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Article
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Nitrogen and Nod factor signaling determine Lotus japonicus root exudate composition and bacterial assembly
Nod factor signaling, and nitrate distinctly affect Lotus japonicus root exudate, microbiome composition and connectivity, emphasizing the role of signaling between plant and distinct members of soil microbiota in shaping the overall assemblies.
- Ke Tao
- , Ib T. Jensen
- & Simona Radutoiu
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Article
| Open Access
A fine-scale Arabidopsis chromatin landscape reveals chromatin conformation-associated transcriptional dynamics
Plants utilize transcriptional dynamics to adapt to cold stress. Here, Zhang et al. describe a network of chromatin interactions between gene promoters across the Arabidopsis genome that could facilitate co-regulation of gene expression during cold stress.
- Yueying Zhang
- , Qianli Dong
- & Huakun Zhang
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| Open Access
Thylakoid protein FPB1 synergistically cooperates with PAM68 to promote CP47 biogenesis and Photosystem II assembly
The assembly of the Photosystem II proximal antenna CP47 remains a challenging question. Here the authors show that FPB1 and PAM68 act coordinately with Alb3 and the SecY/E translocon to facilitate the co-translational integration of specific regions of CP47 into thylakoids.
- Lin Zhang
- , Junxiang Ruan
- & Lianwei Peng
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| Open Access
Rewiring of a KNOXI regulatory network mediated by UFO underlies the compound leaf development in Medicago truncatula
This study reveals a pathway in which the transformation of trifoliate leaves into pinnate-like pentafoliate leaves is regulated by the conserved regulators of floral development (MtUFO) and leaf development (MtKNOXI) in M. truncatula.
- Zhichao Lu
- , Juanjuan Zhang
- & Chuanen Zhou
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| Open Access
Switching action modes of miR408-5p mediates auxin signaling in rice
miR408-5p typically regulates target IAA30 via translation repression, but switches to cleaving IAA30 mRNA under high auxin conditions. miR393, miR156, miR408-5p and their targets could hierarchically act in auxin pathway and regulate leaf inclination.
- Fuxi Rong
- , Yusong Lv
- & Liang Wu
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| Open Access
The spliceosome-associated protein CWC15 promotes miRNA biogenesis in Arabidopsis
CWC15 is a spliceosome-associated protein in Arabidopsis. Here the authors reports a multifaceted role of CWC15 in promoting microRNA (miRNA) biogenesis by binding to miRNA promoters and interacting with microprocessor components.
- Bangjun Zhou
- , Huihui Yu
- & Bin Yu
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| Open Access
Natural variation in OsMYB8 confers diurnal floret opening time divergence between indica and japonica subspecies
Florets of indica rice open earlier than japonica rice, hindering utilization of the cross subspecies heterosis. Here, the authors show that an OsMYB8-OsJAR1 module regulates diurnal floret opening time divergences between the two subspecies.
- Yajun Gou
- , Yueqin Heng
- & Rongxin Shen
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| Open Access
Copine proteins are required for brassinosteroid signaling in maize and Arabidopsis
Brassinosteroids play vital role in plant growth and development. Here, the authors demonstrate that the plasma membrane-associated copine proteins are new components required for the receptor complex functioning in BR signaling in maize and Arabidopsis.
- Teng Jing
- , Yuying Wu
- & Mingyue Gou
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| Open Access
Core clock genes adjust growth cessation time to day-night switches in poplar
Alique et al. show that poplar trees adjust their seasonal growth timing by finely tuning the daily expression level of the photoperiodic integrator FT2 through a mechanism governed by the circadian clock’s core genes.
- Daniel Alique
- , Arturo Redondo López
- & Mariano Perales
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| Open Access
Chromatin attachment to the nuclear matrix represses hypocotyl elongation in Arabidopsis thaliana
The role of the nuclear matrix in plant nuclei is unclear. Here the authors reveal that nuclear matrix-associated proteins act as a regulatory hub, recruiting both DNA and transcriptional repressors to the nuclear matrix
- Linhao Xu
- , Shiwei Zheng
- & Hua Jiang
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| Open Access
C2-methyladenosine in tRNA promotes protein translation by facilitating the decoding of tandem m2A-tRNA-dependent codons
Duan et al. demonstrate that the m2A modification is ubiquitous in plants and tRNA m2A37 promotes a relaxed conformation of tRNA, enhancing translation efficiency by facilitating decoding of tandem m2A-tRNA-dependent codons.
- Hong-Chao Duan
- , Chi Zhang
- & Guifang Jia
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Article
| Open Access
The mechanism of low blue light-induced leaf senescence mediated by GmCRY1s in soybean
This study provides insights into how shade induces leaf senescence in soybean. The reduction of blue light intensity deactivates GmCRY1s, leading to the degradation of GmRGAs and the upregulation of WRKY100, ultimately promoting leaf senescence.
- Zhuang Li
- , Xiangguang Lyu
- & Bin Liu
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Article
| Open Access
Phytophagy impacts the quality and quantity of plant carbon resources acquired by mutualistic arbuscular mycorrhizal fungi
Plant antagonists may disrupt the allocation of carbon resources from plants to mutualistic microorganisms. Here, the authors report how plants attacked by cyst nematodes and aphids maintain carbon transfer to arbuscular mycorrhizal fungi through fatty acid transfer whilst the limiting the loss of sugars.
- C. A. Bell
- , E. Magkourilou
- & K. J. Field
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| Open Access
Discovery of plant chemical defence mediated by a two-component system involving β-glucosidase in Panax species
In this work, the authors discovered that Panax species, the valuable medicinal plants, have evolved a two-component chemical defence system comprising a chloroplast-localized β-glucosidase and 20(S)-protopanaxadiol ginsenosides.
- Li-Juan Ma
- , Xiao Liu
- & Jian-Bo Wan
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Temporally-coordinated bivalent histone modifications of BCG1 enable fungal invasion and immune evasion
Bivalent histone modifications control various cellular processes in eukaryotes. Here, the authors report that a fungal pathogen deploys bivalent histone modification to fine-tune the expression of BCG1, thereby facilitating successful infection and host immunity evasion.
- Xiaozhen Zhao
- , Yiming Wang
- & Qin Gu
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| Open Access
Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL
The authors employ Micro-C-XL to investigate chromatin structures in plants, specifically focusing on nucleosome-resolution chromatin organizations and enhancer-promoter chromatin loops in Arabidopsis, rice, and soybean.
- Linhua Sun
- , Jingru Zhou
- & Hang He
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| Open Access
A micro RNA mediates shoot control of root branching
Plant shoots and roots act in concert to ensure access to soil nutrients by adapting root growth. The manuscript identifies a key shoot signal, a mobile micro RNA, that systemically controls lateral root initiation to optimize nitrate supply.
- Moritz Sexauer
- , Hemal Bhasin
- & Katharina Markmann
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| Open Access
Arabidopsis telomerase takes off by uncoupling enzyme activity from telomere length maintenance in space
Telomeres are proposed to be sentinels for stress. Here, the authors report a strong induction of telomerase in space-flown Arabidopsis without telomere length changes. Instead, telomerase activity is inversely correlated with genome oxidation
- Borja Barbero Barcenilla
- , Alexander D. Meyers
- & Dorothy E. Shippen
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DNA polymerase ε harmonizes topological states and R-loops formation to maintain genome integrity in Arabidopsis
Here the authors show that Inhibition of DNA topoisomerase 1 (TOP1i) increases the defects in root growth of a DNA damage repair-compromised mutant atm. They identify a mutant DNA polymerase ε (POL2A) which rescues the sensitivity of atm to TOP1i by modulating R-loops dynamics near DNA replication origins.
- Qin Li
- , Jincong Zhou
- & Qianwen Sun
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| Open Access
Spatial transcriptomics uncover sucrose post-phloem transport during maize kernel development
Maize kernels have long intrigued researchers due to their complex structure. Through microscopic sectioning and spatial transcriptomics, the authors observed the spatial distribution of RNA through electronic RNA in situ hybridization maps and discovered how storage accumulation occurs.
- Yuxin Fu
- , Wenxin Xiao
- & Wenqin Wang
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| Open Access
Single-cell analysis identifies genes facilitating rhizobium infection in Lotus japonicus
The authors use single-cell analysis to identify genes specifically expressed in plant root cells that respond to infection by nitrogen-fixing rhizobia. They show that one of these genes, SYMRKL1, is required for normal progression of infection.
- Manuel Frank
- , Lavinia Ioana Fechete
- & Stig Uggerhøj Andersen
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Petal size is controlled by the MYB73/TPL/HDA19-miR159-CKX6 module regulating cytokinin catabolism in Rosa hybrida
Expression of MIR159 is attenuated by a MYB73/TPL/HDA19 repression complex during rose petal development. Reduced MIR159 levels lead to accumulation of Cytokinin Oxidase 6, causing cytokinin clearance and subsequent arrest of cell division.
- Weikun Jing
- , Feifei Gong
- & Nan Ma
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Article
| Open Access
Nanobody-based VSR7 tracing shows clathrin-dependent TGN to Golgi recycling
Nanobody-epitope interaction-based analysis of the Arabidopsis VACUOLAR SORTING RECEPTOR7 (VSR7) suggests immobilization-based ligand transport to the TGN/EE and ends due to acidity-driven ligand release and clathrin-dependent receptor recycling.
- Xiaoyu Shao
- , Hao Xu
- & Peter Pimpl
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MSH2 stimulates interfering and inhibits non-interfering crossovers in response to genetic polymorphism
Interhomolog polymorphism, which is detected by MSH2-containing heterodimers, may affect crossover outcomes during meiosis. Here, the authors revealed antagonistic effects of MSH2 on interfering and non-interfering crossover pathways in Arabidopsis.
- Julia Dluzewska
- , Wojciech Dziegielewski
- & Piotr A. Ziolkowski
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| Open Access
Efficient 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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| Open Access
Control 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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| Open Access
Comparative 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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| Open Access
Phosphate 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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| Open Access
Identification 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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| Open Access
Molecular 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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| Open Access
The 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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| Open Access
A 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 Access
Functional annotation of proteins for signaling network inference in non-model species
An artificial-intelligence network is used to generate highly accurate predictions of proteins’ functionality. The predictions on the identity of regulatory proteins is used to create regulatory networks and make discoveries about complex biological systems.
- Lisa Van den Broeck
- , Dinesh Kiran Bhosale
- & Rosangela Sozzani
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| Open Access
ERFVII action and modulation through oxygen-sensing in Arabidopsis thaliana
Oxygen is essential for plant life. Here the authors define new functions and components of the plant oxygen sensing mechanism providing an understanding of the biochemistry of sensing and physiological responses allowing plant roots to survive in the soil.
- Agata Zubrycka
- , Charlene Dambire
- & Michael J. Holdsworth
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| Open Access
The OsSGS3-tasiRNA-OsARF3 module orchestrates abiotic-biotic stress response trade-off in rice
Gu et al. report that the OsSGS3-tasiRNA-OsARF3 module plays an important role in coordinating the trade-off between heat tolerance and disease resistance, which positively regulates thermotolerance but negatively modulates immunity in rice.
- Xueting Gu
- , Fuyan Si
- & Junzhong Liu
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| Open Access
Fungal small RNAs ride in extracellular vesicles to enter plant cells through clathrin-mediated endocytosis
Fungal pathogen Botrytis cinerea can send sRNAs to plant cells to suppress plant immunity. Here the authors demonstrate that B. cinerea utilizes extracellular vesicles (EVs) to secrete Bc-sRNAs, which are then internalized by plant cells through clathrin-mediated endocytosis (CME).
- Baoye He
- , Huan Wang
- & Hailing Jin
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| Open Access
An unconventional proanthocyanidin pathway in maize
Maize has an unconventional proanthocyanidin (PA) biosynthetic pathway which produces rare stereoisomers of PA monomers and dimers, highlighting an opportunity for further improving the nutritional value of maize.
- Nan Lu
- , Ji Hyung Jun
- & Richard A. Dixon
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Article
| Open Access
Manipulating microRNA miR408 enhances both biomass yield and saccharification efficiency in poplar
Modifying plant lignin pathway to enhance saccharification efficiency is often associated with growth penalty. Here, the authors show that overexpression of Pag-miR408 in poplar leads to enhanced saccharification efficiency and growth in both laboratory and field conditions, and laccase genes are the targets of Pag-miR408.
- Yayu Guo
- , Shufang Wang
- & Jinxing Lin
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| Open Access
Cell type-specific mapping of ion distribution in Arabidopsis thaliana roots
Giehl et al. describe a method for simultaneous quantification of up to 11 mineral elements in different root cell types, explore the consequences of perturbed xylem loading and identify a cell type-specific constraint for metal sequestration in roots.
- Ricardo F. H. Giehl
- , Paulina Flis
- & Nicolaus von Wirén
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| Open Access
OsMADS17 simultaneously increases grain number and grain weight in rice
The trade-off between grain number and grain weight is a major obstacle for increasing rice yield. Here, the authors show that variation in 5’ UTR of OsMADS17 can simultaneously increase grain number and grain weight through decreasing mRNA translation efficiency.
- Yuanjie Li
- , Sheng Wu
- & Chuanqing Sun
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Article
| Open Access
An ancient metabolite damage-repair system sustains photosynthesis in plants
Rubisco is responsible for sequestering virtually all of the carbon dioxide in the global carbon cycle. Here, the authors demonstrate that two conserved phosphatases degrade Rubisco misfire products that inhibit photosynthesis in plants.
- Dario Leister
- , Anurag Sharma
- & Thilo Rühle
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Article
| Open Access
Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors
Here, the authors describe a new method to study how some proteins work together to control gene activity. They show that certain protein pairs can recognize new DNA sequences that they can’t recognize individually and control a wider range of genes.
- Miaomiao Li
- , Tao Yao
- & Shao-shan Carol Huang
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| Open Access
Arabidopsis TRB proteins function in H3K4me3 demethylation by recruiting JMJ14
TRB proteins have been shown to recruit PRC2 for H3K27me3 deposition. This work shows that TRBs also recruit JMJ14 to remove H3K4me3, demonstrating that TRBs silence the target genes via a combinatorial histone modification mechanism.
- Ming Wang
- , Zhenhui Zhong
- & Steven E. Jacobsen
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Article
| Open Access
Phytochrome B photobodies are comprised of phytochrome B and its primary and secondary interacting proteins
Phytochrome is a photoreceptor forming a membraneless organelle called a photobody. The authors isolated the photobody and found that the photobody is made of not only phytochrome but also its primary and secondary interacting proteins.
- Chanhee Kim
- , Yongmin Kwon
- & Giltsu Choi
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| Open Access
Distinct roles of Arabidopsis ORC1 proteins in DNA replication and heterochromatic H3K27me1 deposition
The dynamics of DNA replication factors is crucial for cell cycle progression. Arabidopsis encode two origin recognition complex 1 proteins, ORC1a and ORC1b, with distinct roles in DNA replication and deposition of heterochromatic H3K27me1, respectively.
- Zaida Vergara
- , María S. Gomez
- & Crisanto Gutierrez
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| Open Access
The Arabidopsis endosperm is a temperature-sensing tissue that implements seed thermoinhibition through phyB
Piskurewicz et al. show that seed thermoinhibition is controlled by endospermic phytochrome B (phyB). High temperature decreases endospermic phyB signaling, which promotes DELLA- and PIFmediated endospermic ABA release that blocks germination.
- Urszula Piskurewicz
- , Maria Sentandreu
- & Luis Lopez-Molina
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| Open Access
Histone H2A monoubiquitination marks are targeted to specific sites by cohesin subunits in Arabidopsis
How histone H2A monoubiquitination (H2Aub1) is established at specific genomic locations remains unclear. Here, the authors report that Arabidopsis cohesin subunits SCC3 and SYN4 are involved in H2Aub1 through their direct or indirect interaction with BMI1A/B/C subunits of PRC1, the E3 ligases in PRC1 for H2Aub1.
- Yu Zhang
- , Min Ma
- & Yuda Fang
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Article
| Open Access
HSFA1a modulates plant heat stress responses and alters the 3D chromatin organization of enhancer-promoter interactions
Here the authors show genome-wide chromatin changes and transcriptional reprogramming occur in response to heat stress in tomato, leading to the transient formation of promoter-enhancer contacts to drive the expression of heat-stress responsive genes. Furthermore, they show chromatin spatial reorganization requires HSFA1a, a transcription factor (TF) essential for heat stress tolerance in tomato.
- Ying Huang
- , Jing An
- & Moussa Benhamed
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| Open Access
Complementary peptides represent a credible alternative to agrochemicals by activating translation of targeted proteins
Feeding an increasing world population in the context of climate change is one of the grand challenges faced by our generation. Here, the authors show that external application of synthetic complementary peptides can increase the abundance of target proteins to modulate plant growth or stress resistance.
- Mélanie Ormancey
- , Bruno Guillotin
- & Jean-Philippe Combier
The phosphorylation of carboxyl-terminal eIF2α by SPA kinases contributes to enhanced translation efficiency during photomorphogenesis