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Open Access
Abstract: Background and aims: Certain plant species, including some trees, have been observed growing not only in soil but also in soil parent materials. However, the root traits and mechanisms enabling these species to penetrate soil parent materials are not yet thoroughly understood. This systematic review aims to identify and discuss the root traits and mechanisms that allow plant roots to grow into soil parent materials. It will also draw insights from the characteristics and mechanisms that plants employ to overcome the challenges posed by compacted soils. Methods: We adhered to the 'Preferred Reporting Items for Systematic Reviews and Meta-Analyses' (PRISMA) guidelines for our methodology. Results: We identified increased root radial pressure, investment in root biomass, fine root development, root trematotropism, mycorrhizal associations, root hairs, and root exudates as key traits aiding plants in soil penetration. The mentioned root traits and mechanisms have also been shown to help plants overcome compacted soil, except for mycorrhizal associations. Conclusion: The key root traits and mechanisms identified in this review lay the groundwork for a deeper understanding of root-soil parent material interactions and plant adaptations in changing physical environments. This enhances our ability to select the next generation of robust and resilient crops capable of thriving in complex root-soil parent material interactions. Future research on root-parent material interactions in food crops holds promise for improving our understanding of how crops can grow beyond traditional soil limitations (such as soil depth).
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Oct 2025
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I03-Macromolecular Crystallography
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Maria
Meloni
,
Edoardo Jun
Mattioli
,
Silvia
Fanti
,
Ginevra Marie Eloise
Peppi
,
Tancredi
Bin
,
Giuseppe
Gabellini
,
Daniele
Tedesco
,
Julien
Henri
,
Paolo
Trost
,
Stéphane D.
Lemaire
,
Matteo
Calvaresi
,
Simona
Fermani
,
Mirko
Zaffagnini
Diamond Proposal Number(s):
[21741]
Open Access
Abstract: Protein S-nitrosylation is a reversible redox-based post-translational modification that plays an important role in cell signaling by modulating protein function and stability. At the molecular level, S-nitrosylation consists of the formation of a nitrosothiol (-SNO) and is primarily induced by the trans-nitrosylating agent nitrosoglutathione (GSNO). Triosephosphate isomerase (TPI), which catalyzes the interconversion of dihydroxyacetone phosphate and glyceraldehyde-3-phosphate, has been identified as a putative target of S-nitrosylation in both plant and non-plant systems. Here we investigate the molecular basis for GSNO-dependent regulation of chloroplast TPI from the model green alga Chlamydomonas reinhardtii (CrTPI). Molecular modelling identified Cys14 and Cys219 as potential sites for interaction with GSNO, though crystallography of GSNO-treated CrTPI revealed S-nitrosylation only at Cys14. To disclose GSNO target sites, we generated and characterized Cys-to-Ser variants for Cys14 and Cys219, identifying Cys219 as a key residue mediating the GSNO-dependent modulation of CrTPI activity. Molecular dynamics simulations further revealed the stabilizing interactions of nitrosylated cysteines with their local environments. Overall, our results indicate that CrTPI catalysis is modulated by GSNO through a redox-based mechanism involving Cys219, which highlights a conserved regulatory strategy shared with human TPI.
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Sep 2025
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Ekaterina
Kot
,
Matteo P.
Ferla
,
Patricia H.
Hollinshead
,
Charles W. E.
Tomlinson
,
Daren
Fearon
,
Jasmin C.
Aschenbrenner
,
Lizbe
Koekemoer
,
Max
Winokan
,
Michael
Fairhead
,
Xiaomin
Ni
,
Rod
Chalk
,
Katherine S.
England
,
Laura
Ortega Varga
,
Mark
Greer Montgomery
,
Nicholas P.
Mulholland
,
Frank
Von Delft
Diamond Proposal Number(s):
[28172, 34598, 30602, 36049]
Open Access
Abstract: BACKGROUND: In order to alleviate the growing issue of herbicide resistance, diversification of the herbicide portfolio is necessary. A promising yet underutilized mode-of-action is the inhibition of fatty acid thioesterases (FATs), which terminate de novo fatty acid (FA) biosynthesis by releasing FAs from acyl carrier protein (ACP) cofactors. These enzymes impact plant growth and sterility by determining the amount and length of FAs present. In this study we report a crystallographic fragment screening approach for the identification of novel chemical matter targeting FATs. RESULTS: We have solved the crystal structure of Arabidopsis thaliana FatA to 1.5 Å and conducted a crystallographic fragment screen which identified 129 unique fragments bound in 141 different poses. Ten fragments demonstrated on-scale potency, two of these exploiting different interactions to known herbicides. Elaboration of one of the fragments resulted in an improvement of affinity from ~20 μm to ~90 nm KD. Finally, superposition of our crystal structures revealed that some fragments exploit large conformational changes in the substrate binding site. CONCLUSION: We have fully enabled FatA as a target for rapid, rational hit-to-lead development, with robust structural, biophysical and biochemical assays. We provide a set of fragment hits which represent diverse, novel scaffolds that both recapitulate interactions made by current herbicides, and also target novel regions within the active and dimer sites. Our fragments can be readily merged and allow for effective catalogue-based structure–activity relationship (SAR) exploration. Together these data will accelerate the development of novel, alternative herbicides to combat herbicide resistance.
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Sep 2025
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Krios II-Titan Krios II at Diamond
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Diamond Proposal Number(s):
[34108]
Open Access
Abstract: Understanding the molecular basis of regulated nitrogen (N2) fixation is essential for engineering N2-fixing bacteria that fulfill the demand of crop plants for fixed nitrogen, reducing our reliance on synthetic nitrogen fertilizers. In Azotobacter vinelandii and many other members of Proteobacteria, the two-component system comprising the anti-activator protein (NifL) and the Nif-specific transcriptional activator (NifA)controls the expression of nif genes, encoding the nitrogen fixation machinery. The NifL-NifA system evolved the ability to integrate several environmental cues, such as oxygen, nitrogen, and carbon availability. The nitrogen fixation machinery is thereby only activated under strictly favorable conditions, enabling diazotrophs to thrive in competitive environments. While genetic and biochemical studies have enlightened our understanding of how NifL represses NifA, the molecular basis of NifA sequestration by NifL depends on structural information on their interaction. Here, we present mechanistic insights into how nitrogen fixation is regulated by combining biochemical and genetic approaches with a low-resolution cryo-electron microscopy (cryo-EM) map of the oxidized NifL-NifA complex. Our findings define the interaction surface between NifL and NifA and reveal how this interaction can be manipulated to generate bacterial strains with increased nitrogen fixation rates able to secrete surplus nitrogen outside the cell, a crucial step in engineering improved nitrogen delivery to crop plants.
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Sep 2025
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Abstract: Globally, phosphorus (P) is one of the most limiting macronutrients for agricultural production. Humid tropical soils have historically low natural P contents, with most P forming high-binding energy compounds with mineral colloids. No-tillage (NT) systems, where fertilizers are positioned in the furrow, can influence plant nutrient uptake and fertilizer use efficiency. In this study, 31P nuclear magnetic resonance (31P–NMR) and X-ray absorption near-edge structure (XANES) were used to evaluate P species in the soil solid phase and solution, focusing on different positions: crop row, between crop rows, and rhizosphere of soybean [Glycine max (L.) Merr.] and wheat (Triticum spp.) cultivated for 36 years in an Oxisol under NT and conventional tillage (CT, with disc plowing and harrowing). Labile P levels were, on average, 25 % higher in NT compared to CT, mainly due to increases in moderately labile and non-labile fractions (p < 0.05). Total P did not differ between systems, with inorganic P representing 65–69 % of total P. In both crops, P was enriched in the rhizosphere and crop row relative to the between-row position, with orthophosphate accounting for 72–85 % of Na-EDTA-extracted P. XANES and chemical fractionation consistently indicated a predominance of P associated with Fe and Al oxyhydroxides. Additionally, XANES detected phytic acid accumulation in the rhizosphere, suggesting a role for root and microbial processes in shaping organic P dynamics. These results highlight the importance of long-term soil management in enhancing P bioavailability and fertilizer use efficiency in tropical agroecosystems.
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Aug 2025
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DIAD-Dual Imaging and Diffraction Beamline
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James
Le Houx
,
Daniel
Mckay Fletcher
,
Alberto
Leonardi
,
Katherine A.
Williams
,
Nancy
Walker
,
Fernando
Alvarez-Borges
,
Ebrahim
Afsar Dizaj
,
Madhu
Murthy
,
Ronan
Smith
,
Liam
Perera
,
Navid
Aslani
,
Andrew
James
,
Sharif
Ahmed
,
Tiina
Roose
,
Siul
Ruiz
Diamond Proposal Number(s):
[30961, 32138, 33343]
Open Access
Abstract: Soil compaction and escalating global drought increase soil strength and stiffness. It remains unclear which plant root biomechanical mechanisms/traits enable growth in these harsh conditions. Here, we combine synchrotron X-ray computed tomography with spatially resolved X-ray diffraction to characterize the biomechanics of a replica root-soil system. We map the strain field around the root tip analog, finding strong agreement with finite element simulations, thereby demonstrating a promising new in vivo measurement protocol.
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Jul 2025
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Soshichiro
Nagano
,
David
Von Stetten
,
Kaoling
Guan
,
Peng-Yuan
Chen
,
Chen
Song
,
Thomas
Barends
,
Manfred S.
Weiss
,
Christian G.
Feiler
,
Katerina
Dörner
,
Iñaki
De Diego Martinez
,
Robin
Schubert
,
Johan
Bielecki
,
Lea
Brings
,
Huijong
Han
,
Konstantin
Kharitonov
,
Chan
Kim
,
Marco
Kloos
,
Jayanath C. P.
Koliyadu
,
Faisal H. M.
Koua
,
Ekaterina
Round
,
Abhisakh
Sarma
,
Tokushi
Sato
,
Christina
Schmidt
,
Joana
Valerio
,
Agnieszka
Wrona
,
Joachim
Schulz
,
Raphael
De Wijn
,
Romain
Letrun
,
Richard
Bean
,
Adrian
Mancuso
,
Karsten
Heyne
,
Jon
Hughes
Open Access
Abstract: Phytochromes are biliprotein photoreceptors widespread amongst microorganisms and ubiquitous in plants where they control developmental processes as diverse as germination, stem elongation and floral induction through the photoconversion of inactive Pr to the Pfr signalling state. Here we report crystal structures of the chromophore-binding module of soybean phytochrome A, including ~2.2 Å XFEL structures of Pr and Pfr at ambient temperature and high resolution cryogenic structures of Pr. In the Pfr structure, the chromophore is exposed to the medium, the D-ring remaining α-facial following the likely clockwise photoflip. The chromophore shifts within its pocket, while its propionate side chains, their partners as well as three neighbouring tyrosines shift radically. Helices near the chromophore show substantial shifts that might represent components of the light signal. These changes reflect those in bacteriophytochromes despite their quite different signalling mechanisms, implying that fundamental aspects of phytochrome photoactivation have been repurposed for photoregulation in the eukaryotic plant.
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Jun 2025
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B18-Core EXAFS
I14-Hard X-ray Nanoprobe
I20-Scanning-X-ray spectroscopy (XAS/XES)
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Diamond Proposal Number(s):
[25930, 24074, 21441]
Open Access
Abstract: Uranium (U) is a natural radioactive metal and a persistent environmental pollutant. Characterising the influence of arbuscular mycorrhizal fungi (AMF) on U bioaccumulation and partitioning in plants is crucial to understand U soil-to-plant transfer mechanisms. High resolution elemental mapping, spectroscopy and microscopy techniques were conducted on uranyl nitrate dosed Plantago lanceolata roots colonised with Rhizophagus irregularis. U-rich particles accumulated within the root cells, with higher abundance in epidermal and outer cortex cells of mycorrhizal root samples than in non-mycorrhizal roots. Electron microscopy determined two different crystalline U phases, an acicular crystal and a novel rounded aggregate formation, the latter of which was only found within the mycorrhizal root cells. Multiple imaging and spectroscopic techniques enabled the dominant elements with these U biominerals to be determined. Co-localisation between U, phosphorus and oxygen indicated the dominance of U-phosphate biominerals, but metals including calcium and zinc were also found to co-localise. The most dominant U compound was uranyl orthophosphate, likely accompanied by autunite. This study demonstrates alteration in U localisation and U particle morphology within Plantago roots as a direct consequence of AMF colonisation. This knowledge will allow more accurate U food-chain transfer modelling and better assessment of AMF-assisted phytoremediation feasibility.
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Jun 2025
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I04-1-Macromolecular Crystallography (fixed wavelength)
I24-Microfocus Macromolecular Crystallography
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Zak
Mciver
,
Alicia
Moraleda-Montoya
,
Zongjia
Chen
,
Ruwan
Epa
,
David
Starns
,
Matthew
Davy
,
Mikel
Garcia-Alija
,
Arnaud
Basle
,
Mario
Schubert
,
Didier
Ndeh
,
Beatriz
Trastoy
,
Spencer J.
Williams
,
Marcelo E.
Guerin
,
Alan
Cartmell
Diamond Proposal Number(s):
[18598, 30305, 21970]
Open Access
Abstract: Rhamnogalacturonan II is one of the most complex plant cell wall carbohydrates and is composed of 13 different sugars and 21 different glycosidic linkages. It is abundant in fruit and indulgence foods, such as chocolate and wine, making it common in the human diet. The human colonic commensal Bacteroides thetaiotaomicron expresses a consortium of 22 enzymes to metabolise rhamnogalacturonan II, some of which exclusively target sugars unique to rhamnogalacturonan II. Several of these enzyme families remain poorly described, and, consequently, our knowledge of rhamnogalacturonan II metabolism is limited. Chief among the poorly understood activities is glycoside hydrolase (GH) family 139, with targets α1,2-2O-methyl L-fucoside linkages, a sugar residue a sugar not found in any other plant cell wall complex glycans. Although the founding enzyme BT0984 was placed in the RG-II degradative pathway, no GH139 structure or catalytic blueprint had been available. We report the crystal structures of BT0984 and a second homologue, and reveal that the family operates with inverting stereochemistry. Using this data we undertook a mutagenic strategy, backed by molecular dynamics, to identify the important substrate binding and catalytic residues, mapping these residues throughout the GH139 family revealing the importance of the O2 methyl interaction of the substrate. We propose a catalytic mechanism that uses a non-canonical Asn as a catalytic base and shares similarity with L-fucosidases/L-galactosidases of family GH95.
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Jun 2025
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I18-Microfocus Spectroscopy
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Diamond Proposal Number(s):
[33049]
Open Access
Abstract: Risk management for agricultural use of digested sewage sludge requires better understanding of the behaviour and fate of contaminant metals in the plant root zone. A study employing rhizo-pot and plug-tray experiments was conducted to identify the zone near spring barley roots (Hordeum vulgare) where concentration and speciation of Cu and Zn are affected. Cu and Zn bonding environments in the root epidermis/cortex and vascular tissue were also identified. In the digested sludge-amended soil, spring barley absorbed Cu only from the immediate vicinity of the roots (<< 1 mm), but Zn was taken up from further afield (> 1 mm). In the rhizosphere Cu was predominately present as Cu(I) oxides or as Cu(II) absorbed/bonded to phosphate, whereas Zn was present as Zn(II) in inner-sphere complexes with metal oxide surfaces, as Zn(II) sulphides or Zn(II) bonded to/incorporated into carbonates. Cu taken-up by spring barley roots was largely sequestered in the root epidermis and/or cortex predominately in the coordination environments similar to those seen in the rhizosphere. Only a small proportion of the Cu was translocated into the vascular tissue (where it is in the same two bonding environments). Zn taken-up by spring barley roots was present as Zn(II) sulphides, Zn(II) absorbed to/incorporated into carbonates, or Zn(II)-organic complexes. Zn was readily translocated from roots to shoots. Better understanding of these differences in the mobility and uptake of Cu and Zn in sludge-amended agricultural soils could be used to undertake element specific risk assessments.
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May 2025
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