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Article
| Open AccessDefense against phytopathogens relies on efficient antimicrobial protein secretion mediated by the microtubule-binding protein TGNap1
Defining plant defense machinery against pathogens is significant in cell biology and crop yield. TGNap1, a TGN and microtubule-binding protein, is required for defense and efficient anti-microbial protein secretion, linking secretion and cytoskeleton.
- Deepak D. Bhandari
- , Dae Kwan Ko
- & Federica Brandizzi
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Article
| Open AccessUV-B irradiation-activated E3 ligase GmILPA1 modulates gibberellin catabolism to increase plant height in soybean
Gibberellins (GA) negatively regulate UVB-mediated suppression of plant height in plants. Here, the authors show that GmILPA1-mediated degradation of GmGA2ox-like protein counteract the UV-B-mediated reduction of bioactive GAs contributing to the linkage between the affection of UV-B and GA on plant height of soybean.
- Jiaqi Sun
- , Shiyu Huang
- & Fengning Xiang
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Article
| Open AccessThe pan-genome and local adaptation of Arabidopsis thaliana
Single reference genomes and short-read sequencing data are not enough to harness the full genetic variation of a species. Here, the authors report pan-genome of Arabidopsis thaliana based on chromosomal-level genomes of 32 accessions and identify variations associated with local adaptation.
- Minghui Kang
- , Haolin Wu
- & Jianquan Liu
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Article
| Open AccessA natural mutation in the promoter of Ms-cd1 causes dominant male sterility in Brassica oleracea
A dominant genic male sterility (DGMS) mutant of Brassica oleracea was identified in 1970s and has been widely used for hybrid cabbage breeding, but its genetic basis is unclear. Here, the authors reveal that a 1-bp deletion in the promoter of the gene encoding a PHD-finger motif transcription factor is responsible for DGMS.
- Fengqing Han
- , Kaiwen Yuan
- & Honghao Lv
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Article
| Open AccessEfficient plant genome engineering using a probiotic sourced CRISPR-Cas9 system
In the field of plant genome engineering, new nucleases with improved editing efficiency and alterative PAM requirements are needed. Here, the authors report a probiotic sourced CRISPR-LrCas9 system with similar PAM requirement to Cas12a and show its high efficiencies in various genome editing applications.
- Zhaohui Zhong
- , Guanqing Liu
- & Yong Zhang
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Article
| Open AccessCloning of the wheat leaf rust resistance gene Lr47 introgressed from Aegilops speltoides
Leaf rust is one of the most severe foliar diseases of wheat. Here, the authors report the cloning of Lr47, a broadly effective leaf rust resistance gene introgressed into wheat from Aegilops speltoides, and show it encodes a coiled-coil nucleotide-binding leucine-rich repeat protein.
- Hongna Li
- , Lei Hua
- & Shisheng Chen
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Article
| Open AccessA global-temporal analysis on Phytophthora sojae resistance-gene efficacy
Rps genes are used to manage the major soybean pathogen Phytophthora sojae, which causes Phytophthora stem and root rot (PRR). Here, the authors show that widely used Rps genes are no longer effective for managing PRR in the United States, Canada and Argentina.
- Austin G. McCoy
- , Richard R. Belanger
- & Martin I. Chilvers
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Article
| Open AccessAlphaFold-Multimer predicts cross-kingdom interactions at the plant-pathogen interface
AlphaFold-Multimer was used to screen of 1,879 small secreted proteins from plant pathogens to be inhibitors of six tomato defense enzymes. Four of these inhibit subtilase P69B, showing the use of AI to predict cross-kingdom protein interactions.
- Felix Homma
- , Jie Huang
- & Renier A. L. van der Hoorn
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Article
| Open AccessEarthworms contribute significantly to global food production
Earthworms contribute to plant growth. Here, Fonte et al. conduct a global meta-analysis and estimate that earthworms contribute to roughly 6.5% of global grain (maize, rice, wheat, barley) production and 2.3% of legume yields, equivalent to over 140 million metric tons annually.
- Steven J. Fonte
- , Marian Hsieh
- & Nathaniel D. Mueller
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Article
| Open AccessA de novo evolved gene contributes to rice grain shape difference between indica and japonica
Genetic bases of grain shape differentiation between the two subspecies of Asian cultivated rice have not been fully elucidated. Here, the authors report GSE9, a de novo gene evolved from a non-coding region of wild rice through acquisition of start codon, contributes to the grain shape difference between the two subspecies.
- Rujia Chen
- , Ning Xiao
- & Zefeng Yang
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Article
| Open AccessSeasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation
Long-term monitoring of plants in field fluctuating environments remains challenging. Here, the authors develop PlantServation, a machine learning-based phenotyping method, and estimate environmental and genotypic effects on the pigment anthocyanin content of diploid and polyploid Arabidopsis.
- Reiko Akiyama
- , Takao Goto
- & Kentaro K. Shimizu
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Article
| Open AccessThe CBL1/9-CIPK1 calcium sensor negatively regulates drought stress by phosphorylating the PYLs ABA receptor
ABA signaling and Ca2+ signaling regulatory networks are crucial for how plants respond to drought stress. Here, the authors reported that the functional module of the CBL1/9-CIPK1-PYLs regulatory network plays a negative role in ABA signaling and its response to drought stress.
- Zhang You
- , Shiyuan Guo
- & Cun Wang
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Article
| Open AccessMechanodetection of neighbor plants elicits adaptive leaf movements through calcium dynamics
Pantazopoulou et al. discovered that leaves sense neighbors by mutual touching of hairs on their surface, called trichomes. Using fluorescent biosensors, they show that this triggers a calcium wave to activate leaf movement away from competitors
- Chrysoula K. Pantazopoulou
- , Sara Buti
- & Ronald Pierik
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Article
| Open AccessNET4 and RabG3 link actin to the tonoplast and facilitate cytoskeletal remodelling during stomatal immunity
Protein tethers can bridge the actin cytoskeleton with cellular membranes. Here, the authors show that two members of the NETWORKED family, NET4A and NET4B, tether actin filaments and the tonoplast through interaction with RABG3b and are essential for actin reorganization during stomatal closure in plant immunity.
- Timothy J. Hawkins
- , Michaela Kopischke
- & Silke Robatzek
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Article
| Open AccessAuxin-producing bacteria promote barley rhizosheath formation
The rhizosheath, or the soil layer closely attached to roots, can help plants tolerate drought. Here, the authors show that rhizosheath formation in barley is promoted by soil bacteria that produce indole-3-acetic acid, a common auxin.
- Feiyun Xu
- , Hanpeng Liao
- & Weifeng Xu
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Article
| Open AccessNatural plant growth and development achieved in the IPK PhenoSphere by dynamic environment simulation
The PhenoSphere is a unique plant cultivation facility in which field-like environments can be simulated. Here, the authors find that a single season simulation is superior to an averaged season and to a climatized glasshouse cultivation to elicit field-like phenotypes evaluated in 11 maize lines.
- Marc C. Heuermann
- , Dominic Knoch
- & Thomas Altmann
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Article
| Open AccessControl of arbuscule development by a transcriptional negative feedback loop in Medicago
Zhang et al. report that Medicago AR2/ERF transcription regulators WRI5a-ERM1-ERF12 form a transcriptional negative feedback loop to coordinate arbuscular lipid supply, enabling the maintenance of a stable, reciprocally beneficial symbiosis.
- Qiang Zhang
- , Shuangshuang Wang
- & Yina Jiang
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Article
| Open AccessUstilago maydis PR-1-like protein has evolved two distinct domains for dual virulence activities
Plant PR-1 proteins participate in defense responses against pathogens. Here, the authors show that PR-1-like proteins from the plant pathogenic fungus Ustilago maydis are important for virulence by detecting plant-derived phenolics and modulating plant PR-1-mediated defenses.
- Yu-Han Lin
- , Meng-Yun Xu
- & Lay-Sun Ma
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Article
| Open AccessArabidopsis TCP4 transcription factor inhibits high temperature-induced homeotic conversion of ovules
Global warming threatens food security and plant survival. This paper demonstrates that Class II TCP transcription factors are critical for specifying ovule identity and inhibiting the conversion of ovules into carpelloids under high temperature.
- Jingqiu Lan
- , Ning Wang
- & Genji Qin
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Article
| Open AccessHigh-efficiency green management of potato late blight by a self-assembled multicomponent nano-bioprotectant
Unlike the other plant pathogens, Phytophtora infestans, the causative pathogen of potato late blight, can hardly take up dsRNA, which is a key obstacle in using dsRNA for disease control. Here, the authors design a self-assembled multicomponent nano-bioprotectant for potato late blight management.
- Yuxi Wang
- , Mingshan Li
- & Xiaodan Wang
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Article
| Open AccessPhylotranscriptomics unveil a Paleoproterozoic-Mesoproterozoic origin and deep relationships of the Viridiplantae
Evolutionary relationships among green plants are unresolved and, in particular, the phylogenetic position of Prasinodermophyta remains controversial. Here, the authors conduct phylogenomic analyses to resolve relationships within Viridiplantae, suggesting that this group diverged between the Great Oxidation Event and the Neoproterozoic Oxygenation Event.
- Zhiping Yang
- , Xiaoya Ma
- & Bojian Zhong
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Article
| Open AccessUnderstanding the mechanism of red light-induced melatonin biosynthesis facilitates the engineering of melatonin-enriched tomatoes
Melatonin is a physiological regulator in many organisms including plants. Here, the authors demonstrate a molecular mechanism of red light-induced melatonin biosynthesis in tomato fruit which could guide the engineering of melatonin-enriched tomatoes.
- Zixin Zhang
- , Xin Zhang
- & Yang Zhang
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Article
| Open AccessPlant immunity suppression by an exo-β-1,3-glucanase and an elongation factor 1α of the rice blast fungus
Fungal cell walls release β-1,3-glucan fragments that trigger plant immunity. Here, the authors show that a glucanase (Ebg1) of the blast fungus Magnaporthe oryzae suppresses plant immunity by hydrolyzing β-1,3-glucan. At the same time, Ebg1 induces plant immune responses that are dampened by a fungal protein that interacts with Ebg1.
- Hang Liu
- , Xunli Lu
- & You-Liang Peng
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Article
| Open AccessGenomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation
Existing genetics and genomics studies of peppers mainly focus on single species. Here, the authors report a pepper graph pan-genome and a genome variation map of 500 accessions from five domesticated species and close wild relatives to reveal their domestication, introgression and population differentiation.
- Feng Liu
- , Jiantao Zhao
- & Xuexiao Zou
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Article
| Open AccessA fungal sesquiterpene biosynthesis gene cluster critical for mutualist-pathogen transition in Colletotrichum tofieldiae
Plant-associated fungi range from pathogens to mutualists. Here the authors identify a gene cluster in a Colletotrichum tofieldiae strain that is required to allow the fungus to transition from a mutualist to a pathogen depending on the nutritional status of the host.
- Kei Hiruma
- , Seishiro Aoki
- & Yusuke Saijo
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Article
| Open AccessA pathogen-induced putative NAC transcription factor mediates leaf rust resistance in barley
Rph7 is a previously mapped barley leaf rust resistance locus, but the causal resistance gene remains unclear. Here, combining a fine mapping approach with RNA-Seq based analysis, the authors clone Rph7 and show it encodes putative NAC transcription factor containing a C-terminal BED domain.
- Chunhong Chen
- , Matthias Jost
- & Peter M. Dracatos
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Article
| Open AccessEnhancing photosynthetic CO2 fixation by assembling metal-organic frameworks on Chlorella pyrenoidosa
Concentrating CO2 around Rubisco is critical to improve photosynthetic efficiency for biomass yield. Here, the authors report the self-assembly of metal-organic frameworks (MOFs) on the surface of green alga Chlorella pyrenoidosa to enhance the photosynthetic carbon fixation.
- Dingyi Li
- , Hong Dong
- & Can Li
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Article
| Open AccessExtrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants
Epigenetic control of extrachromosomal circular DNA (eccDNA) compartment and the relationships between eccDNA and plant genome stability remain unclear. Here, the authors investigate eccDNA and structural variations in Arabidopsis epigenetic mutants to reveal the eccDNA repertoire and its impact on genome stability.
- Panpan Zhang
- , Assane Mbodj
- & Marie Mirouze
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Article
| Open AccessQTG-Miner aids rapid dissection of the genetic base of tassel branch number in maize
The lack of large-scale QTL cloning method hampers systematic dissection of genetic base of quantitative traits. Here, the authors develop a multi-omics data-based technique for large-scale and rapid cloning of quantitative genes of tassel branch number and discovery of selection signatures in maize breeding.
- Xi Wang
- , Juan Li
- & Lin Li
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Article
| Open AccessComparative genomic analyses reveal the genetic basis of the yellow-seed trait in Brassica napus
Yellow-seed trait is preferred in rapeseed breeding as it can greatly improve seed oil yield and quality. Here, the authors assemble the genome of two rapeseed lines with yellow-seed and black-seed phenotypes, and clone an R2R3-MYB-type transcription factor encoding gene as a key regulator of seed color.
- Cunmin Qu
- , Meichen Zhu
- & Jiana Li
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Article
| Open AccessAdoption of climate-resilient groundnut varieties increases agricultural production, consumption, and smallholder commercialization in West Africa
The adoption of climate-resilient crop varieties has the potential to build farmers’ climate resilience. Here, the authors show that adoption of climate-resilient groundnut varieties in West Africa benefits all households, with the biggest gains accruing to small-scale farmers.
- Martin Paul Jr Tabe-Ojong
- , Jourdain C. Lokossou
- & Hippolyte D. Affognon
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Article
| Open AccessAcidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections
We have limited knowledge on how soil conditions affect microbiota and plant health. Here, the authors find that soil acidification impacts bacterial communities and reduces the capacity of soils to combat fungal pathogens such as Fusarium.
- Xiaogang Li
- , Dele Chen
- & Manuel Delgado-Baquerizo
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Article
| Open AccessCharacterization of two O-methyltransferases involved in the biosynthesis of O-methylated catechins in tea plant
Tea contains catechins such as (−)-epigallocatechin gallate (EGCG) which have antioxidant activity and potential health benefits. Here the authors characterise two enzymes that produce O-methylated EGCG, a modified form found in some tea cultivars that has improved bioavailability.
- Ji-Qiang Jin
- , Fu-Rong Qu
- & Liang Chen
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Article
| Open AccessPhosphate starvation response precedes abscisic acid response under progressive mild drought in plants
Even mild drought impacts crop production significantly. Here, the authors develop an experimental mild drought system induced by ridges in the field and find that phosphate starvation response occurs before ABA response in early mild drought.
- Yukari Nagatoshi
- , Kenta Ikazaki
- & Yasunari Fujita
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Article
| Open AccessSCFRMF mediates degradation of the meiosis-specific recombinase DMC1
In eukaryotes the recombinase DMC1 is required for meiotic recombination, but it remains unclear how DMC1 stability is regulated. Here the authors identify a SCF complex which mediates ubiquitination and proteasomal degradation of DMC1.
- Wanyue Xu
- , Yue Yu
- & Yingxiang Wang
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Article
| Open AccessExo84c interacts with VAP27 to regulate exocytotic compartment degradation and stigma senescence
The exocyst complex is essential for plant development. Here the authors reveal a link between the exocyst complex and the ER network in regulating the degradation of exocytic compartments, stigma senescence and flower receptivity
- Tong Zhang
- , Yifan Li
- & Pengwei Wang
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Article
| Open AccessIdentification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism
The use of automated tools to reconstruct lipid metabolic pathways is not warranted in plants. Here, the authors construct Plant Lipid Module for Arabidopsis rosette using constraint-based modeling, demonstrate its integration in other plant metabolic models, and use it to dissect the genetic architecture of lipid metabolism.
- Sandra Correa Córdoba
- , Hao Tong
- & Zoran Nikoloski
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Article
| Open AccessDivergent sequences of tetraspanins enable plants to specifically recognize microbe-derived extracellular vesicles
Extracellular vesicles (EVs) are important in plant-microbe interactions. Here we show that the divergent sequences within tetraspanins localized at EV membranes enable plant innate immune system to distinguish between self and non-self EVs.
- Jinyi Zhu
- , Qian Qiao
- & Yuanchao Wang
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Article
| Open AccessMolecular mechanism underlying regulation of Arabidopsis CLCa transporter by nucleotides and phospholipids
CLC transporters are regulated by nucleotides and phospholipids. Here cryo-EM structure of Arabidopsis CLCa in complex with ATP and PIP2 and electrophysiological analysis suggests the underlying regulatory mechanisms of both nucleotides and phospholipids.
- Zhao Yang
- , Xue Zhang
- & Peng Zhang
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Article
| Open AccessA lignin-derived material improves plant nutrient bioavailability and growth through its metal chelating capacity
Biorefinery lignin waste has little value in the market. Here, Liu et al. find that water-soluble lignin, converted from sulfuric acid lignin, improves plant iron bioavailability and growth through a metal chelating capacity comparable to the metal chelator EDTA.
- Qiang Liu
- , Tsubasa Kawai
- & Baohai Li
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Article
| Open AccessSubtelomeric 5-enolpyruvylshikimate-3-phosphate synthase copy number variation confers glyphosate resistance in Eleusine indica
Resistance to herbicide glyphosate can be evolved trough copy number variation (CNV) of its target gene EPSPS in goosegrass. Here, the authors assemble the genomes of glyphosate susceptible and resistance lines and provide evidence of sub-telomeric-repeat driven CNV of EPSPS could lead to glyphosate resistance.
- Chun Zhang
- , Nicholas A. Johnson
- & Eric L. Patterson
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Article
| Open AccessDeSUMOylation of a Verticillium dahliae enolase facilitates virulence by derepressing the expression of the effector VdSCP8
Verticillium dahliae, a soil-borne fungal pathogen, causes vascular wilt in a wide variety of economically important crops. This study reveals a sophisticated pathogenic mechanism of VdUlpB-deSUMOylated enolase to facilate fungal virulence by derepressing the expression of the effector VdSCP8.
- Xue-Ming Wu
- , Bo-Sen Zhang
- & Hui-Shan Guo
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Article
| Open AccessA BLADE-ON-PETIOLE orthologue regulates corolla differentiation in the proximal region in Torenia fournieri
Flowers manifest enormous diversity and shape is determined by morphogenesis along different independent axes. Here Su et al. report a shared BOP-ALOG module that regulates corolla differentiation in the proximal region axis.
- Shihao Su
- , Yawen Lei
- & Tetsuya Higashiyama
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Article
| Open AccessAutophagy promotes jasmonate-mediated defense against nematodes
Autophagy plays a critical role in plant immunity. Here the authors show that in tomato, autophagy promotes defense against root-knot nematodes by promoting degradation of negative regulators of jasmonic acid signaling.
- Jinping Zou
- , Xinlin Chen
- & Jie Zhou
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Article
| Open AccessThe NAC transcription factors SNAP1/2/3/4 are central regulators mediating high nitrogen responses in mature nodules of soybean
Symbiotic nitrogen fixation (SNF) in legumes is suppressed by the presence of soil inorganic. nitrogen (N). Here the authors characterize a transcriptional regulatory network underlying the N-inhibition of SNF in soybean nodules.
- Xin Wang
- , Zhimin Qiu
- & Yuefeng Guan
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Article
| Open AccessA translational regulator MHZ9 modulates ethylene signaling in rice
The authors identify a GYF domain-containing protein MHZ9 in rice, which regulates ethylene signaling by directly binding to OsEBF1/2 and other mRNAs thus regulating their translation efficiency in P-body via interacting with OsEIN2.
- Yi-Hua Huang
- , Jia-Qi Han
- & Jin-Song Zhang
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Article
| Open AccessFunctional divergence of CYP76AKs shapes the chemodiversity of abietane-type diterpenoids in genus Salvia
Functional divergence of CYP76AK subfamily, accompanied by oxidation variations at C-20, leads to diverse abietane-type diterpenoids in Salvia species. Enzyme activity loss contributes to this unique chemical diversity within the lineage.
- Jiadong Hu
- , Shi Qiu
- & Wansheng Chen
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Article
| Open AccessXCP1 cleaves Pathogenesis-related protein 1 into CAPE9 for systemic immunity in Arabidopsis
The protein PR1 is crucial for plant immunity but has unclear bioactivity. Here PR1 is shown to release a phytocytokine CAPE and trigger systemic acquired resistance (SAR) via a caspase-like enzyme specific for CAPE production (ESCAPE).
- Ying-Lan Chen
- , Fan-Wei Lin
- & Yet-Ran Chen
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Article
| Open AccessThe Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis
The Ycf48 accessory factor is important for the assembly and repair of the photosystem II (PSII) complex of oxygenic photosynthesis. Here, the authors show that Ycf48 occupies the binding site of the oxygen evolving Mn cluster early in PSII biogenesis.
- Ziyu Zhao
- , Irene Vercellino
- & Josef Komenda
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