IDEF1

2022-11-15 | Categories genes  | Tags transcription factor  Al tolerance  endosperm  seed  reproductive  leaf  vascular bundle  iron  seedling  pollen  vegetative  lateral root  biomass  seed germination  homeostasis  root  growth  jasmonate  Ubiquitin 

• Information
  • Symbol: IDEF1
  • MSU: LOC_Os08g01090
  • RAPdb: Os08g0101000
• PSP score
  • LOC_Os08g01090.2: 0.8932
  • LOC_Os08g01090.1: 0.9531
• PLAAC score
  • LOC_Os08g01090.2: 0
  • LOC_Os08g01090.1: 14.846
• pLDDT score
  • 60.1
• Protein Structure from AlphaFold and UniProt
  • 
• Publication
  • The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes, 2009, Plant J.
  • The rice transcription factor IDEF1 directly binds to iron and other divalent metals for sensing cellular iron status, 2012, Plant J.
  • The spatial expression and regulation of transcription factors IDEF1 and IDEF2, 2010, Ann Bot.
  • The transcription factor IDEF1 regulates the response to and tolerance of iron deficiency in plants, 2007, Proc Natl Acad Sci U S A.
  • Jasmonate signaling is activated in the very early stages of iron deficiency responses in rice roots., 2016, Plant Mol Biol.
• Genbank accession number
  • AK107456
• Key message
  • The transcription factor IDEF1 regulates the response to Fe deficiency in Oryza sativa (rice) by recognizing CATGC sequences within the Fe deficiency-responsive cis-acting element IDE1
  • The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes
  • Transgenic rice plants expressing an introduced IDEF1 exhibit substantial tolerance to iron deficiency in both hydroponic culture and calcareous soil
  • During seed germination, IDEF1 and IDEF2 were expressed in the endosperm and embryo
  • We identified the rice transcription factor IDEF1, which specifically binds the iron deficiency-responsive cis-acting element IDE1
  • IDEF1 belongs to an uncharacterized branch of the plant-specific transcription factor family ABI3/VP1 and exhibits the sequence recognition property of efficiently binding to the CATGC sequence within IDE1
  • IDEF1 overexpression leads to the enhanced expression of the iron deficiency-induced transcription factor gene OsIRO2, suggesting the presence of a sequential gene regulatory network
  • The transcription factor IDEF1 regulates the response to and tolerance of iron deficiency in plants
  • The spatial expression and regulation of transcription factors IDEF1 and IDEF2
  • Proximal regions of IDEF1-regulated gene promoters also showed enrichment of RY elements (CATGCA), which regulate gene expression during seed maturation
  • The expression of several genes encoding late embryogenesis abundant proteins, including Osem, was induced in Fe-deficient roots and/or leaves in an IDEF1-dependent manner, suggesting a possible function of seed maturation-related genes in Fe-deficient vegetative organs
  • CONCLUSIONS: IDEF1 and IDEF2 are constitutively expressed during both vegetative and reproductive stages
  • IDEF1 and IDEF2 expression was dominant in leaf mesophyll and vascular cells, respectively
  • KEY RESULTS: IDEF1 and IDEF2 were highly expressed in the basal parts of the lateral roots and vascular bundles
  • The Oryza sativa (rice) transcription factor IDEF1 plays a crucial role in regulating iron deficiency-induced genes involved in iron homeostasis
  • Transgenic rice plants constitutively overexpressing IDEF1 without these metal-binding domains failed to cause pleiotropic effects conferred by overexpression of full-length IDEF1, including a low germination rate, impaired seedling growth, tolerance to iron deficiency in hydroponic culture, and enhanced expression of various iron deficiency-inducible genes
  • Impairment of the transcriptional regulation of IDEF1 by deletion of the metal-binding domains occurred primarily at an early stage of iron deficiency
  • These results suggest that the histidine-asparagine and proline-rich regions in rice IDEF1 directly bind to divalent metals and sense the cellular metal ion balance caused by changes in iron availability
  • The rice transcription factor IDEF1 directly binds to iron and other divalent metals for sensing cellular iron status
  • IDEF1 was strongly expressed in pollen, ovaries, the aleurone layer and embryo
  • The iron deficiency-responsive cis-acting element binding factors 1 and 2 (IDEF1 and IDEF2) regulate transcriptional response to iron deficiency in rice roots
  • Expression patterns of the target genes of IDEF1 and IDEF2 were analysed using transformants with induced or repressed expression of IDEF1 or IDEF2 grown in iron-rich or in iron-deficient solutions for 1 d
  • Expression of IDEF1 target genes was regulated in iron-rich roots similar to early iron-deficiency stages
  • The spatial expression patterns and gene regulation of IDEF1 and IDEF2 in roots are generally conserved under conditions of iron sufficiency and deficiency, suggesting complicated interactions with unknown factors for sensing and transmitting iron-deficiency signals
  • Manipulation of IDEF1 also provides another approach for producing crops tolerant of iron deficiency to enhance food and biomass production in calcareous soils
  • IDEF1 transcripts are constitutively present in rice roots and leaves
  • Transgenic tobacco plants expressing IDEF1 under the control of the constitutive cauliflower mosaic virus 35S promoter transactivate IDE1-mediated expression only in iron-deficient roots
  • Many jasmonate-inducible genes were also negatively regulated by the ubiquitin ligases OsHRZ1 and OsHRZ2 and positively regulated by the transcription factor IDEF1
  • These results indicate that jasmonate signaling is activated during the very early stages of iron deficiency, which is partly regulated by IDEF1 and OsHRZs
• Connection
  • IDEF1, OsIRO2, The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes, Time-course expression analyses using quantitative reverse-transcriptase PCR revealed that the IDEF1 expression level was positively correlated with the level of induction of the Fe utilization-related genes OsIRO2, OsYSL15, OsIRT1, OsYSL2, OsNAS1, OsNAS2, OsNAS3 and OsDMAS1, just after the onset of Fe starvation
  • IDEF1, OsNAS1, The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes, Time-course expression analyses using quantitative reverse-transcriptase PCR revealed that the IDEF1 expression level was positively correlated with the level of induction of the Fe utilization-related genes OsIRO2, OsYSL15, OsIRT1, OsYSL2, OsNAS1, OsNAS2, OsNAS3 and OsDMAS1, just after the onset of Fe starvation
  • IDEF1, OsIRT1, The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes, Time-course expression analyses using quantitative reverse-transcriptase PCR revealed that the IDEF1 expression level was positively correlated with the level of induction of the Fe utilization-related genes OsIRO2, OsYSL15, OsIRT1, OsYSL2, OsNAS1, OsNAS2, OsNAS3 and OsDMAS1, just after the onset of Fe starvation
  • IDEF1, OsNAS3, The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes, Time-course expression analyses using quantitative reverse-transcriptase PCR revealed that the IDEF1 expression level was positively correlated with the level of induction of the Fe utilization-related genes OsIRO2, OsYSL15, OsIRT1, OsYSL2, OsNAS1, OsNAS2, OsNAS3 and OsDMAS1, just after the onset of Fe starvation
  • IDEF1, OsYSL15, The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes, Time-course expression analyses using quantitative reverse-transcriptase PCR revealed that the IDEF1 expression level was positively correlated with the level of induction of the Fe utilization-related genes OsIRO2, OsYSL15, OsIRT1, OsYSL2, OsNAS1, OsNAS2, OsNAS3 and OsDMAS1, just after the onset of Fe starvation
  • IDEF1, OsNAS2, The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes, Time-course expression analyses using quantitative reverse-transcriptase PCR revealed that the IDEF1 expression level was positively correlated with the level of induction of the Fe utilization-related genes OsIRO2, OsYSL15, OsIRT1, OsYSL2, OsNAS1, OsNAS2, OsNAS3 and OsDMAS1, just after the onset of Fe starvation
  • IDEF1, OsYSL2, The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes, Time-course expression analyses using quantitative reverse-transcriptase PCR revealed that the IDEF1 expression level was positively correlated with the level of induction of the Fe utilization-related genes OsIRO2, OsYSL15, OsIRT1, OsYSL2, OsNAS1, OsNAS2, OsNAS3 and OsDMAS1, just after the onset of Fe starvation
  • IDEF1, IDEF2, The spatial expression and regulation of transcription factors IDEF1 and IDEF2, The iron deficiency-responsive cis-acting element binding factors 1 and 2 (IDEF1 and IDEF2) regulate transcriptional response to iron deficiency in rice roots
  • IDEF1, IDEF2, The spatial expression and regulation of transcription factors IDEF1 and IDEF2, Clarification of the functions of IDEF1 and IDEF2 could uncover the gene regulation mechanism
  • IDEF1, IDEF2, The spatial expression and regulation of transcription factors IDEF1 and IDEF2, METHODS: Spatial patterns of IDEF1 and IDEF2 expression were analysed by histochemical staining of IDEF1 and IDEF2 promoter-GUS transgenic rice lines
  • IDEF1, IDEF2, The spatial expression and regulation of transcription factors IDEF1 and IDEF2, Expression patterns of the target genes of IDEF1 and IDEF2 were analysed using transformants with induced or repressed expression of IDEF1 or IDEF2 grown in iron-rich or in iron-deficient solutions for 1 d
  • IDEF1, IDEF2, The spatial expression and regulation of transcription factors IDEF1 and IDEF2, KEY RESULTS: IDEF1 and IDEF2 were highly expressed in the basal parts of the lateral roots and vascular bundles
  • IDEF1, IDEF2, The spatial expression and regulation of transcription factors IDEF1 and IDEF2, IDEF1 and IDEF2 expression was dominant in leaf mesophyll and vascular cells, respectively
  • IDEF1, IDEF2, The spatial expression and regulation of transcription factors IDEF1 and IDEF2, During seed germination, IDEF1 and IDEF2 were expressed in the endosperm and embryo
  • IDEF1, IDEF2, The spatial expression and regulation of transcription factors IDEF1 and IDEF2, CONCLUSIONS: IDEF1 and IDEF2 are constitutively expressed during both vegetative and reproductive stages
  • IDEF1, IDEF2, The spatial expression and regulation of transcription factors IDEF1 and IDEF2, The spatial expression patterns of IDEF1 and IDEF2 overlap with their target genes in restricted cell types, but not in all cells
  • IDEF1, IDEF2, The spatial expression and regulation of transcription factors IDEF1 and IDEF2, The spatial expression patterns and gene regulation of IDEF1 and IDEF2 in roots are generally conserved under conditions of iron sufficiency and deficiency, suggesting complicated interactions with unknown factors for sensing and transmitting iron-deficiency signals
  • IDEF1, IDEF2, The spatial expression and regulation of transcription factors IDEF1 and IDEF2, The spatial expression and regulation of transcription factors IDEF1 and IDEF2
  • IDEF1, OsHRZ1, Jasmonate signaling is activated in the very early stages of iron deficiency responses in rice roots., Many jasmonate-inducible genes were also negatively regulated by the ubiquitin ligases OsHRZ1 and OsHRZ2 and positively regulated by the transcription factor IDEF1
  • IDEF1, OsHRZ2, Jasmonate signaling is activated in the very early stages of iron deficiency responses in rice roots., Many jasmonate-inducible genes were also negatively regulated by the ubiquitin ligases OsHRZ1 and OsHRZ2 and positively regulated by the transcription factor IDEF1
  • CSN6, IDEF1, CSN6, a subunit of the COP9 signalosome, is involved in early response to iron deficiency in Oryza sativa., In contrast to CSN6, the IDEF1 protein and expression of several iron uptake/utilisation-related genes are increased in response to -Fe
  • CSN6, IDEF1, CSN6, a subunit of the COP9 signalosome, is involved in early response to iron deficiency in Oryza sativa., Thus, we constructed CSN6 transgenic sense and antisense lines and found that experimental depletion of CSN6 results in accumulation of the IDEF1 protein and up-regulation of several iron uptake/utilisation-related genes
  • CSN6, IDEF1, CSN6, a subunit of the COP9 signalosome, is involved in early response to iron deficiency in Oryza sativa., Collectively, the cellular CSN6 level is decreased during early stages of -Fe to ensure the rapid accumulation of IDEF1, which in turn up-regulates several iron uptake/utilisation-related genes to help overcome -Fe stress in rice

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