FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (OsFIT) interacts with OsIRO2 to regulate iron homeostasis

ABSTRACTThere are two Fe-uptake strategies for maintaining Fe homeostasis in plants. As a special graminaceous plant, rice applies both strategies. However, it remains unclear how these two strategies are regulated in rice. IRON-RELATED BHLH TRANSCRIPTION FACTOR 2 (OsIRO2) is critical for regulating Fe uptake in rice. In this study, we identified an interacting partner of OsIRO2, Oryza sativa FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (OsFIT), which encodes a bHLH transcription factor. The OsIRO2 protein is localized in the cytoplasm and nucleus, but OsFIT facilitates the accumulation of OsIRO2 in the nucleus. Loss-of-function mutations to OsFIT result in decreased Fe accumulation, severe Fe-deficiency symptoms, and disrupted expression of Fe-uptake genes. In contrast, OsFIT overexpression promotes Fe accumulation and the expression of Fe-uptake genes. Genetic analyses indicated that OsFIT and OsIRO2 function in the same genetic node. Further analysis suggested that OsFIT and OsIRO2 form a functional transcription activation complex to initiate the expression of Fe-uptake genes. Our findings provide a mechanism understanding of how rice maintains Fe homeostasis.One-sentence summaryOsFIT interacts with and facilitates the accumulation of OsIRO2 in the nucleus where the OsFIT-OsIRO2 transcription complex initiates the transcription of Fe deficiency responsive genes.

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FIT, a regulatory hub for iron deficiency and stress signaling in roots, and FIT-dependent and -independent gene signatures

Journal of Experimental Botany ◽

10.1093/jxb/eraa012 ◽

2020 ◽

Vol 71 (5) ◽

pp. 1694-1705 ◽

Cited By ~ 8

Author(s):

Birte Schwarz ◽

Petra Bauer

Keyword(s):

Transcription Factor ◽

Protein Interactions ◽

Fe Deficiency ◽

Bhlh Transcription Factor ◽

Root Cells ◽

Gene Signatures ◽

Helix Loop Helix ◽

Independent Gene ◽

Fe Uptake ◽

Fe Acquisition

Abstract Iron (Fe) is vital for plant growth. Plants balance the beneficial and toxic effects of this micronutrient, and tightly control Fe uptake and allocation. Here, we review the role of the basic helix–loop–helix (bHLH) transcription factor FIT (FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR) in Fe acquisition. FIT is not only essential, it is also a central regulatory hub in root cells to steer and adjust the rate of Fe uptake by the root in a changing environment. FIT regulates a subset of root Fe deficiency (–Fe) response genes. Based on a combination of co-expression network and FIT-dependent transcriptome analyses, we defined a set of FIT-dependent and FIT-independent gene expression signatures and co-expression clusters that encode specific functions in Fe regulation and Fe homeostasis. These gene signatures serve as markers to integrate novel regulatory factors and signals into the –Fe response cascade. FIT forms a complex with bHLH subgroup Ib transcription factors. Furthermore, it interacts with key regulators from different signaling pathways that either activate or inhibit FIT function to adjust Fe acquisition to growth and environmental constraints. Co-expression clusters and FIT protein interactions suggest a connection of –Fe with ABA responses and root cell elongation processes that can be explored in future studies.

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Oryza sativa FER‐LIKE FE DEFICIENCY‐INDUCED TRANSCRIPTION FACTOR (OsFIT/OsbHLH156) interacts with OsIRO2 to regulate iron homeostasis

Journal of Integrative Plant Biology ◽

10.1111/jipb.12933 ◽

2020 ◽

Vol 62 (5) ◽

pp. 668-689 ◽

Cited By ~ 8

Author(s):

Gang Liang ◽

Huimin Zhang ◽

Yang Li ◽

Mengna Pu ◽

Yujie Yang ◽

...

Keyword(s):

Transcription Factor ◽

Oryza Sativa ◽

Iron Homeostasis ◽

Fe Deficiency

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Putative cis-regulatory elements predict iron deficiency responses in Arabidopsis roots

10.1101/603290 ◽

2019 ◽

Author(s):

Birte Schwarz ◽

Christina B. Azodi ◽

Shin-Han Shiu ◽

Petra Bauer

Keyword(s):

Transcription Factor ◽

Iron Deficiency ◽

Large Scale ◽

Computational Models ◽

Regulatory Elements ◽

Transport Systems ◽

Fe Deficiency ◽

Grass Species ◽

Bhlh Transcription Factor ◽

Fe Uptake

AbstractIron (Fe) is a key cofactor in many cellular redox processes, including respiration and photosynthesis. Plant Fe deficiency (-Fe) activates a complex regulatory network which coordinates root Fe uptake and distribution to sink tissues, while avoiding over-accumulation of Fe and other metals to toxic levels. In Arabidopsis (Arabidopsis thaliana), FIT (FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR), a bHLH transcription factor (TF), is required for up-regulation of root Fe acquisition genes. However, other root and shoot -Fe-induced genes involved in Fe allocation and signaling are FIT-independent. The cis-regulatory code, i.e. the cis-regulatory elements (CREs) and their combinations that regulate plant -Fe-responses, remains largely elusive. Using Arabidopsis genome and transcriptome data, we identified over 100 putative CREs (pCREs) that were predictive of -Fe-induced up-regulation of genes in root tissue. We used large-scale in vitro TF binding data, association with FIT-dependent or FIT-independent co-expression clusters, positional bias, and evolutionary conservation to assess pCRE properties and possible functions. In addition to bHLH and MYB TFs, also B3, NAC, bZIP, and TCP TFs might be important regulators for -Fe responses. Our approach uncovered IDE1 (Iron Deficiency-responsive Element 1), a -Fe response CRE in grass species, to be conserved in regulating genes for biosynthesis of Fe-chelating compounds also in Arabidopsis. Our findings provide a comprehensive source of cis-regulatory information for -Fe-responsive genes, that advances our mechanistic understanding and informs future efforts in engineering plants with more efficient Fe uptake or transport systems.One sentence summary>100 putative cis-regulatory elements robustly predict Arabidopsis root Fe deficiency-responses in computational models, and shed light on the mechanisms of transcriptional regulation.

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IRON MAN interacts with BRUTUS to maintain iron homeostasis in Arabidopsis

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2109063118 ◽

2021 ◽

Vol 118 (39) ◽

pp. e2109063118

Author(s):

Yang Li ◽

Cheng Kai Lu ◽

Chen Yang Li ◽

Ri Hua Lei ◽

Meng Na Pu ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Transcription Factors ◽

Iron Homeostasis ◽

Fe Deficiency ◽

Small Peptides ◽

Interaction Domain ◽

C Terminus ◽

Positive Regulators ◽

Fe Homeostasis ◽

And Function

IRON MAN (IMA) peptides, a family of small peptides, control iron (Fe) transport in plants, but their roles in Fe signaling remain unclear. BRUTUS (BTS) is a potential Fe sensor that negatively regulates Fe homeostasis by promoting the ubiquitin-mediated degradation of bHLH105 and bHLH115, two positive regulators of the Fe deficiency response. Here, we show that IMA peptides interact with BTS. The C-terminal parts of IMA peptides contain a conserved BTS interaction domain (BID) that is responsible for their interaction with the C terminus of BTS. Arabidopsis thaliana plants constitutively expressing IMA genes phenocopy the bts-2 mutant. Moreover, IMA peptides are ubiquitinated and degraded by BTS. bHLH105 and bHLH115 also share a BID, which accounts for their interaction with BTS. IMA peptides compete with bHLH105/bHLH115 for interaction with BTS, thereby inhibiting the degradation of these transcription factors by BTS. Genetic analyses suggest that bHLH105/bHLH115 and IMA3 have additive roles and function downstream of BTS. Moreover, the transcription of both BTS and IMA3 is activated directly by bHLH105 and bHLH115 under Fe-deficient conditions. Our findings provide a conceptual framework for understanding the regulation of Fe homeostasis: IMA peptides protect bHLH105/bHLH115 from degradation by sequestering BTS, thereby activating the Fe deficiency response.

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Glutathione regulates subcellular iron homeostasis via transcriptional activation of iron responsive genes in Arabidopsis

10.1101/2021.05.09.443283 ◽

2021 ◽

Author(s):

Ranjana Shee ◽

Soumi Ghosh ◽

Pinki Khan ◽

Salman Sahid ◽

Chandan Roy ◽

...

Keyword(s):

Transcription Factors ◽

Transcriptional Activation ◽

Iron Homeostasis ◽

Fe Deficiency ◽

Fe Content ◽

Increased Sensitivity ◽

Fe Homeostasis ◽

Bhlh Transcription Factors ◽

Dependent Pathway

Glutathione (GSH) is a ubiquitous molecule known to regulate various physiological and developmental phenomena in plants. Recently, its involvement in regulating iron (Fe) deficiency response was established in Arabidopsis. However, the role of GSH in modulating subcellular Fe homeostasis remained elusive. In this study, we dissected the role of GSH in regulating Fe homeostasis in Arabidopsis shoots under Fe limited conditions. The two GSH depleted mutants, cad2-1 and pad2-1 displayed increased sensitivity to Fe deficiency with smaller rosette diameter and higher chlorosis level compared with the Col-0 plants. Interestingly, the expression of the vacuolar Fe exporters, AtNRAMP3 and AtNRAMP4, chloroplast Fe importer, AtPIC1, along with AtFer1 and AtIRT1 were significantly down-regulated in these mutants. The expression of these genes were up-regulated in response to exogenous GSH treatment while treatment with BSO, a GSH inhibitor, down-regulated their expression. Moreover, the mutants accumulated higher Fe content in the vacuole and lower in the chloroplast compared with Col-0 under Fe limited condition suggesting a role of GSH in modulating subcellular Fe homeostasis. This regulation was, further, found to involve a GSNO-dependent pathway. Promoter analysis revealed that GSH induced the transcription of these genes presumably via S-nitrosylation of different Fe responsive bHLH transcription factors.

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bHLH transcription factor bHLH115 regulates iron homeostasis in Arabidopsis thaliana

Journal of Experimental Botany ◽

10.1093/jxb/erx043 ◽

2017 ◽

Vol 68 (7) ◽

pp. 1743-1755 ◽

Cited By ~ 57

Author(s):

Gang Liang ◽

Huimin Zhang ◽

Xiaoli Li ◽

Qin Ai ◽

Diqiu Yu

Keyword(s):

Arabidopsis Thaliana ◽

Transcription Factor ◽

Iron Homeostasis ◽

Bhlh Transcription Factor

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Annotation and Molecular Characterisation of the TaIRO3 and TaHRZ Iron Homeostasis Genes in Bread Wheat (Triticum aestivum L.)

Genes ◽

10.3390/genes12050653 ◽

2021 ◽

Vol 12 (5) ◽

pp. 653

Author(s):

Oscar Carey-Fung ◽

Jesse T. Beasley ◽

Alexander A. T. Johnson

Keyword(s):

Triticum Aestivum ◽

Bread Wheat ◽

Iron Homeostasis ◽

Zinc Finger Protein ◽

Expression Profiles ◽

Diploid Species ◽

Triticum Aestivum L ◽

Fe Deficiency ◽

Pcr Analysis ◽

Fe Homeostasis

Effective maintenance of plant iron (Fe) homoeostasis relies on a network of transcription factors (TFs) that respond to environmental conditions and regulate Fe uptake, translocation, and storage. The iron-related transcription factor 3 (IRO3), as well as haemerythrin motif-containing really interesting new gene (RING) protein and zinc finger protein (HRZ), are major regulators of Fe homeostasis in diploid species like Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa L.), but remain uncharacterised in hexaploid bread wheat (Triticum aestivum L.). In this study, we have identified, annotated, and characterised three TaIRO3 homoeologs and six TaHRZ1 and TaHRZ2 homoeologs in the bread wheat genome. Protein analysis revealed that TaIRO3 and TaHRZ proteins contain functionally conserved domains for DNA-binding, dimerisation, Fe binding, or polyubiquitination, and phylogenetic analysis revealed clustering of TaIRO3 and TaHRZ proteins with other monocot IRO3 and HRZ proteins, respectively. Quantitative reverse-transcription PCR analysis revealed that all TaIRO3 and TaHRZ homoeologs have unique tissue expression profiles and are upregulated in shoot tissues in response to Fe deficiency. After 24 h of Fe deficiency, the expression of TaHRZ homoeologs was upregulated, while the expression of TaIRO3 homoeologs was unchanged, suggesting that TaHRZ functions upstream of TaIRO3 in the wheat Fe homeostasis TF network.

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Loss of function of bHLH transcription factor Nrd1 in tomato induces an arabinogalactan protein-encoding gene and enhances resistance to Pseudomonas syringae pv. tomato

10.1101/2021.11.08.467746 ◽

2021 ◽

Author(s):

Ning Zhang ◽

Chloe Hecht ◽

Xuepeng Sun ◽

Zhangjun Fei ◽

Gregory B Martin

Keyword(s):

Transcription Factor ◽

Pseudomonas Syringae ◽

Transcript Abundance ◽

Negative Regulator ◽

Arabinogalactan Protein ◽

Bhlh Transcription Factor ◽

Dependent Manner ◽

Rna Seq ◽

Loss Of Function ◽

Encoding Gene

Basic helix-loop-helix (bHLH) transcription factors constitute a superfamily in eukaryotes but their roles in plant immunity remain largely uncharacterized. We found that the transcript abundance in tomato leaves of one bHLH transcription factor-encoding gene, Nrd1 (negative regulator of resistance to DC3000 1), was significantly increased after treatment with the immunity-inducing flgII-28 peptide. Plants carrying a loss-of-function mutation in Nrd1 (Δnrd1) showed enhanced resistance to Pseudomonas syringae pv. tomato (Pst) DC3000 although early pattern-triggered immunity responses such as generation of reactive oxygen species and activation of mitogen-activated protein kinases after treatment with flagellin-derived flg22 and flgII-28 peptides were unaltered compared to wild-type plants. An RNA-Seq analysis identified a gene, Agp1, whose expression is strongly suppressed in an Nrd1-dependent manner. Agp1 encodes an arabinogalactan protein and overexpression of the Agp1 gene in Nicotiana benthamiana led to ~10-fold less Pst growth compared to the control. These results suggest that the Nrd1 protein promotes tomato susceptibility to Pst by suppressing the defense gene Agp1. RNA-Seq also revealed that loss of Nrd1 function has no effect on the transcript abundance of immunity-associated genes including Bti9, Core, Fls2, Fls3 and Wak1 upon Pst inoculation, suggesting that the enhanced immunity observed in the Δnrd1 mutants is due to the activation of key PRR signaling components as well as loss of Nrd1-regulated suppression of Agp1.

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