in yeast and insect cells demonstrated that at least one of the candidates ABA-IMPORTING TRANSPORTER (AIT) 1, which had been characterized as the low-affinity nitrate transporter NRT1.2, mediates cellular ABA uptake. Compared with WT, the ait1/nrt1.2 mutants were less sensitive to exogenously applied ABA during seed germination and/or postgermination growth, whereas overexpression of AIT1/NRT1.2 resulted in ABA hypersensitivity in the same conditions. Interestingly, the inflorescence stems of ait1/ nrt1.2 had a lower surface temperature than those of the WT because of excess water loss from open stomata. We detected promoter activities of AIT1/NRT1.2 around vascular tissues in inflorescence stems, leaves, and roots. These data suggest that the function of AIT1/NRT1.2 as an ABA importer at the site of ABA biosynthesis is important for the regulation of stomatal aperture in inflorescence stems.guard cells | liquid chromatography-tandem mass spectrometry | water stress

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The FOX hunting system: an alternative gain‐of‐function gene hunting technique

Cited by 219 publications

References 45 publications

Organelle–nucleus cross-talk regulates plant intercellular communication via plasmodesmata

Organelle–nucleus cross-talk regulates plant intercellular communication via plasmodesmata

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

Identification of an abscisic acid transporter by functional screening using the receptor complex as a sensor

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