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<jats:title>SUMMARY</jats:title><jats:p>Wheat yellow mosaic virus (WYMV) causes severe wheat viral disease in Asia. However, the viral suppressor of RNA silencing (VSR) encoded by WYMV has not been identified. Here, the P1 protein encoded by WYMV RNA2 was shown to suppress RNA silencing in <jats:italic>Nicotiana benthamiana</jats:italic>. Mutagenesis assays revealed that the alanine substitution mutant G175A of P1 abolished VSR activity and mutant Y10A VSR activity remained only in younger leaves. P1, but not G175A, interacted with gene silencing‐related protein, <jats:italic>N. benthamiana</jats:italic> calmodulin‐like protein (NbCaM), and calmodulin‐binding transcription activator 3 (NbCAMTA3), and Y10A interacted with NbCAMTA3 only. Competitive Bimolecular fluorescence complementation and co‐immunoprecipitation assays showed that the ability of P1 disturbing the interaction between NbCaM and NbCAMTA3 was stronger than Y10A, Y10A was stronger than G175A. <jats:italic>In vitro</jats:italic> transcript inoculation of infectious WYMV clones further demonstrated that VSR‐defective mutants G175A and Y10A reduced WYMV infection in wheat (<jats:italic>Triticum aestivum</jats:italic> L.), G175A had a more significant effect on virus accumulation in upper leaves of wheat than Y10A. Moreover, RNA silencing, temperature, and autophagy have significant effects on the accumulation of P1 in <jats:italic>N. benthamiana.</jats:italic> Taken together, WYMV P1 acts as VSR by interfering with calmodulin‐associated antiviral RNAi defense to facilitate virus infection in wheat, which has provided clear insights into the function of P1 in the process of WYMV infection.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Black pepper (<jats:italic>Piper nigrum</jats:italic> L.), the world renown as the King of Spices, is not only a flavorsome spice but also a traditional herb. Piperine, a species‐specific piper amide, is responsible for the major bioactivity and pungent flavor of black pepper. However, several key steps for the biosynthesis of piperoyl‐CoA (acyl‐donor) and piperidine (acyl‐acceptor), two direct precursors for piperine, remain unknown. In this study, we used guilt‐by‐association analysis of the combined metabolome and transcriptome, to identify two feruloyldiketide‐CoA synthases responsible for the production of the C5 side chain scaffold feruloyldiketide‐CoA intermediate, which is considered the first and important step to branch metabolic fluxes from phenylpropanoid pathway to piperine biosynthesis. In addition, we also identified the first two key enzymes for piperidine biosynthesis derived from lysine in <jats:italic>P. nigrum</jats:italic>, namely a lysine decarboxylase and a copper amine oxidase. These enzymes catalyze the production of cadaverine and 1‐piperideine, the precursors of piperidine. <jats:italic>In vivo</jats:italic> and <jats:italic>in vitro</jats:italic> experiments verified the catalytic capability of them. In conclusion, our findings revealed enigmatic key steps of piperine biosynthetic pathway and thus provide a powerful reference for dissecting the biosynthetic logic of other piper amides.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Lipocalins constitute a conserved protein family that binds to and transports a variety of lipids while fatty acid desaturases (FADs) are required for maintaining the cell membrane fluidity under cold stress. Nevertheless, it remains unclear whether plant lipocalins promote FADs for the cell membrane integrity under cold stress. Here, we identified the role of OsTIL1 lipocalin in FADs‐mediated glycerolipid remodeling under cold stress. Overexpression and CRISPR/Cas9 mediated gene edition experiments demonstrated that <jats:italic>OsTIL1</jats:italic> positively regulated cold stress tolerance by protecting the cell membrane integrity from reactive oxygen species damage and enhancing the activities of peroxidase and ascorbate peroxidase, which was confirmed by combined cold stress with a membrane rigidifier dimethyl sulfoxide or a H<jats:sub>2</jats:sub>O<jats:sub>2</jats:sub> scavenger dimethyl thiourea. <jats:italic>OsTIL1</jats:italic> overexpression induced higher 18:3 content, and higher 18:3/18:2 and (18:2 + 18:3)/18:1 ratios than the wild type under cold stress whereas the gene edition mutant showed the opposite. Furthermore, the lipidomic analysis showed that <jats:italic>OsTIL1</jats:italic> overexpression led to higher contents of 18:3‐mediated glycerolipids, including galactolipids (monoglactosyldiacylglycerol and digalactosyldiacylglycerol) and phospholipids (phosphatidyl glycerol, phosphatidyl choline, phosphatidyl ethanolamine, phosphatidyl serine and phosphatidyl inositol) under cold stress. RNA‐seq and enzyme linked immunosorbent assay analyses indicated that <jats:italic>OsTIL1</jats:italic> overexpression enhanced the transcription and enzyme abundance of four ω‐3 FADs (<jats:italic>OsFAD3‐1/3‐2</jats:italic>, <jats:italic>7</jats:italic>, and <jats:italic>8</jats:italic>) under cold stress. These results reveal an important role of <jats:italic>OsTIL1</jats:italic> in maintaining the cell membrane integrity from oxidative damage under cold stress, providing a good candidate gene for improving cold tolerance in rice.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>The characterization of <jats:italic>cis</jats:italic>‐regulatory DNA elements (CREs) is essential for deciphering the regulation of gene expression in eukaryotes. Although there have been endeavors to identify CREs in plants, the properties of CREs in polyploid genomes are still largely unknown. Here, we conducted the genome‐wide identification of DNase I‐hypersensitive sites (DHSs) in leaf and stem tissues of the auto‐octoploid species <jats:italic>Saccharum officinarum</jats:italic>. We revealed that DHSs showed highly similar distributions in the genomes of these two <jats:italic>S. officinarum</jats:italic> tissues. Notably, we observed that approximately 74% of DHSs were located in distal intergenic regions, suggesting considerable differences in the abundance of distal CREs between <jats:italic>S. officinarum</jats:italic> and other plants. Leaf‐ and stem‐dependent transcriptional regulatory networks were also developed by mining the binding motifs of transcription factors (TFs) from tissue‐specific DHSs. Four TEOSINTE BRANCHED 1, CYCLOIDEA, and PCF1 (TCP) TFs (TCP2, TCP4, TCP7, and TCP14) and two ethylene‐responsive factors (ERFs) (ERF109 and ERF03) showed strong causal connections with short binding distances from each other, pointing to their possible roles in the regulatory networks of leaf and stem development. Through functional validation in transiently transgenic protoplasts, we isolate a set of tissue‐specific promoters. Overall, the DHS maps presented here offer a global view of the potential transcriptional regulatory elements in polyploid sugarcane and can be expected to serve as a valuable resource for both transcriptional network elucidation and genome editing in sugarcane breeding.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Chromoplasts act as a metabolic sink for carotenoids, in which plastoglobules serve as versatile lipoprotein particles. PGs in chloroplasts have been characterized. However, the features of PGs from non‐photosynthetic plastids are poorly understood. We found that the development of chromoplast plastoglobules (CPGs) in globular and crystalloid chromoplasts of citrus is associated with alterations in carotenoid storage. Using Nycodenz density gradient ultracentrifugation, an efficient protocol for isolating highly purified CPGs from sweet orange (<jats:italic>Citrus sinensis</jats:italic>) pulp was established. Forty‐four proteins were defined as likely comprise the core proteome of CPGs using comparative proteomics analysis. Lipidome analysis of different chromoplast microcompartments revealed that the nonpolar microenvironment within CPGs was modified by 35 triacylglycerides, two sitosterol esters, and one stigmasterol ester. Manipulation of the CPG‐localized gene <jats:italic>CsELT1</jats:italic> (<jats:styled-content>e</jats:styled-content>sterase/<jats:styled-content>l</jats:styled-content>ipase/<jats:styled-content>t</jats:styled-content>hioesterase) in citrus calli resulted in increased lipids and carotenoids, which is further evidence that the nonpolar microenvironment of CPGs contributes to carotenoid accumulation and storage in the chromoplasts. This multi‐feature analysis of CPGs sheds new light on the role of chromoplasts in carotenoid metabolism, paving the way for manipulating carotenoid content in citrus fruit and other crops.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Plants grown under low magnesium (Mg) soils are highly susceptible to encountering light intensities that exceed the capacity of photosynthesis (<jats:italic>A</jats:italic>), leading to a depression of photosynthetic efficiency and eventually to photooxidation (i.e., leaf chlorosis). Yet, it remains unclear which processes play a key role in limiting the photosynthetic energy utilization of Mg‐deficient leaves, and whether the plasticity of <jats:italic>A</jats:italic> in acclimation to irradiance could have cross‐talk with Mg, hence accelerating or mitigating the photodamage. We investigated the light acclimation responses of rapeseed (<jats:italic>Brassica napus</jats:italic>) grown under low‐ and adequate‐Mg conditions. Magnesium deficiency considerably decreased rapeseed growth and leaf <jats:italic>A</jats:italic>, to a greater extent under high than under low light, which is associated with higher level of superoxide anion radical and more severe leaf chlorosis. This difference was mainly attributable to a greater depression in dark reaction under high light, with a higher Rubisco fallover and a more limited mesophyll conductance to CO<jats:sub>2</jats:sub> (<jats:italic>g</jats:italic><jats:sub>m</jats:sub>). Plants grown under high irradiance enhanced the content and activity of Rubisco and <jats:italic>g</jats:italic><jats:sub>m</jats:sub> to optimally utilize more light energy absorbed. However, Mg deficiency could not fulfill the need to activate the higher level of Rubisco and Rubisco activase in leaves of high‐light‐grown plants, leading to lower Rubisco activation and carboxylation rate. Additionally, Mg‐deficient leaves under high light invested more carbon per leaf area to construct a compact leaf structure with smaller intercellular airspaces, lower surface area of chloroplast exposed to intercellular airspaces, and CO<jats:sub>2</jats:sub> diffusion conductance through cytosol. These caused a more severe decrease in within‐leaf CO<jats:sub>2</jats:sub> diffusion rate and substrate availability. Taken together, plant plasticity helps to improve photosynthetic energy utilization under high light but aggravates the photooxidative damage once the Mg nutrition becomes insufficient.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Chloroplasts are essential organelles in plants that contain chlorophylls and facilitate photosynthesis for growth and development. As photosynthetic efficiency significantly impacts crop productivity, understanding the regulatory mechanisms of chloroplast development has been crucial in increasing grain and biomass production. This study demonstrates the involvement of <jats:italic>OsGATA16</jats:italic>, an ortholog of Arabidopsis <jats:italic>GATA, NITRATE INDUCIBLE, CARBON‐METABOLISM INVOLVED</jats:italic> (<jats:italic>GNC</jats:italic>), and <jats:italic>GNC‐LIKE/CYTOKININ‐RESPONSIVE GATA FACTOR 1</jats:italic> (<jats:italic>GNL/CGA1</jats:italic>), in chlorophyll biosynthesis and chloroplast development in rice (<jats:italic>Oryza sativa</jats:italic>). The <jats:italic>osgata16‐1</jats:italic> knockdown mutants produced pale‐green leaves, while <jats:italic>OsGATA16</jats:italic>‐overexpressed plants (<jats:italic>OsGATA16</jats:italic>‐OE1) generated dark‐green leaves, compared to their parental <jats:italic>japonica</jats:italic> rice. Reverse transcription and quantitative PCR analysis revealed downregulation of genes related to chloroplast division, chlorophyll biosynthesis, and photosynthesis in the leaves of <jats:italic>osgata16‐1</jats:italic> and upregulation in those of <jats:italic>OsGATA16</jats:italic>‐OE1. Additionally, <jats:italic>in vivo</jats:italic> binding assays showed that OsGATA16 directly binds to the promoter regions of <jats:italic>OsHEMA</jats:italic>, <jats:italic>OsCHLH</jats:italic>, <jats:italic>OsPORA</jats:italic>, <jats:italic>OsPORB</jats:italic>, and <jats:italic>OsFtsZ</jats:italic>, and upregulates their expression. These findings indicate that OsGATA16 serves as a positive regulator controlling chlorophyll biosynthesis and chloroplast development in rice.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Inter‐virus relationships in mixed infections and virus‐drought relationships are important in agriculture and natural vegetation. In this quantitative review, we sampled published factorial experiments to probe for relationships against the null hypothesis of additivity. Our sample captured antagonistic, additive and synergistic inter‐virus relationships in double infections. Virus‐drought relationships in our sample were additive or antagonistic, reinforcing the notion that viruses have neutral or positive effects on droughted plants, or that drought enhances plant tolerance to viruses. Both inter‐virus and virus‐drought relationships vary with virus species, host plant to the level of cultivar or accession, timing of infection, plant age and trait and growing conditions. The trait‐dependence of these relationships has implications for resource allocation in plants. Owing to lagging theories, more experimental research in these fields is bound to return phenomenological outcomes. Theoretical work can advance in two complementary directions. First, the effective theory models the behaviour of the system without specifying all the underlying causes that lead to system state change. Second, mechanistic theory based on a nuanced view of the plant phenotype that explicitly considers downward causation; the influence of the plant phenotype on inter‐virus relations and vice versa; the impact of timing, intensity and duration of drought interacting with viruses to modulate the plant phenotype; both the soil (moisture) and atmospheric (vapour pressure deficit) aspects of drought. Theories should scale in time, from short term to full growing season, and in levels of organisation up to the relevant traits: crop yield in agriculture and fitness in nature.</jats:p>