Shedding light on iron nutrition: exploring intersections of transcription factor cascades in light and iron deficiency signaling

Abstract

In the dynamic environment of plants, the interplay between light-dependent growth and iron nutrition is a recurring challenge. Plants respond to low iron levels by adjusting growth and physiology through enhanced iron acquisition from the rhizosphere and internal iron pool reallocation. Iron deficiency response assays and gene co-expression networks aid in documenting physiological reactions and unraveling gene-regulatory cascades, offering insight into the interplay between hormonal and external signaling pathways. However, research directly exploring the significance of light in iron nutrition remains limited. This review provides an overview on iron deficiency regulation and its cross-connection with distinct light signals, focusing on transcription factor cascades and long-distance signaling. The circadian clock and retrograde signaling influence iron uptake and allocation. The light-activated shoot-to-root mobile transcription factor ELONGATED HYPOCOTYL5 (HY5) affects iron homeostasis responses in roots. Blue light triggers the formation of biomolecular condensates containing iron deficiency-induced protein complexes. The potential of exploiting the connection between light and iron signaling remains underutilized. With climate change and soil alkalinity on the rise, there is a need to develop crops with improved nutrient use efficiency and modified light dependencies. More research is needed to understand and leverage the interplay between light signaling and iron nutrition.

Keywords: BTS; FIT; HY5; SR45; bHLH; biomolecular condensate; blue light; circadian clock; iron; long-distance signaling.

Fig. 1.

Overview of iron acquisition and allocation and iron deficiency response assays (example of Arabidopsis thaliana). (A) Iron is mobilized in the rhizosphere, acquired by roots, and transported from root to shoot. A. thaliana is a Strategy I plant, that secretes coumarins, acidifies the rhizosphere, reduces ferric iron (Fe³⁺), and takes up ferrous iron (Fe²⁺). PM, plasma membrane; FRO2, FERRIC REDUCTASE OXIDASE2; IRT1, IRON-REGULATED TRANSPORTER1. (B) Iron deficiency responses are studied by growing plants on agar plates or in hydroponic medium and exposing plants to iron-sufficient and -deficient conditions. Various responses can be qualitatively and quantitatively analyzed in shoots and roots. The figure has been created with Biorender.com. Iron-deficient and -sufficient plant growth phenotypes are shown for hydroponic growth.

Fig. 2.

bHLH transcription factor cascade regulating plant iron homeostasis. The iron homeostasis pathway in plants is tightly regulated by bHLH transcription factors, E3 ligases, and other proteins. (A) E3 ligases, such as BTS (BRUTUS) and BTSL (BTS-like) proteins, can control the protein levels of bHLH IVc transcription factors by targeting them for proteasomal degradation. During iron deficiency, IMA (IRON MAN) proteins may repress BTS/L function by direct binding and serving as an alternative target for degradation, thereby increasing the abundance of bHLH IVc proteins. (B) Transcriptional cascade leading to iron deficiency responses. Interaction of bHLH IVc and IVb transcription factors leads to downstream targeting of another bHLH subgroup IVb member PYE (POPEYE) and the bHLH subgroup Ib (bHLH38, bHLH39, bHLH100, and bHLH101) for transcriptional regulation; for example, bHLH IVc plus URI (UPSTREAM REGULATOR OF IRT1)/bHLH121 leads to activation, while bHLH IVc plus bHLH11 leads to de-activation. Active PYE protein represses the expression of certain target genes, FRO3 (FERRIC REDUCTASE OXIDASE3), NAS4 (NICOTIANAMINE SYNTHASE4), ZIF1 (ZINC FACILITATOR1), and BHLH IB, which causes iron redistribution. On the other hand, bHLH Ib transcription factors activate root iron acquisition by heterodimerization with a central regulator, FIT (FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR), leading to the activation of root-induced genes FRO2 (FERRIC REDUCTASE OXIDASE2) and IRT1 (IRON-REGULATED TRANSPORTER1). The dashed line indicates that regulation of target genes by bHLH IVc and IVb is also possible. The color code indicates distinct patterns of gene regulation: ‘blue’ color, iron deficiency-induced and FIT-dependent, acting primarily in seedling roots; ‘red’ color, iron deficiency-induced, but not dependent on FIT, acting in seedling roots and shoots; ‘rose’ color, not induced by iron deficiency, not dependent on FIT, acting in seedling roots and shoots. References are mentioned in the text. The figure has been created with Biorender.com.

Fig. 3.

Light-dependent regulation of iron homeostasis. Different light conditions or darkness can influence iron acquisition and allocation positively or negatively, as indicated by black arrows. Red and blue light, in contrast to darkness and far-red light, can up- and down-regulate genes as represented by green and red arrows. The color code of iron deficiency components is as in Fig. 2. The circadian clock regulates iron homeostasis. Iron deficiency results in lengthening of the circadian period. The circadian clock components, CCA1 (CIRCADIAN CLOCK ASSOCIATED1) and TIC (TIME FOR COFFEE), may directly interfere with promoters of iron deficiency response genes or the iron sufficiency marker FER1 (FERRITIN1). Retrograde signaling in chloroplasts, high light, and ethylene may intersect and control iron homeostasis. References are mentioned in the text. The figure has been created with Biorender.com.

Fig. 4.

Long-distance signaling of the iron status, indicating the presence of diverse systemic iron signals. (A–C) Examples of three methods employed to reveal the importance of systemic shoot-to-root iron signals. (A) Reciprocal grafting using leaf iron-overaccumulating mutants such as brz (bronze) and dgl (degenerate leaflet) of pea (Pisum sativum) showed the existence of a long-distance shoot-to-root iron deficiency signal constitutively promoting root iron uptake and allocation towards leaves. (B) Foliar iron application to iron-deficient plants leads to a down-regulation of root iron uptake responses due to iron sufficiency signals. However, foliar application does not rescue the pea dgl and Arabidopsis thaliana opt3 mutant defective in OLIGOPEPTIDE TRANSPORTER3, a component involved in the transmission of the long-distance iron sufficiency signal in the phloem. (C) Split root assays have demonstrated that iron uptake can be increased in response to local and systemic iron deficiency signals in root halves exposed to iron but not in root halves maintained in iron deficiency conditions. (D) HY5 (ELONGATED HYPOCOTYL5) is a regulator of iron homeostasis in roots. Light leads to activation of various photoreceptors, for example in response to red and blue light. Active photoreceptors inhibit the COP1 (CONSTITUTIVE PHOTOMORPHOGENIC1)–SPA (SUPPRESSOR OF PHYTOCHROME A) complex, thereby preventing degradation of HY5. A small pool of HY5 remains phosphorylated under the activity of SPA and is inactive even in the light. PPK1 is a photoregulatory protein kinase acting upon HY5. Active non-phosphorylated HY5 accumulates in light conditions and acts as a mobile signal in roots to induce various responses related to iron, as shown by studies in A. thaliana, tomato (Solanum lycopersicum), and apple (Malus baccata). In A. thaliana, HY5 can directly control expression of some genes for iron acquisition and allocation. Alternatively, HY5 may also indirectly control iron homeostasis as a consequence of its functioning in hormone and copper homeostasis. In tomato, HY5 can interfere with the action of FER, an ortholog of FIT. In apple, HY5 acts on a YELLOWSTRIPE-LIKE transporter gene (YSL7). References are mentioned in the text. The figure has been created with Biorender.com.

Fig. 5.

Blue light-dependent accumulation of iron deficiency response regulators in subnuclear biomolecular condensates. FIT and bHLH39 can form condensates, which are light inducible, reversible, highly dynamic, and probably formed due to liquid–liquid phase separation. The subnuclear bodies may contain speckle components, such as SR45 (ARGININE/SERINE-RICH45), and photobody components such as PIF (PHYTOCHROME-INTERACTING TRANSCRIPTION FACTOR) proteins. The figure has been created with Biorender.com.