Plant molecular biology articles within Nature Communications

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  • Article
    | Open Access

    TUTase mediated uridylation of mRNA promotes degradation. Here, Scheer, de Almeida et al. show that Arabidopsis TUTase URT1 interacts directly with the translation inhibitor and decay factor DECAPPING5 and suppresses siRNA biogenesis by preventing accumulation of deadenylated mRNAs

    • Hélène Scheer
    • , Caroline de Almeida
    •  & Dominique Gagliardi

  • Article
    | Open Access

    The nucleolus organizing region (NOR) consists of multiple, highly repetitive rDNA genes. Here Sims et al. use both long- and short-read sequencing to determine the organization and sequence of Arabidopsis NOR2 rDNA and show that different rRNA gene variants are integrated into translating ribosomes in a tissue-specific manner.

    • Jason Sims
    • , Giovanni Sestini
    •  & Peter Schlögelhofer

  • Article
    | Open Access

    Introducing the pyrenoid-based CO2-concentrating mechanism of green algae into crops could greatly improve photosynthesis. Here, the authors show that expression of the algal linker protein EPYC1 and a plant-algal hybrid Rubisco in Arabidopsis chloroplasts leads to formation of a phase separated algal-like proto-pyrenoid.

    • Nicky Atkinson
    • , Yuwei Mao
    •  & Alistair J. McCormick

  • Article
    | Open Access

    Histone 3 Lys 27 trimethylation (H3K27me3) mediates epigenetic silencing of gene expression. Here, Zhang et al. show that in Arabidopsis, the BAH-domain H3K27me3-reader protein AIPP3 forms a complex with PHD proteins and CPL2, a plant-specific Pol II phosphatase, to inhibit Pol II activity by dephosphorylation.

    • Yi-Zhe Zhang
    • , Jianlong Yuan
    •  & Cheng-Guo Duan

  • Article
    | Open Access

    Dioecy has evolved independently from hermaphroditic ancestors in different plant lineages. Here, the authors assemble Populus deltoides male and female genomes, and show the putative roles of a femaleness gene and a maleness gene in sex determination, which suggests independent evolution in different poplar species.

    • Liangjiao Xue
    • , Huaitong Wu
    •  & Tongming Yin

  • Article
    | Open Access

    The meiotic transmissibility and progeny phenotypic influence of graft-mediated epigenetic changes remain unclear. Here, the authors use the msh1 mutant in the rootstock to trigger heritable enhanced growth vigor in Arabidopsis and tomato, and show it is associated with the RNA-directed DNA methylation pathway.

    • Hardik Kundariya
    • , Xiaodong Yang
    •  & Sally A. Mackenzie

  • Article
    | Open Access

    The secondary structure of miRNA precursor sequences is known to affect processing by DICER-like proteins. Here Rojas et al. show that additional sequence features also play a regulatory role in plants with nucleotide identity at unpaired positions substantially impacting processing efficiency.

    • Arantxa M. L. Rojas
    • , Salvador I. Drusin
    •  & Javier F. Palatnik

  • Article
    | Open Access

    Electrons enter the mitochondrial respiratory chain via complex I. Here, the authors report high-resolution structures of mature plant complex I and one of its assembly intermediates, highlighting plant-specific features including an ancestral carbonic anhydrase domain.

    • Heddy Soufari
    • , Camila Parrot
    •  & Yaser Hashem

  • Article
    | Open Access

    Transcriptional factors (TFs) bind in a combinatorial fashion to specify the on-and-off states of genes in a complex and redundant regulatory network. Here, the authors construct the transcription regulatory network in maize leaf using 104 TFs ChIP-seq data and train machine learning models to predict TF binding and colocalization.

    • Xiaoyu Tu
    • , María Katherine Mejía-Guerra
    •  & Silin Zhong

  • Article
    | Open Access

    MAPK signaling suppresses autoimmunity mediated by the SUMM2 receptor in Arabidopsis. Here Huang et al. show that a trimeric complex consisting of the GPI anchored protein LLG1, and the two receptor-like proteins LET1 and LET2, promotes activation of SUMM2 according to MAPK signaling status.

    • Yanyan Huang
    • , Chuanchun Yin
    •  & Ping He

  • Article
    | Open Access

    Protein-protein interactions are thought to channel substrates between consecutive enzymes during glycolysis. Here the authors show that Arabidopsis phosphoglycerate mutase and enolase can form a substrate-channelling metabolon and also play a moonlighting role in promoting colocalization of chloroplasts and mitochondria.

    • Youjun Zhang
    • , Arun Sampathkumar
    •  & Alisdair R. Fernie

  • Article
    | Open Access

    The heterochromatic knob (hk4S) on Arabidopsis chromosome 4 prevents the recombination between accessions with and without hk4S. Here, via egg-cell specific expression of the Cas9 nuclease, the authors demonstrate targeted reversal of the 1.1 Mb long hk4S-inversion in Col-0 and restore the crossovers with Ler-1.

    • Carla Schmidt
    • , Paul Fransz
    •  & Holger Puchta

  • Article
    | Open Access

    MicroRNA2118 induces the production of phased small interfering RNAs (phaisRNAs) in plants. Here the authors show that rice miR2118 is required for both male and female fertility and supports the production of atypical U-rich 21 nt phasiRNAs that are abundant in anther walls.

    • Saori Araki
    • , Ngoc Tu Le
    •  & Reina Komiya

  • Article
    | Open Access

    Mediator is a multiprotein complex required to activate gene transcription by RNAPII. Here, the authors report that MED12 and MED13 are conditional positive regulators that facilitate the expression of genes depleted in active chromatin marks and the induction of gene expression in response to environmental stimuli in Arabidopsis.

    • Qikun Liu
    • , Sylvain Bischof
    •  & Steven E. Jacobsen

  • Article
    | Open Access

    Gene isoforms result from variable transcription start sites (TSSs) and polyadenylation sites (PASs) at the end of transcripts. Here, the authors perform transcript isoform sequencing and find widespread promoter- proximal transcriptional termination in Arabidopsis, suggesting this may represent a checkpoint that regulates plant gene expression.

    • Quentin Angelo Thomas
    • , Ryan Ard
    •  & Sebastian Marquardt

  • Article
    | Open Access

    Enzymatic inactivation of gibberellins and auxin, via GA2ox3 and DAO respectively, contributes to hormone homeostasis in plants. Here Takehara et al. show that both enzymes multimerize in a substrate-concentration-dependent manner, and that this multimerization leads to increased enzyme activity.

    • Sayaka Takehara
    • , Shun Sakuraba
    •  & Miyako Ueguchi-Tanaka

  • Article
    | Open Access

    The flowering regulator FLC shows upregulation and downregulation phases along with long-term past temperature in Arabidopsis halleri. Here, the authors reveal that H3K27me3-mediated chromatin regulation at AhgFLC provides the ability to respond to both the seasonal temperature trends and the perennial life cycle.

    • Haruki Nishio
    • , Diana M. Buzas
    •  & Hiroshi Kudoh

  • Article
    | Open Access

    SnRK2 protein kinases play key roles in signaling during plant responses to abiotic stress. Here Soma et al. report three Arabidopsis Raf-like MAP kinase kinase kinases phosphorylate and activate a subclass of SnRK2s that rapidly respond to osmotic stress independently of ABA signaling.

    • Fumiyuki Soma
    • , Fuminori Takahashi
    •  & Kazuko Yamaguchi-Shinozaki

  • Article
    | Open Access

    RNA-directed DNA methylation (RdDM) is thought to silence newly inserted transposable elements (TEs) with RNA-independent mechanisms becoming more prominent as TEs age. Here, the authors show that RdDM continues to silence the oldest intact distal TEs in tomato and Arabidopsis suggesting a second, later phase of RdDM.

    • Zhengming Wang
    •  & David C. Baulcombe

  • Article
    | Open Access

    Existing examples of targeted gene insertion in plants either rely on a selectable marker gene or result in short DNA inserts. Here, the authors use an optimized CRISPR-Cas9 method to insert a 5.2 kb carotenoid biosynthesis cassette into genomic safe harbors in rice, and obtain marker-free lines with high carotenoid content.

    • Oliver Xiaoou Dong
    • , Shu Yu
    •  & Pamela C. Ronald

  • Article
    | Open Access

    Conventional methods cannot reveal transient transcription factors (TFs) and targets interactions. Here, Alvarez et al. capture both stable and transient TF-target interactions by time-series ChIP-seq and/or DamID-seq in a cell-based TF perturbation system and show NLP7 as a master TF to initiate a rapid nitrogen-response cascade.

    • José M. Alvarez
    • , Anna-Lena Schinke
    •  & Gloria M. Coruzzi

  • Article
    | Open Access

    Plants deploy numerous receptor-like kinases (RLKs) to respond to pathogens. Here the authors show that NIK1, an RLK that positively regulates antiviral immunity, negatively regulates the response to bacteria by modulating FLS2/BAK1 complex formation, suggesting crosstalk between bacterial and viral immunity.

    • Bo Li
    • , Marco Aurélio Ferreira
    •  & Elizabeth P. B. Fontes

  • Article
    | Open Access

    Plant hypoxia responses are controlled by oxygen and nitric oxide (NO)-dependent proteolysis of ERFVII transcription factors. Here Hartman et al. show that passive ethylene entrapment during root submergence enhances NO-scavenger PHYTOGLOBIN1, ERFVII stability and promotes subsequent hypoxia tolerance.

    • Sjon Hartman
    • , Zeguang Liu
    •  & Laurentius A. C. J. Voesenek

  • Article
    | Open Access

    RNA polymerase V transcription in plants, which is needed DNA methylation and transcriptional silencing, requires components of the DDR complex. Here the authors show that all components of the DDR complex co-localize with Pol V and report the cryoEM structures of two complexes associated with Pol V recruitment.

    • Somsakul Pop Wongpalee
    • , Shiheng Liu
    •  & Steven E. Jacobsen

  • Article
    | Open Access

    Cytosolic RNA degradation by the RNA exosome requires the Ski complex. Here the authors show that the proteins RST1 and RIPR assist the RNA exosome and the Ski complex in RNA degradation, thereby preventing the production of secondary siRNAs from endogenous mRNAs.

    • Heike Lange
    • , Simon Y. A. Ndecky
    •  & Dominique Gagliardi

  • Article
    | Open Access

    The SWI2/SNF2-Related 1 chromatin remodeling complex (SWR1-C) is important for gene regulation, but its composition remains largely uncharacterized in plants. Here, the authors report that methyl-CpG-binding domain 9 (MBD9) is a SWR1-C interacting protein required for histone H2A.Z deposition in Arabidopsis.

    • Magdalena E. Potok
    • , Yafei Wang
    •  & Steven E. Jacobsen

  • Article
    | Open Access

    The distribution of H3K36me3 varies between species. Here Liu et al. show that the OsSUF4 transcription factor binds its target motif via a zinc finger domain to promote H3K36 methyltransferase targeting close to the transcription start site of genes including the flowering regulators RFT1 and Hd3a.

    • Bing Liu
    • , Yuhao Liu
    •  & Aiwu Dong

  • Article
    | Open Access

    Plants are dependent on controlled sugar uptake via Monosaccharide Transporters, such as STP10, for correct organ development, sugar accumulation in fruits and microbial defense. Here authors present the crystal structure of STP10 bound to glucose which sheds light on the fundamental principles of sugar transport in the plant-unique MST superfamily.

    • Peter Aasted Paulsen
    • , Tânia F. Custódio
    •  & Bjørn Panyella Pedersen

  • Article
    | Open Access

    Boron is essential for plant survival but high levels can impair growth and cause DNA damage. Here the authors show that Arabidopsis can ameliorate Boron toxicity via proteasomal degradation of BRAHMA to minimize open chromatin and reduce the likelihood of DNA double strand breaks.

    • Takuya Sakamoto
    • , Yayoi Tsujimoto-Inui
    •  & Toru Fujiwara

  • Article
    | Open Access

    A small RNA-based signaling cascade prevents the induction of plant resistance genes (R-genes) in the absence of pathogen challenge. Here Cai et al. show that nuclear accumulation of the R protein SNC1 can activate immunity by suppressing small RNA production and releasing R-gene repression.

    • Qiang Cai
    • , Chao Liang
    •  & Xuemei Chen

  • Article
    | Open Access

    The function of most lncRNA is unknown. Here, the authors show that transcriptional read-through at the Arabidopsis SVALKA locus produces a cryptic lncRNA that overlaps with the neighboring cold-responsive CBF1 gene and limits CBF1 expression via an RNA polymerase II collision-based mechanism.

    • Peter Kindgren
    • , Ryan Ard
    •  & Sebastian Marquardt

  • Article
    | Open Access

    Humidity has been shown to influence many aspects of plant physiology. Here Mwimba et al. show that oscillating humidity entrains the circadian clock under constant light conditions and enhances clock amplitude in simulated natural environments, while also improving immunity and overall growth.

    • Musoki Mwimba
    • , Sargis Karapetyan
    •  & Xinnian Dong

  • Article
    | Open Access

    Molecular mechanism of how temperature-mediated control of bud break in perennial plants remains unclear. Here, the author show that transcriptional factor SHORT VEGETATIVE PHASE-LIKE and its downstream target TCP18 are negative regulators of hybrid aspen bud break.

    • Rajesh Kumar Singh
    • , Jay P. Maurya
    •  & Rishikesh P. Bhalerao

  • Article
    | Open Access

    Small RNA degrading nucleases (SDNs) can degrade short RNAs. Here the authors report the crystal structure of Arabidopsis SDN1 in complex with a single-stranded RNA, and provide new insight into 3′ end trimming mechanism of 3′ to 5′ riboexonucleases in the metabolism of various species of small RNAs.

    • Jiayi Chen
    • , Li Liu
    •  & Jinbiao Ma

  • Article
    | Open Access

    Parasitic lifestyles leave unique genomic footprints. Here, the authors describe the genome sequence of a parasitic plant, Cuscuta campestris, and find that gene losses and host gene acquisitions reflect the independence from photosynthesis and the ability to retain and express chunks of foreign genomic DNA.

    • Alexander Vogel
    • , Rainer Schwacke
    •  & Kirsten Krause

  • Article
    | Open Access

    Histone mark reader proteins bind to particular histone modifications and regulate chromatin state. Here, Qian et al. show that the SHORT LIFE reader has a unique ability to recognize both activating and repressive histone marks and that these interactions enable SHORT LIFE to repress flowering in plants.

    • Shuiming Qian
    • , Xinchen Lv
    •  & Jiamu Du

  • Article
    | Open Access

    Geminiviruses are an important plant pathogen that causes large food crop losses globally. Here the authors describe a high resolution cryo-EM structure of the Ageratum yellow vein virus and reveal the molecular details of how a single capsid protein sequence can adopt the different conformations needed to build that geminate capsid.

    • Emma L. Hesketh
    • , Keith Saunders
    •  & Neil A. Ranson

  • Article
    | Open Access

    In plants, variation in DNA methylation can influence agronomically important traits. Here the authors show that expression of a human Ten-eleven translocation enzyme can generate heritable hypomethylation alleles in Arabidopsis, providing a novel method to manipulate DNA methylation for breeding and research purposes.

    • Lexiang Ji
    • , William T. Jordan
    •  & Robert J. Schmitz

  • Article
    | Open Access

    Cell-type transcriptome profiling greatly elucidate organismal development. Here, the authors report a spatiotemporally resolved comprehensive transcriptome analysis of tomato fruit ontogeny and suggest a new model of fruit maturation which initiates in internal tissues then radiates outwards.

    • Yoshihito Shinozaki
    • , Philippe Nicolas
    •  & Jocelyn K. C. Rose

  • Article
    | Open Access

    The plastid-encoded RNA polymerase PEP is regulated according to plastid redox state. Here, the authors show that the redox-regulated PRIN2 protein is reduced to monomeric form in a thiol-dependent manner in response to light and that PRIN2 monomers are required for PEP activity and retrograde signaling.

    • Manuel Guinea Díaz
    • , Tamara Hernández-Verdeja
    •  & Åsa Strand

  • Article
    | Open Access

    A subset of α/β hydrolases is known to suppress the pathogen-triggered hypersensitive response (HR) in plants, but their mechanism of action remains unclear. The authors present two crystal structures and functional analyses of these enzymes, showing that HR is suppressed by a previously unknown family of deacetylases.

    • Marco Bürger
    • , Björn C. Willige
    •  & Joanne Chory

  • Article
    | Open Access

    The yeast and human RNA exosome is structurally related to prokaryotic phosphorylases but degrades RNA only via associated hydrolytic activities. Here the authors show that the RNA exosome of plants, and likely those of a few basal eukaryotes, combines phosphorolytic and hydrolytic activities to degrade RNA.

    • Natalia Sikorska
    • , Hélène Zuber
    •  & Dominique Gagliardi

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