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| Open AccessIntegrated omics networks reveal the temporal signaling events of brassinosteroid response in Arabidopsis
Brassinosteroids (BR) regulate plant development and stress responses. Here, by integrating multiple omics datasets and inferring networks, the authors profile BR signaling in Arabidopsis and characterize BRONTOSAURUS, a BR-regulated transcription factor that impacts cell division in roots.
- Natalie M. Clark
- , Trevor M. Nolan
- & Justin W. Walley
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Article
| Open AccessCytokinin regulates vegetative phase change in Arabidopsis thaliana through the miR172/TOE1-TOE2 module
The antagonistic activities of miR156 and miR172 regulate juvenile-to-adult phase transition during plant shoot growth. Here the authors show that cytokinin promotes this transition by increasing miR172 abundance which in turn represses the activity of the transcriptional regulators TOE1 and TOE2.
- Sören Werner
- , Isabel Bartrina
- & Thomas Schmülling
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Article
| Open AccessAn ethylene biosynthesis enzyme controls quantitative variation in maize ear length and kernel yield
Considerable genetic variation exists in maize ear size and kernel number. Here the authors show that variation in a gene encoding an ethylene biosynthetic enzyme impacts ear length, flower fertility and kernel yield suggesting an important role for ethylene signaling during inflorescence development.
- Qiang Ning
- , Yinan Jian
- & Zuxin Zhang
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Article
| Open AccessRewetting does not return drained fen peatlands to their old selves
Whether rewetting leads to effective restoration of drained peatlands is unclear. Here the authors analyse a large number of near-natural and rewetted fen peatland sites in Europe, finding persistent differences in plant community composition and ecosystem functioning, and higher variance in the restored sites.
- J. Kreyling
- , F. Tanneberger
- & G. Jurasinski
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Article
| Open AccessThe identification of grain size genes by RapMap reveals directional selection during rice domestication
Cloning quantitative trait loci (QTL) in crops is often slow and laborious. Here, the authors describe RapMap, a method to rapidly clone multiple QTL based on F2 gradient populations coupled with a co-segregation standard, and show how it can be used to identify genes controlling grain size in rice.
- Juncheng Zhang
- , Dejian Zhang
- & Yibo Li
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Article
| Open AccessDirect photoresponsive inhibition of a p53-like transcription activation domain in PIF3 by Arabidopsis phytochrome B
Photoactivated phytochrome B regulates gene expression by interacting with PIF transcription factors. Here the authors show that PIF3 contains a p53-like transcription activation domain (AD) and that PHYB can directly suppress PIF3 transactivation activity by binding adjacent to the AD.
- Chan Yul Yoo
- , Jiangman He
- & Meng Chen
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Article
| Open AccessSterols are required for the coordinated assembly of lipid droplets in developing seeds
Lipid droplet biogenesis originates at the endoplasmic reticulum and is defined by a specific set of lipids and proteins. Here, the authors show that sterols play an important role in coordinating oil and oleosin biosynthesis for the formation of lipid droplets in plant leaves and seeds.
- Linhui Yu
- , Jilian Fan
- & Changcheng Xu
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Article
| Open AccessThe Arabidopsis MIK2 receptor elicits immunity by sensing a conserved signature from phytocytokines and microbes
Peptide signals generated during plant microbe interactions can trigger immune responses in plants. Here the authors show that SCOOP12, a member of a family of peptides present in Brassicaceae plants, and SCOOP12-like motifs in Fusarium fungi, can trigger immune responses following perception by the MIK2 receptor kinase.
- Shuguo Hou
- , Derui Liu
- & Ping He
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Article
| Open AccessStructural insight into the mechanism of energy transfer in cyanobacterial phycobilisomes
The major light-harvesting systems for photosynthesis in cyanobacteria and red algae are phycobilisomes (PBS). Here, the authors present the cryo-EM structures of two cyanobacterial PBS from Anabaena 7120 and Synechococcus 7002 and discuss their energy transfer pathways.
- Lvqin Zheng
- , Zhenggao Zheng
- & Ning Gao
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Article
| Open AccessIncipient diploidization of the medicinal plant Perilla within 10,000 years
Perilla is a young allotetraploid species within the mint family Lamiaceae. Here, the authors assemble the genomes of a tetraploid species and its diploid progenitor, characterize the incipient diploidization of the tetraploid, conduct population genetics analyses, and identify loci associate with pigmentation and oil content.
- Yujun Zhang
- , Qi Shen
- & Shilin Chen
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Article
| Open AccessA bacterial kinase phosphorylates OSK1 to suppress stomatal immunity in rice
XopC2 effectors are present in many plant bacterial pathogens. Here the authors show that XopC2 has kinase activity and enhances disease susceptibility by phosphorylating the OSK1 protein, which increases its interaction with the jasmonate receptor COI1b to promote JA signaling and stomatal opening.
- Shanzhi Wang
- , Shuai Li
- & Wenxian Sun
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Article
| Open AccessAnalysis of 427 genomes reveals moso bamboo population structure and genetic basis of property traits
Moso bamboo is an economically and ecologically important nontimber forestry species. Here, the authors analyze 427 genomes collected from 15 representative geographic areas, and identify genes under balancing selection, putative patterns of historic demography, and candidate genes associated with important traits.
- Hansheng Zhao
- , Shuai Sun
- & Zhimin Gao
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Article
| Open AccessLocal auxin biosynthesis acts downstream of brassinosteroids to trigger root foraging for nitrogen
Flowering plants elongate their lateral roots under mild nitrogen deficiency to enhance nutrient acquisition. Here the authors show that natural variation of this response depends on local auxin biosynthesis that acts downstream of brassinosteroids to determine lateral root extension.
- Zhongtao Jia
- , Ricardo F. H. Giehl
- & Nicolaus von Wirén
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Article
| Open AccessGenetic basis and adaptation trajectory of soybean from its temperate origin to tropics
How soybean, a temperate origin crop, adapted to a tropical environment remains unclear. Here, the authors report Tof16, an ortholog of LHY, and the previously identified J locus, control soybean yield under short-day condition and loss of function of these two genes contributes to the adaptation to tropics.
- Lidong Dong
- , Chao Fang
- & Baohui Liu
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Article
| Open AccessFunctional basis of electron transport within photosynthetic complex I
Photosynthetic Complex I (PS-CI) is proposed to couple ferredoxin oxidation and plastoquinone reduction to proton pumping across thylakoid membranes. Here the authors determine the reduction potentials of the iron-sulphur clusters of PS-CI and thus the bioenergetics of the electron transfer relay.
- Katherine H. Richardson
- , John J. Wright
- & Maxie M. Roessler
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Article
| Open AccessAridity-driven shift in biodiversity–soil multifunctionality relationships
Biodiversity-ecosystem functioning relationships may vary with climate. Here, the authors study relationships of plant and soil microbial diversity with soil nutrient multifunctionality in 130 dryland sites in China, finding a shift towards greater importance of soil microbial diversity in arid conditions.
- Weigang Hu
- , Jinzhi Ran
- & Jianming Deng
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Article
| Open AccessCO2, nitrogen deposition and a discontinuous climate response drive water use efficiency in global forests
Water use efficiency is a key measure of plant responses to climate change. Here, the authors investigate its control by CO2, nitrogen deposition, and water availability using a global tree-ring dataset. They find an aridity threshold and quantify changes in control over the past 50 years.
- Mark A. Adams
- , Thomas N. Buckley
- & Tarryn L. Turnbull
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Article
| Open AccessDynamics of moisture diffusion and adsorption in plant cuticles including the role of cellulose
The plant cuticle provides a barrier between internal leaf tissues and the environment. Here the authors develop a mathematical model of water movement through the cuticle and describe a prominent role for cellulose in controlling the dynamics of moisture diffusion and adsorption.
- E. C. Tredenick
- & G. D. Farquhar
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Article
| Open AccessParallel adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles
Relative contributions of pre-existing versus de novo genomic variation to adaptation remain unclear. Here, the authors address this problem by examining the adaptation of autotetraploid Arabidopsis arenosa to serpentine soils and find that both types of variations contribute to rapid adaptation.
- Veronika Konečná
- , Sian Bray
- & Filip Kolář
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Article
| Open AccessExcessive ammonium assimilation by plastidic glutamine synthetase causes ammonium toxicity in Arabidopsis thaliana
Ammonium is an important nitrogen source for plants but excess ammonium impairs growth. Here the authors show that ammonium toxicity results from assimilation by GLUTAMINE SYNTHETASE 2 in the plastids which results in excess proton accumulation and acidity stress.
- Takushi Hachiya
- , Jun Inaba
- & Hitoshi Sakakibara
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Article
| Open AccessPre-meiotic 21-nucleotide reproductive phasiRNAs emerged in seed plants and diversified in flowering plants
Pre-meiotic anthers of monocots accumulate phased, small interfering RNAs (phasiRNAs) that are absent in many well-studied model eudicots. Here, the authors show that such 21-nt phasiRNAs are in fact present in diverse eudicot species including strawberry, in which production is triggered by miR11308.
- Suresh Pokhrel
- , Kun Huang
- & Blake C. Meyers
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Article
| Open AccessGlobal variation in the fraction of leaf nitrogen allocated to photosynthesis
The fraction of leaf nitrogen allocated to RuBisCO indicates differing nitrogen use strategies of plants and varies considerably. Here the authors show that this variation is largely driven by leaf thickness and phosphorus content with light intensity, atmospheric dryness and soil pH also having considerable influence.
- Xiangzhong Luo
- , Trevor F. Keenan
- & Yao Zhang
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Article
| Open AccessWarm temperature triggers JOX and ST2A-mediated jasmonate catabolism to promote plant growth
Plants undergo morphological changes to enhance cooling at warm temperatures. Here Zhu et al. show that JOXs and ST2A enzymes, which mediate jasmonate catabolism, contribute to this process by reducing the level of bioactive jasmonate facilitating growth responses.
- Tingting Zhu
- , Cornelia Herrfurth
- & Ive De Smet
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Article
| Open AccessThe intervening domain is required for DNA-binding and functional identity of plant MADS transcription factors
MADS transcription factors regulate multiple aspects of plant development. Here the authors show that the intervening I domain is conserved in both type I and type II plant MADS lineages and contributes to the functional identity of the protein by influencing both DNA binding activity and dimerisation specificity.
- Xuelei Lai
- , Rosario Vega-Léon
- & Chloe Zubieta
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Article
| Open AccessNatural variation in a type-A response regulator confers maize chilling tolerance
The genetic basis of low-temperature tolerance in maize is unclear. Here, the authors show that the type-A Response Regulator 1 (ZmRR1) and mitogen-activated protein kinase (MPK8) are positive and negative regulators of maize chilling tolerance, and ZmRR1 is phosphorylated by ZmMPK8 during cold treatment.
- Rong Zeng
- , Zhuoyang Li
- & Shuhua Yang
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Article
| Open AccessNon-invasive hydrodynamic imaging in plant roots at cellular resolution
Existing methods for non-invasively monitoring water flow in plants have limited spatial/temporal resolution. Here, the authors report that Raman microspectroscopy, complemented by hydrodynamic modelling, can monitor hydrodynamics within living root tissues at cell- and sub-second-scale resolutions.
- Flavius C. Pascut
- , Valentin Couvreur
- & Kevin F. Webb
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Article
| Open AccessDiffusion-mediated HEI10 coarsening can explain meiotic crossover positioning in Arabidopsis
Crossover numbers and positions are tightly controlled but the mechanism involved is still obscure. Here, the authors, using quantitative super-resolution cytogenetics and mathematical modelling, show that diffusion mediated coarsening of HEI10, an E3-ligase domain containing protein, may explain meiotic crossover positioning in Arabidopsis.
- Chris Morgan
- , John A. Fozard
- & Martin Howard
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Article
| Open AccessDiversification of mandarin citrus by hybrid speciation and apomixis
To explore the nature of wild and cultivated mandarins, the authors carry out genomic analysis of diverse east Asian citrus. The discovery of a wild species Citrus ryukyuensis native to the Ryukyu islands and a new population of wild mainland Asian mandarin explains the origin and diversity of mandarins and their ability to reproduce apomictically.
- Guohong Albert Wu
- , Chikatoshi Sugimoto
- & Daniel S. Rokhsar
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Article
| Open AccessA minus-end directed kinesin motor directs gravitropism in Physcomitrella patens
Gravitropism is the process by which plants perceive and respond to gravity. Here the authors identify a minus-end-directed kinesin required for gravity-triggered actin filament rearrangement and negative gravitropic response in the moss Physcomitrella patens, thus linking a microtubule-based cellular motor to gravitropism via actin.
- Yufan Li
- , Zhaoguo Deng
- & Haodong Chen
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Article
| Open AccessStructure and function of an Arabidopsis thaliana sulfate transporter
Plant sulfate transporters mediate absorption and distribution of sulfate. Here the authors present functional assays and a cryo-EM structure of the Arabidopsis SULTR4;1 transporter identifying key domains for dimerization, substrate binding and coupling of transport activity to a proton gradient.
- Lie Wang
- , Kehan Chen
- & Ming Zhou
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Article
| Open AccessSpecies-specific gamete recognition initiates fusion-driving trimer formation by conserved fusogen HAP2
HAP2 is essential for gamete fusion during fertilization and is conserved among eukaryotes. Here the authors show that species-specific adhesion between Chlamydomonas plus and minus gametes initiates HAP2 to undergo a fusogenic conformational change into homotrimers via a molecular mechanism akin to that of enveloped viruses.
- Jun Zhang
- , Jennifer F. Pinello
- & William J. Snell
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Article
| Open AccessLanthanum(III) triggers AtrbohD- and jasmonic acid-dependent systemic endocytosis in plants
Rare earth elements are widely used in agriculture to promote plant growth. Here the authors show that aerial application of a rare earth element to the leaves triggers a graft-transmissible, RbohD- and jasmonic acid-dependent systemic signal that triggers endocytosis and mineral nutrient uptake in roots.
- Mengzhu Cheng
- , Lihong Wang
- & Zhenbiao Yang
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Article
| Open AccessCoordination of biradial-to-radial symmetry and tissue polarity by HD-ZIP II proteins
The apical style in Arabidopsis is formed following a bilateral-to-radial symmetry transition in the gynoecium. Here the authors show that the final step in style radialization is coordinated by the adaxial regulators HAT3 and ATHB4, which are induced by the SPT and HEC transcription factors.
- Monica Carabelli
- , Luana Turchi
- & Laila Moubayidin
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Article
| Open AccessGeminiviruses encode additional small proteins with specific subcellular localizations and virulence function
Geminiviruses are small plant-infecting viruses. Here the authors screen the geminivirus genome for small open reading frames that may have been previously overlooked and show that one encodes a protein named V3 that localizes to the Golgi and acts as an RNA silencing suppressor.
- Pan Gong
- , Huang Tan
- & Xueping Zhou
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Article
| Open AccessSphingolipids mediate polar sorting of PIN2 through phosphoinositide consumption at the trans-Golgi network
Lipid composition impacts the function of cellular membranes. Here the authors show that a reduction in sphingolipid acyl-chain length promotes phosphoinositide consumption by phospholipase C at the Arabidopsis trans-Golgi network which in turn regulates sorting of the auxin efflux carrier PIN2.
- Yoko Ito
- , Nicolas Esnay
- & Yohann Boutté
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Article
| Open AccessArabidopsis MORC proteins function in the efficient establishment of RNA directed DNA methylation
MORC ATPases are required for transposable element silencing and heterochromatin condensation in plants and animals. Here the authors show that Arabidopsis MORCs colocalize with sites of RNA-directed DNA methylation and provide evidence that they act as molecular tethers to efficiently establish DNA methylation.
- Yan Xue
- , Zhenhui Zhong
- & Steven E. Jacobsen
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Article
| Open AccessThe Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts
Welwitschia mirabilis is a unique plant that only has two leaves, but it can survive in hostile conditions of the African desert. Here, the authors report its chromosome-level genome assembly and discuss how gene function and regulation have given rise to its unique morphology and environmental adaptions.
- Tao Wan
- , Zhiming Liu
- & Qingfeng Wang
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Article
| Open AccessChaperone-like protein DAY plays critical roles in photomorphogenesis
Chloroplast development and brassinosteroid (BR) signaling both regulate plant photomorphogenesis. Here the authors show that DAY, a DnaJ-like domain-containing membrane protein, regulates both processes by binding and stabilizing both BRI1, the BR receptor, and POR, a key enzyme in chlorophyll biosynthesis.
- Ho-Seok Lee
- , Ilyeong Choi
- & Hyun-Sook Pai
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Article
| Open AccessA nonS-locus F-box gene breaks self-incompatibility in diploid potatoes
Diploid potatoes are typically self-incompatible, complicating efforts to breed diploid cultivars. Here the authors report map-based cloning of the S-locus inhibitor (Sli) gene in potato which encodes a non S-locus F-box protein that is expressed in pollen and can functions like a general S-RNase inhibitor to overcome self-incompatibility.
- Ling Ma
- , Chunzhi Zhang
- & Yi Shang
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Article
| Open AccessNeofunctionalisation of the Sli gene leads to self-compatibility and facilitates precision breeding in potato
The S-locus inhibitor (Sli) gene could allow potato breeding by facilitating production of diploid inbred lines. Here the authors show that Sli encodes an F-box protein with a promoter insertion enhancing expression in pollen can overcome pollen rejection in the styles of diploid potato.
- Ernst-Jan Eggers
- , Ate van der Burgt
- & Pim Lindhout
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Article
| Open AccessFour chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding
Pecan is an important specialty crop that has experienced extensive interspecific hybridization and nearly-obligate outcrossing. Here, the authors assemble diploid genomes of four outbred genotypes, identify interspecific introgressions through comparative genomics analyses, and map QTLs associated with pest resistance.
- John T. Lovell
- , Nolan B. Bentley
- & Jennifer J. Randall
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Article
| Open AccessXanthomonas effector XopR hijacks host actin cytoskeleton via complex coacervation
Bacterial pathogens can subvert host cell processes through secreted proteins but the precise mechanisms and repertoire of proteins remains unclear. Here the authors report that a bacterial effector protein of Xanthomonas campestris, XopR, undergoes liquid-liquid phase separation to hijack the host cell actin cytoskeleton.
- He Sun
- , Xinlu Zhu
- & Yansong Miao
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Article
| Open AccessLEAFY COTYLEDON1 expression in the endosperm enables embryo maturation in Arabidopsis
The LEC1 transcription factor is expressed in both embryo and endosperm during seed development. Here the authors show that LEC1 expression in the endosperm is necessary and sufficient for embryo maturation and that LEC1 protein is trafficked to the embryo to activate seed maturation.
- Jingpu Song
- , Xin Xie
- & Yuhai Cui
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Article
| Open AccessPopulation genomics of apricots unravels domestication history and adaptive events
The evolutionary and domestication history of apricots is poorly understood. Here, the authors provide four apricot high-quality genome assemblies, the genomes of 578 accessions from natural and cultivated populations, and show that Chinese and European apricots constitute two different gene pools, resulting from independent domestication events.
- Alexis Groppi
- , Shuo Liu
- & Véronique Decroocq
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Article
| Open AccessPGRL2 triggers degradation of PGR5 in the absence of PGRL1
It is currently thought that the thylakoid proteins PGRL1 and PGR5 form a complex to mediate cyclic electron flow (CEF) around photosystem I. Here the authors show that CEF can in fact be mediated by PGR5 alone and that PGRL1 and the homologous PGRL2 modify the process by modulating PGR5 activity and stability.
- Thilo Rühle
- , Marcel Dann
- & Dario Leister
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Article
| Open AccessRETRACTED ARTICLE: Selective inheritance of target genes from only one parent of sexually reproduced F1 progeny in Arabidopsis
Unlike insects and mice, CRISPR/Cas9-based gene drives have not been achieved in plants. Here, the authors demonstrate homozygous F1 Arabidopsis plants can be obtained through zygotic conversion using CRISPR/Cas9-mediated homology-directed repair.
- Tao Zhang
- , Michael Mudgett
- & Yunde Zhao
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Article
| Open AccessRapid evolution of bacterial mutualism in the plant rhizosphere
Beneficial plant-microbe interactions are common in nature, but direct evidence for the evolution of mutualism is scarce. Here, Li et al. experimentally evolve a rhizospheric bacterium and find that it can evolve into a mutualist on a relatively short timescale.
- Erqin Li
- , Ronnie de Jonge
- & Alexandre Jousset
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Article
| Open AccessEvolution of an assembly factor-based subunit contributed to a novel NDH-PSI supercomplex formation in chloroplasts
The chloroplast NDH complex interacts with Photosystem I to form the NDH-PSI supercomplex. Here the authors show that Arabidopsis NDF5 shares a common ancestor with the NDH subunit PnsB2 and acts as an NDH assembly factor initiating the assembly of PnsB2 and the evolutionarily distinct PnsB3.
- Yoshinobu Kato
- , Masaki Odahara
- & Toshiharu Shikanai
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Article
| Open AccessAn anchoring complex recruits katanin for microtubule severing at the plant cortical nucleation sites
Katanin severs microtubules to facilitate array reorientation and amplification. Here the authors show that a conserved centrosomal complex of Msd1 and Wdr8 recruits katanin to cortical nucleation sites in acentrosomal plant cells and stabilizes daughter microtubules until they are severed by katanin.
- Noriyoshi Yagi
- , Takehide Kato
- & Takashi Hashimoto
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