Uptake mechanism of iron-phytosiderophore from the soil based on the structure of yellow stripe transporter

Atsushi Yamagata (), Yoshiko Murata, Kosuke Namba, Tohru Terada, Shuya Fukai and Mikako Shirouzu
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Atsushi Yamagata: RIKEN Center for Biosystems Dynamics Research
Yoshiko Murata: Suntory Foundation for Life Sciences
Kosuke Namba: Tokushima University
Tohru Terada: The University of Tokyo
Shuya Fukai: Kyoto University
Mikako Shirouzu: RIKEN Center for Biosystems Dynamics Research

Nature Communications, 2022, vol. 13, issue 1, 1-12

Abstract: Abstract Calcareous soils cover one-third of all land and cause severe growth defects in plants due to the poor water solubility of iron at high pH. Poaceae species use a unique chelation strategy, whereby plants secrete a high-affinity metal chelator, known as phytosiderophores (mugineic acids), and reabsorb the iron-phytosiderophore complex by the yellow stripe 1/yellow stripe 1-like (YS1/YSL) transporter for efficient uptake of iron from the soil. Here, we present three cryo-electron microscopy structures of barley YS1 (HvYS1) in the apo state, in complex with an iron-phytosiderophore complex, Fe(III)-deoxymugineic acid (Fe(III)–DMA), and in complex with the iron-bound synthetic DMA analog (Fe(III)–PDMA). The structures reveal a homodimeric assembly mediated through an anti-parallel β-sheet interaction with cholesterol hemisuccinate. Each protomer adopts an outward open conformation, and Fe(III)–DMA is bound near the extracellular space in the central cavity. Fe(III)–PDMA occupies the same binding site as Fe(III)–DMA, demonstrating that PDMA can function as a potent fertilizer in an essentially identical manner to DMA. Our results provide a structural framework for iron-phytosiderophore recognition and transport by YS1/YSL transporters, which will enable the rational design of new, high-potency fertilizers.

Date: 2022
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DOI: 10.1038/s41467-022-34930-1

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