Mariette A, Kang HS, Calabria J
… +9 more, Rautengarten C, Keynton ACW, Czyz A, Rollnik T, Fröhlich A, McFarlane HE, Heazlewood JL, Sampathkumar A, Ebert B
The nucleotide sugar UDP-L-arabinofuranose is made in the cytosol through the interconversion of UDP-L-arabinopyranose by UDP-arabinomutases and subsequently transported into the Golgi lumen by nucleotide sugar transport...The nucleotide sugar UDP-L-arabinofuranose is made in the cytosol through the interconversion of UDP-L-arabinopyranose by UDP-arabinomutases and subsequently transported into the Golgi lumen by nucleotide sugar transporters to provide substrate for arabinosyltransferases, a similar organization seen for many nucleotide sugars. The transport of nucleotide sugars is assumed to be a bottleneck in the biosynthesis of cell wall polysaccharides. Using a biochemical approach, we previously identified four nucleotide sugar transporters that specifically transport UDP-L-arabinofuranose in vitro. However, single loss-of-function mutants affecting these transporters did not show significant reductions in L-arabinose in cell wall extracts or obvious phenotypic differences compared to the wild type. Here we present physiological insights into the role of UDP-L-arabinofuranose transporters in planta through a detailed characterization of higher-order Arabidopsis thaliana mutants. Higher-order mutants contain reduced L-arabinose content, which correlates with developmental phenotypes including reduced plant growth, decreased hypocotyl elongation in the dark and defects in epidermal cells. Similar to the UDP-arabinomutase double mutant, a quadruple mutant of the UDP-L-arabinofuranose transporters is gametophytic male lethal and has collapsed pollen grains. Additionally, analysis of the nucleotide sugar pool in mutant leaves revealed that nucleotide sugar interconversion is affected. Together, our findings demonstrate that the transport of UDP-L-arabinofuranose from the cytosol into the Golgi lumen is a critical step in cell wall biosynthesis and is essential for plant growth, development and reproduction.
Climate change threatens global forest biodiversity, particularly affecting long-lived, endangered tree species. However, the molecular mechanisms underlying their population evolution and environmental adaptation remain...Climate change threatens global forest biodiversity, particularly affecting long-lived, endangered tree species. However, the molecular mechanisms underlying their population evolution and environmental adaptation remain unclear. Here, we employed multi-omics analyses, including pan-genomes, transcriptomics, metabolomics, population genomics, and epigenomics, to decipher nervonic acid biosynthesis and population evolutionary history of the endangered tree Acer miaotaiense. A high-quality, chromosome-level genome of A. miaotaiense was first assembled (645.94 Mb). Pan-genome characterization showed that core genes and structural variation of seven Acer species were enriched in long-chain fatty acid metabolism. Metabolomic and transcriptomic analyses identified AmiaKCS7 and AmiaKCS9 as key regulators of nervonic acid biosynthesis. Population genomics demonstrated east-west divergence, with eastern populations showing elevated inbreeding and deleterious mutations. Especially, the eastern marginal populations represented priority conservation units under global warming due to their heightened genomic vulnerability. Landscape genomics revealed 747 candidate genes involved in local adaptation, particularly to temperature fluctuations and drought stress (eg heat shock protein 20 and major intrinsic protein). Integrated epigenomic analyses further confirmed transposon-associated methylation and lncRNAs modulated heat-responsive environmental adaptation. Our findings establish a foundational resource for understanding the adaptive evolution of A. miaotaiense and pinpoint critical genes and populations essential for its future conservation.
Liu Y, Shi K, Zhang M
… +5 more, Wei J, Feng M, Dayan FE, Tao X, Feng Z
Plant Physiol
· 2026 Jun · PMID 42161891
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Herbicide resistance challenges sustainable weed management in crop fields. However, the lack of gene manipulation tools for weeds hinders studies of herbicide resistance evolution and regulation. Here, we identified tha...Herbicide resistance challenges sustainable weed management in crop fields. However, the lack of gene manipulation tools for weeds hinders studies of herbicide resistance evolution and regulation. Here, we identified that tobacco mosaic virus (TMV) can systemically infect Galium aparine, a noxious broadleaf weed common in wheat and rapeseed fields, among 13 broadleaf weeds. The TMV-based expression system can be used to elucidate herbicide resistance in G. aparine. We demonstrated that virus-based expression of BAR, ALS, and its site-directed mutagenized form in G. aparine plants can impart herbicide resistance. To expand the application of this system in metabolic resistance studies, 10 upregulated P450 genes in the tribenuron-methyl-resistant G. aparine population plants were identified. Expression of these P450 genes in G. aparine via this system enhanced tribenuron-methyl resistance in G. aparine plants. Additionally, we confirmed Eleusine indica CYP81A104 functions in herbicide resistance through heterologous expression in G. aparine plants, suggesting that this system can be used to investigate the roles of genes from other weed species. The TMV vector-based assay system enabled the functional validation of weed genes within 2 months, which is shorter than the time required in other heterologous expression systems (ie, stable expression of weed genes in rice or Arabidopsis). Thus, this virus-based system provides insights into target-site and/or metabolic-based resistance mechanisms to herbicides in G. aparine and possibly in other weed species.
Zhang T, Peng JT, Chu J
… +8 more, Luo S, Lee J, Sánchez Rodríguez DB, Gundran K, Xia X, Garay-Arroyo A, Richardson JA, Dickinson AJ
Plant Physiol
· 2026 May · PMID 42160262
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Citric acid is an integral component of primary metabolism and cellular energetics and plays extensive roles in other cellular processes, such as signaling, chelating, and exudation. Here, we characterized the unique eff...Citric acid is an integral component of primary metabolism and cellular energetics and plays extensive roles in other cellular processes, such as signaling, chelating, and exudation. Here, we characterized the unique effects that citric acid has on Arabidopsis (Arabidopsis thaliana) root structure and development. In particular, we investigated how citric acid modifies 2 root types in opposing ways: by inhibiting primary root growth while promoting anchor root growth. To understand the mechanisms driving these different growth patterns within the same organism, we analyzed nutrient and transcriptomic responses to citric acid treatment in anchor roots and primary roots. High-spatial resolution elemental analysis revealed that root meristems and the root-hypocotyl junction are regions of strong nutrient enrichment, but that citric acid treatment has little effect on nutrient levels in these regions. Transcriptional analysis revealed major differences between primary roots and anchor roots in response to citric acid. In particular, citric acid acted as a reactive oxygen species (ROS) scavenger through increased Class III peroxidase transcription, effectively reducing H2O2 levels both in vitro and in vivo. Altering the ROS balance at the root-hypocotyl junction was sufficient to induce anchor root formation. Citric acid treatment also differentially upregulated lignin biosynthesis, lignin assembly, and ETHYLENE RESPONSE FACTOR 115 expression in primary roots and anchor roots. ETHYLENE RESPONSE FACTOR 115 regulates the quiescent center and root columella, and we found that citric acid treatment induces developmental defects in this tissue. Overall, this study reveals that a vital organic acid produced and secreted at relatively high concentrations has both widespread and specific effects on plant development and root architecture.
Rice (Oryza sativa) is a major staple crop providing both calories and essential microelements such as Zn for humans. Understanding the molecular mechanisms involved in the control of Zn homeostasis may aid in optimizing...Rice (Oryza sativa) is a major staple crop providing both calories and essential microelements such as Zn for humans. Understanding the molecular mechanisms involved in the control of Zn homeostasis may aid in optimizing Zn levels to improve rice growth and maximize its nutritional value. In this study, we aimed to decipher the precise function of ZRT/IRT-like protein 1 (OsZIP1) in Zn uptake and the signaling pathways through which OsZIP1 responds to fluctuations in Zn bioavailability. In contrast to other members of the OsZIP family, OsZIP1 was an atypical low-affinity zinc transporter that did not respond to Zn deficiency through binding of basic leucine zipper transcription factor 50/48 (bZIP50/48) to canonical ZDRE elements. However, OsZIP1 was induced by both depletion and excess of Zn. Excessive Zn triggered Fe deficiency signaling and induced the accumulation of positive regulator of iron deficiency response 2 (OsPRI2), which in turn activated abscisic acid insensitive 5 (OsABI5) expression and drove the upregulation of OsZIP1. By contrast, Zn depletion upregulated the expression of OsZIP1 via unfolded protein response (UPR) signaling. The nuclear isoform of bZIP74, which was generated by alternative splicing in response to Zn depletion, bound to the modified unfolded protein response element (mUPRE) in the promoter of OsZIP1 and enhanced its expression. Our study reveals a pivotal role of a low-affinity transporter in fine-tuning Zn homeostasis and provides an essential node in the control of cellular Zn homeostasis at fluctuating Zn bioavailability.
Plant intracellular immune receptors, mostly nucleotide-binding leucine-rich repeat (NLR) proteins, are tightly regulated to maintain low expression levels under non-infection conditions and to allow induced expression b...Plant intracellular immune receptors, mostly nucleotide-binding leucine-rich repeat (NLR) proteins, are tightly regulated to maintain low expression levels under non-infection conditions and to allow induced expression by pathogens. The extensively studied NLR gene SUPPRESSOR OF NPR1, CONSTITUTIVE 1 (SNC1) is transcriptionally regulated by transcription factors, histone-modifying enzymes, and chromatin remodelers in Arabidopsis (Arabidopsis thaliana). Here, we identified a putative histone chaperone protein, CABIN1 (CALCINEURIN BINDING PROTEIN 1), as a negative regulator of SNC1-mediated plant immunity through a sensitized genetic screen. The cabin1 mutant exhibited enhanced resistance to the bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000. This was accompanied by elevated expression of SNC1 and many defense genes even in the absence of pathogen infection. The enhanced disease resistance in the cabin1 mutant depended on a functional SNC1 gene, and CABIN1 physically bound to the SNC1 promoter region, indicating that SNC1 directly mediates autoimmunity in cabin1. The Arabidopsis CABIN1 protein interacted with HISTONE REGULATOR A (HIRA), similarly in animals. The hira mutant also exhibited enhanced disease resistance and a higher SNC1 expression than the wild type; however, the resistance enhancement did not depend on SNC1 alone. This work identifies regulators of plant immunity and implicates histone chaperones in the regulation of immune gene expression.
Peng H, Huang W, Wang S
… +7 more, Han Z, Li X, Tang H, Ye X, Lu Y, Xu L, Wang K
Plant Physiol
· 2026 May · PMID 42148553
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Engineered wheat produces natural antioxidant pigments in whole plants and flour, enabling healthier, visually distinctive foods and offering a tool to study gene activity in specific tissues.Engineered wheat produces natural antioxidant pigments in whole plants and flour, enabling healthier, visually distinctive foods and offering a tool to study gene activity in specific tissues.
Sun W, Lu Y, Cao Z
… +6 more, Xin C, Fan K, Kong X, Chen X, Zhang M, Chen QJ
Plant Physiol
· 2026 May · PMID 42148549
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An uncleavable fusion of prime editors with the Csy4 CRISPR RNA endonuclease efficiently generates heritable mutations in Arabidopsis with reduced Csy4-associated toxicity.An uncleavable fusion of prime editors with the Csy4 CRISPR RNA endonuclease efficiently generates heritable mutations in Arabidopsis with reduced Csy4-associated toxicity.
Paul K, Kasera M, Takahashi Y
… +3 more, Joo H, Hsu PK, Schroeder JI
Plant Physiol
· 2026 May · PMID 42148548
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A study has suggested that specific protein phosphatases are central CO sensors that control CO2 regulation of stomatal conductance, which could not be unequivocally confirmed here.A study has suggested that specific protein phosphatases are central CO sensors that control CO2 regulation of stomatal conductance, which could not be unequivocally confirmed here.
Calcium (Ca2+) plays a pivotal role in plant reproduction. Pollen tubes exhibit polarized growth regulated, among other factors, by an apical oscillatory Ca2+ gradient. This gradient is controlled by the Ca2+ influx from...Calcium (Ca2+) plays a pivotal role in plant reproduction. Pollen tubes exhibit polarized growth regulated, among other factors, by an apical oscillatory Ca2+ gradient. This gradient is controlled by the Ca2+ influx from the apoplast mediated by plasma membrane channels and the efflux from the cytosol to organelles and the apoplast, which is controlled by pumps and exchangers. Nevertheless, the precise mechanism by which Ca2+ efflux is regulated during pollen tube growth remains unclear. Here, we study the function of the pollen-expressed Arabidopsis thaliana autoinhibited Ca2+ ATPases (ACAs), particularly those localized in the vacuole (ACA4 and ACA11) and in the endoplasmic reticulum (ER) (ACA2 and ACA7). We found that double mutants (aca4-1 aca11-1, aca2-2 aca7-1, and aca2-2 aca11-1) and triple mutants (aca2-2 aca4-1 aca11-1 and aca2-2 aca7-1 aca11-1) show reduced pollen tube growth velocity compared with WT. Moreover, we found that aca4-1 aca11-1 displays a higher frequency of pollen tube growth and cytosolic Ca2+ oscillations, higher amplitude values of Ca2+ oscillations, and slower pollen tube growth compared with WT. Our results suggest that the absence of the 2 pollen vacuolar ACAs (ACA4 and ACA11) has a more pronounced impact on cytosolic Ca2+ dynamics and pollen tube growth than that of the ER ACAs (ACA2 and ACA7). Our findings align with a model in which Ca2+ is transported to internal stores, vacuoles, and the ER, thereby regulating the establishment and maintenance of the Ca2+ gradient during pollen tube growth.
The establishment of a specific pollen wall pattern is essential for pollen development in flowering plants. This process largely depends on the formation of a temporary wall surrounding microspores in tetrads, known as...The establishment of a specific pollen wall pattern is essential for pollen development in flowering plants. This process largely depends on the formation of a temporary wall surrounding microspores in tetrads, known as the primexine, which is primarily composed of Arabinogalactan proteins (AGPs) and polysaccharides. NEF1, a gene identified two decades ago in Arabidopsis thaliana, is required for primexine formation; however, its precise functional mechanism remains unclear. In this study, we generated a nef1 knockout mutant (nef1-2) that exhibits a complete absence of primexine and male sterility. Immuno-fluorescence analysis revealed severe defects in primexine components, including pectin, xylan, and AGPs, in the nef1-2 mutant. Notably, AGPs accumulated abnormally in the tapetum, where material transport was severely disrupted, suggesting that defective AGP accumulation may underlie the primexine deficiency. Fluorescence observations demonstrated that NEF1 is specifically expressed in the tapetum and localizes to the Endoplasmic Reticulum (ER) and Golgi apparatus. Furthermore, when GFP was fused to the N-terminus of NEF1, the protein failed to localize to the Golgi apparatus. Consequently, transgenic plants expressing pNEF1:GFP-NEF1 displayed impaired deposition of both primexine polysaccharides and AGPs, further confirming that proper NEF1 localization is essential for its function. This study improves our understanding of NEF1's role in primexine formation and highlights the contribution of AGPs in pollen wall pattern establishment.
Light intensities in nature fluctuate; however, our understanding of how plants acclimate to changing photon fluxes remains limited. Various chloroplast-located proteins contribute to the ability to tolerate fluctuating...Light intensities in nature fluctuate; however, our understanding of how plants acclimate to changing photon fluxes remains limited. Various chloroplast-located proteins contribute to the ability to tolerate fluctuating light (FL). Here, we show that an Arabidopsis (Arabidopsis thaliana) protein outside chloroplasts is involved in acclimation to FL. Early-Response to Dehydration 6-Like 14 (ERDL14) is a tonoplast-located sugar/H+ antiporter able to pump glucose and sucrose into the vacuole. The ERDL14 promoter contains several elements that enable its activation under high light (HL) and FL conditions, in which standard light intensities (3 mins at 120 µE) are periodically interrupted by short high-light phases (1 min at 1.000 µE). erdl14 loss-of-function mutants do not show phenotypic peculiarities under HL, which coincides with a marked down-regulation of ERDL14 gene expression after 2 days at HL. In contrast, FL treatment impairs erdl14 mutant development, most likely caused by down-regulation of the abundance of proteins involved in primary photosynthetic processes, leading to reduced photosynthetic quantum yield. This decreased abundance of proteins involved in primary photosynthetic processes is connected to increased cytosolic sugar levels in erdl14, indicating a "high-sugar repression", which is prevented in the wild type by the pumping activity of ERDL14. Knock-out mutants lacking other vacuolar sugar importers, i.e. tst1 and tst2, are not as strongly impaired in their ability to cope with FL, indicating a specific function of ERDL14.
Kong D, Meng J, Wang Y
… +4 more, Liu J, Cui W, Li L, Ju C
Plant Physiol
· 2026 May · PMID 42127317
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The ethylene signaling transcription factor EIN3 regulates rooting structure development in a conserved manner in land plants.The ethylene signaling transcription factor EIN3 regulates rooting structure development in a conserved manner in land plants.
Root hairs absorb water and mineral nutrients while anchoring growing root tips. They must navigate through soils of varying mechanical properties. Mechanical changes in their microenvironment affect root hair shape and...Root hairs absorb water and mineral nutrients while anchoring growing root tips. They must navigate through soils of varying mechanical properties. Mechanical changes in their microenvironment affect root hair shape and growth rate, but what underlies these responses has remained elusive. To uncover these mechanisms, we grew seedlings of Arabidopsis thaliana (Col-0) in media with increasing mechanical stiffness. Col-0 seedlings showed both shorter and fewer root hairs with increasing mechanical resistance. We used incipient plasmolysis to estimate turgor pressure in trichoblasts and found that it also decreased with increasing media stiffness. Because cellulose is the major load-bearing polymer in the cell wall and influences cell expansion, we quantified cellulose orientation in root hairs. We found that cellulose fibrils were oriented at steeper angles relative to the growth axis in root hairs grown in stiffer media, suggesting a response to mechanical stress. Cell wall thickness also increased with increasing media stiffness. Microtubule orientations followed patterns that were similar to those of cellulose fibrils, but at a smaller angle relative to the growth axis, whereas microtubule density decreased with increasing media stiffness. Unexpectedly, we observed that root hairs grew faster in stiffer media, implying that their growth is misregulated, potentially triggering wall integrity signaling that causes early growth arrest. Finite element modeling of root hairs predicted decreased surface stress, explaining these growth phenotypes. These findings help establish mechanistic links among mechanotransduction, cytoskeletal dynamics, and cell wall assembly during root hair growth.