Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon

Mönke, Gudrun; Seifert, Michael; Keilwagen, Jens; Mohr, Michaela; Große, Ivo; Hähnel, Urs; Junker, Astrid; Weißhaar, Bernd; Conrad, Udo; Bäumlein, Helmut; Altschmied, Lothar

doi:10.1093/nar/gks594

Cited by 162 publications

(193 citation statements)

References 99 publications

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“…In Arabidopsis, weak alleles of ABI3 are fully desiccation tolerant but have reduced storability, making it one of the major regulators of longevity (Ooms et al, 1993;Sugliani et al, 2009;Verdier et al, 2013). In wkry3 and nfxl1 mutant seeds, dry weight accumulation and other developmental processes regulated by ABI3, such as chlorophyll degradation and the accumulation of nonreducing soluble sugar contents, were not affected in mature seeds, and NFXL1, WRKY3, or WRKY33 have not been identified as targets of ABI3, LEC1, or LEC2 (Braybrook et al, 2006;Junker et al, 2012;Mönke et al, 2012). In M. truncatula, our transcriptome data on abi3 mutant seeds and ectopic expression of ABI3 using a hairy root system demonstrate that NFXL and WRKY33 transcript levels were not deregulated by ABI3, making these TF putative regulators of an ABI3-independent pathway involved in longevity.…”

Section: Discussion Translational Biology Between M Truncatula and Amentioning

confidence: 99%

Inference of Longevity-Related Genes from a Robust Coexpression Network of Seed Maturation Identifies Regulators Linking Seed Storability to Biotic Defense-Related Pathways

Righetti¹,

Vu²,

Pelletier³

et al. 2015

Plant Cell

121

191

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Seed longevity, the maintenance of viability during storage, is a crucial factor for preservation of genetic resources and ensuring proper seedling establishment and high crop yield. We used a systems biology approach to identify key genes regulating the acquisition of longevity during seed maturation of Medicago truncatula. Using 104 transcriptomes from seed developmental time courses obtained in five growth environments, we generated a robust, stable coexpression network (MatNet), thereby capturing the conserved backbone of maturation. Using a trait-based gene significance measure, a coexpression module related to the acquisition of longevity was inferred from MatNet. Comparative analysis of the maturation processes in M. truncatula and Arabidopsis thaliana seeds and mining Arabidopsis interaction databases revealed conserved connectivity for 87% of longevity module nodes between both species. Arabidopsis mutant screening for longevity and maturation phenotypes demonstrated high predictive power of the longevity cross-species network. Overrepresentation analysis of the network nodes indicated biological functions related to defense, light, and auxin. Characterization of defense-related wrky3 and nf-x1-like1 (nfxl1) transcription factor mutants demonstrated that these genes regulate some of the network nodes and exhibit impaired acquisition of longevity during maturation. These data suggest that seed longevity evolved by co-opting existing genetic pathways regulating the activation of defense against pathogens.

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Section: Discussion Translational Biology Between M Truncatula and Amentioning

confidence: 99%

Inference of Longevity-Related Genes from a Robust Coexpression Network of Seed Maturation Identifies Regulators Linking Seed Storability to Biotic Defense-Related Pathways

Righetti¹,

Vu²,

Pelletier³

et al. 2015

Plant Cell

121

191

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“…These proteins include putative ABI3 targets (Mönke et al, 2012) and those related to ABA biosynthesis and signaling (Tables I and II). We also noted changes in the levels for proteins involved in lipid metabolism.…”

Section: An Isobaric Tags For Relative and Absolute Quantitation Expementioning

confidence: 99%

“…We found that several seed storage proteins, including SEED STORAGE ALBUMIN1 (SESA1), SESA12, and SESA3 and two oleosin proteins, were down regulated in the cer9-2 mutant (Table II). These proteins are involved in oil body formation and are also ABI3 putative targets (Mönke et al, 2012; Table II).…”

Section: An Isobaric Tags For Relative and Absolute Quantitation Expementioning

confidence: 99%

The Putative E3 Ubiquitin Ligase ECERIFERUM9 Regulates Abscisic Acid Biosynthesis and Response during Seed Germination and Postgermination Growth in Arabidopsis

et al. 2014

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The ECERIFERUM9 (CER9) gene encodes a putative E3 ubiquitin ligase that functions in cuticle biosynthesis and the maintenance of plant water status. Here, we found that CER9 is also involved in abscisic acid (ABA) signaling in seeds and young seedlings of Arabidopsis (Arabidopsis thaliana). The germinated embryos of the mutants exhibited enhanced sensitivity to ABA during the transition from reversible dormancy to determinate seedling growth. Expression of the CER9 gene is closely related to ABA levels and displays a similar pattern to that of ABSCISIC ACID-INSENSITIVE5 (ABI5), which encodes a positive regulator of ABA responses in seeds. cer9 mutant seeds exhibited delayed germination that is independent of seed coat permeability. Quantitative proteomic analyses showed that cer9 seeds had a protein profile similar to that of the wild type treated with ABA. Transcriptomics analyses revealed that genes involved in ABA biosynthesis or signaling pathways were differentially regulated in cer9 seeds. Consistent with this, high levels of ABA were detected in dry seeds of cer9. Blocking ABA biosynthesis by fluridone treatment or by combining an ABA-deficient mutation with cer9 attenuated the phenotypes of cer9. Whereas introduction of the abi1-1, abi3-1, or abi4-103 mutation could completely eliminate the ABA hypersensitivity of cer9, introduction of abi5 resulted only in partial suppression. These results indicate that CER9 is a novel negative regulator of ABA biosynthesis and the ABA signaling pathway during seed germination.

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“…Recent work using chromatin immunoprecipitation (ChIP) and expression analysis is revealing how some of these factors control development and how they interact (Braybrook et al, 2006;Kaufmann et al, 2009;Zheng et al, 2009;Mönke et al, 2012). Here, we report the genome-wide identification of in vivo binding sites for FUS3 in an embryonic culture tissue system that allows robust ChIP.…”

mentioning

confidence: 98%

Identification of Direct Targets of FUSCA3, a Key Regulator of Arabidopsis Seed Development

2013

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FUSCA3 (FUS3) is a B3 domain transcription factor that is a member of the LEAFY COTYLEDON (LEC) group of genes. The LEC genes encode proteins that also include LEC2, a B3 domain factor related to FUS3, and LEC1, a CCAAT box-binding factor. LEC1, LEC2, and FUS3 are essential for plant embryo development. All three loss-of-function mutants in Arabidopsis (Arabidopsis thaliana) prematurely exit embryogenesis and enter seedling developmental programs. When ectopically expressed, these genes promote embryo programs in seedlings. We report on chromatin immunoprecipitation-tiling array experiments to globally map binding sites for FUS3 that, along with other published work to assess transcriptomes in response to FUS3, allow us to determine direct from indirect targets. Many transcription factors associated with embryogenesis are direct targets of FUS3, as are genes involved in the seed maturation program. FUS3 regulates genes encoding microRNAs that, in turn, control transcripts encoding transcription factors involved in developmental phase changes. Examination of direct targets of FUS3 reveals that FUS3 acts primarily or exclusively as a transcriptional activator. Regulation of microRNA-encoding genes is one mechanism by which FUS3 may repress indirect target genes. FUS3 also directly up-regulates VP1/ABI3-LIKE1 (VAL1), encoding a B3 domain protein that functions as a repressor of transcription. VAL1, along with VAL2 and VAL3, is involved in the transition from embryo to seedling development. Many genes are responsive to FUS3 and to VAL1/VAL2 but with opposite regulatory consequences. The emerging picture is one of complex cross talk and interactions among embryo transcription factors and their target genes.

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Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon

Cited by 162 publications

References 99 publications

Inference of Longevity-Related Genes from a Robust Coexpression Network of Seed Maturation Identifies Regulators Linking Seed Storability to Biotic Defense-Related Pathways

Inference of Longevity-Related Genes from a Robust Coexpression Network of Seed Maturation Identifies Regulators Linking Seed Storability to Biotic Defense-Related Pathways

The Putative E3 Ubiquitin Ligase ECERIFERUM9 Regulates Abscisic Acid Biosynthesis and Response during Seed Germination and Postgermination Growth in Arabidopsis

Identification of Direct Targets of FUSCA3, a Key Regulator of Arabidopsis Seed Development

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