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Transcript profiling of crown rootless1 mutant stem base reveals new elements associated with crown root development in rice

ABSTRACT: Expression data from rice crownrootless1 mutant and corresponding WT stem bases

ORGANISM(S): Oryza sativa

PROVIDER: GSE30818 | GEO | 2011/07/20

SECONDARY ACCESSION(S): PRJNA144199

REPOSITORIES: GEO

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Transcript profiling of crown rootless1 mutant stem base reveals new elements associated with crown root development in rice

Project description:Expression data from rice crownrootless1 mutant and corresponding WT stem bases crl1 mutant and WT stem base transcriptomes were compared to identify genes whose expression is altered by crl1 mutation

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Transcript profiling in rice stem base of wild type and crown root less 1 mutant after auxin treatment

Project description:Lateral Organ Boundary Domain (LBD) transcription factors are specific of plants and are involved in the control of development. One LBD clade is related to the control of root development (Coudert et al., 2013, Mol. Biol. Evol. 30, 569-572). Belonging to this clade, CROWN ROOT LESS 1 controls the initiation of crown roots in rice and its expression is induced by auxin (Inukai Plant Cell, 17, 1387-1396, Liu et al., 2005, Plant J., 43, 47-56). The aim of this study was to identify CRL1-dependant auxin responsive genes. Transcriptome analysis in wild-type and crl1 mutant stem bases after exogenous auxin treatment of plantlets revealed 126 CRL1-dependant auxin responsive genes including a large part of genes encoding proteins involved in signal transduction pathways that may be related to cell division, expansion and differentiation, and root development.

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Project description:Crown roots constitute the main part of the rice root system. Several key genes involved in crown root initiation and development have been identified by genetics and functional genomics approaches. The CROWN ROOTLESS1 (CRL1) transcription factor is necessary for crown root initiation in rice. The basic helix-loop-helix 044 (OsbHLH044) transcription factor was identified as a CRL1-regulated gene. In this study, we aimed to determine OsbHLH044-regulated genes, with transcriptome analysis of OsbHLH44 overexpressing plants in crl1 mutant background. We analysed the transcriptional profile of overexpressing lines stem bases in comparison with corresponding null segregant sister control lines. Affymetrix microarrays were processed in the Microarray Core Facility “Transcriptome“ of the Institute in Regenerative Medicine and Biotherapy, CHU de Montpellier-INSERM-UM Montpellier, http://irmb.chu-montpellier.fr/ .

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Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice.

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Project description:As a signal molecular in aerobic organism, how reactive oxygen species (ROS) regulates normal life is a fundamental biological question. Locally accumulated ROS have been reported to balance cell division and differentiation in root apical meristem. However, the underlying molecular mechanism is unclear. Here, we reveal that developmentally produced H2O2 in plant root apical meristem (RAM) triggers reversible acetylation modification of proteins which involved in protein synthesis and cell proliferation. WOX11, an essential transcription factor for crown roots (CRs) formation, modulates ROS homeostasis by directly regulating class III peroxidases. HDACs (histone deacetylases) sense cellular redox status to enhance their enzyme activities, which drives protein acetylation level alterations in rice roots. Oxidation-dependent on WOX11 triggered protein acetylation modification leads to a robust root system in rice. Our study revealed a novel regulatory mechanism which cellular redox status via a WOX11-dependent manner regulates protein acetylation during rice crown root development. The molecular link between the redox status and HDACs activities through WOX11-dependent pathway may provide new insight into which plants exploit developmentally produced ROS to direct organogenesis. Additionally, HDACs reversible enzyme activity via redox-regulated endows with the flexibility of protein modification control in dealing with developmental and changing environmental cues.

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