ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology

Construction of multi-targeted CRISPR libraries in tomato to overcome functional redundancy at genome-scale level

Genetic variance is vital for breeding programs and mutant screening, yet traditional mutagenesis methods wrestle with genetic redundancy and a lack of specificity in gene targeting. CRISPR-Cas9 offers precise, site-specific gene editing, but its application in crop improvement has been limited by scalability challenges. In this study, we develop genome-wide multi-targeted CRISPR libraries in tomato, enhancing the scalability of CRISPR gene editing in crops and addressing the challenges of redundancy while maintaining its precision. We design 15,804 unique single guide RNAs (sgRNAs), each targeting multiple genes within the same gene families. These sgRNAs are classified into 10 sub-libraries based on gene function. We generate approximately 1300 independent CRISPR lines and successfully identify mutants with distinct phenotypes related to fruit development, fruit flavor, nutrient uptake, and pathogen response. Additionally, we develop CRISPR-GuideMap, a double-barcode tagging system to enable large-scale sgRNA tracking in generated plants. Our results demonstrate that multi-targeted CRISPR libraries are scalable and effective for large-scale gene editing and offer an approach to overcome gene functional redundancy in basic plant research and crop breeding.

Expression profiling and transcriptional regulation of the SRS transcription factor gene family of common bean (Phaseolus vulgaris) in symbiosis with Rhizobium etli

The SRS/STY transcription factors from the model legumes: Lotus japonicus and Medicago truncatula, are part of regulatory networks that play relevant roles for nodule development during the N-fixing symbiosis with rhizobia. In this work we analyzed the participation of the PvSRS transcription factors from common bean (Phaseolus vulgaris), a most important legume crop, in the symbiosis with Rhizobium etli. Our phylogenetic analysis of SRS TFs across five plant species, including four legumes and Arabidopsis thaliana, identified clades that group SRS proteins that are highly expressed in legume nodules and in Arabidopsis roots. A qRT-PCR expression analysis of the 10 PvSRS in root/nodule of inoculated plants, revealed that all the PvSRS genes are expressed at different stages of the symbiosis, albeit at different levels. Based on what is known for L. japonicus, we demonstrated that the PvSRS10 gene -with highest expression during symbiosis- is transcriptionally activated by NF-Y transcription factor, thus indicating its participation in the NIN-NF-Y regulatory cascade. Based on our previous work about the relevant role of members from the MADS-domain/AGL transcription factors as regulators of the N-fixing symbiosis, in this work we demonstrated the transcriptional regulation of PvSRS10 by the MADS-TF PvFUL-like. Analysis of protein-protein interaction networks predicted thatPvSRS5 and PvSRS6 interact with proteins involved in transcriptional regulation and the auxin-activated signaling pathway. The regulatory mechanisms of PvSRS TF in common bean symbiosis may be related to auxin biosynthesis regulation, that is essential for determinate nodules development. Our study highlights the role of PvSRS TF in the N-/fixing symbiosis, a relevant process for sustainable agriculture.

Chloroplastic Aspartyl-tRNA Synthetase Is Required for Chloroplast Development, Photosynthesis and Photorespiratory Metabolism

Photorespiration is a complex metabolic process linked to primary plant metabolism and influenced by environmental factors, yet its regulation remains poorly understood. In this study, we identified the asprs3-1 mutant, which displays a photorespiratory phenotype with leaf chlorosis, stunted growth, and diminished photosynthesis under ambient CO2, but normal growth under elevated CO2 conditions. Map-based cloning and genetic complementation identified AspRS3 as the mutant gene, encoding an aspartyl-tRNA synthetase. AspRS3 is localised in both chloroplasts and mitochondria, with the chloroplast being the primary site of its physiological function. The AspRS3 mutation impacts the expression of plastid-encoded and photosynthesis-related genes, leading to decreased levels of chloroplast-encoded proteins such as ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (RBCL) and ferredoxin-dependent glutamate synthase (Fd-GOGAT). Furthermore, we observed an accumulation of photorespiratory intermediates, including glycine and glycerate, and reactive oxygen species (ROS) in asprs3-1. However, under high CO2, the expression of these proteins, the accumulation of photorespiratory intermediates, and ROS levels in asprs3-1 did not significantly differ from those in the wild type. We propose that elevated CO2 mitigates the asprs3-1 phenotype by inhibiting Rubisco oxygenation and photorespiratory metabolism. This study highlights the role of aminoacyl-tRNA synthetases in regulating photorespiration and provides new insights into its metabolic control.

Exploring the modulation of phosphorylation and SUMOylation-dependent NPR1 conformational switching on immune regulators TGA3 and WRKY70 through molecular simulation

NPR1 (Nonexpressor pathogenesis-related genes 1) is regulated by multisite phosphorylation and SUMOylation, serving as a master switch for effector-triggered plant immunity through a transcriptional activator (TGA3) and repressor (WRKY70) are experimentally well studied. However, the conformational relationship between the various phosphorylation, un-phosphorylation states, and SUMOylation's role in the functional switch remains unclear. Using deep learning-based molecular modeling, docking, and multi-nanosecond simulations (totaling 2 μs) with end-state free energy calculations, we unveil how different phosphorylation states impact the dynamic stability of NPR1's four phospho-serine residues (Ser11, Ser15, Ser55, & Ser59) and binding of the TGA3-WRKY70 over SUMOylation. Results from our simulations show that the salicylic-acid induced P-Ser11/15NPR1-SUMO3 stabilizes helices and the flexible activation loop (α22Lys423 - α1Arg50 & L35Asp467-Arg51α51, and Gly27L3), thereby switching association with TGA3. The inter-helix salt-bridge formed (L10Arg99-Glu323α9 and α14Glu280-Pro264L6) between the phosphorylated NPR1-SUMO3-TGA3 engage in tight control of conformational regulation were disengaged in the unphosphorylated system. The P-Ser55/59NPR1-SUMO3-WRKY70 reorients itself and forms an electrostatic and hydrogen bond with Lys145α7 - L2Asp26, L6Arg99 - Leu293L18 and Lys262L15 - Glu241L15, α13Val239 (α310), & L17Leu267 keeps complex stable and quiescent compare to unphosphorylated NPR1-WRKY70. Subsequently, the essential dynamic and secondary structural analysis reveals that the phosphorylation inhibits the α516 (long helix) formation and reduces the communication space between the 460α25-βturn3-α30-L42590 (NPR1) and 90L9-L10107 (SUMO3), making the binding more suitable for TGA3 (260βturn-L6270) and WRKY70 (230L15-L16265) via activation loop. These findings, which reveal the atomic and structural details of the NPR1's post-translational modification, will illuminate future investigations into enhancing plant immunity.

Integrated analysis of transcriptome and metabolome reveals the molecular basis of quality differences in Alpinia oxyphylla Miq. From geo-authentic and non-authentic areas

Alpinia oxyphylla Miq., a well-accepted medicinal and edible plant in south China. The primary ingredients of this medicine vary significantly depending on their origin, which profoundly impacts its quality. In this study, a principal component analysis was performed on 17 different planting areas of A. oxyphylla, with nootkatone and kaempferol identified as representative sesquiterpenoids and flavonoids, respectively. To investigate the genes involved in nootkatone and kaempferol biosynthesis, a combined transcriptome and metabolome profiling was carried out on materials sourced from geo-authentic and non-authentic areas. The transcriptome analysis of these two types of accessions identified 96,691 unigenes, with 13,589 genes showing differential expression in both regions. Metabolome analysis revealed 2859 differentially accumulated metabolites across the four pairwise comparisons. Correlation analysis uncovered a number of genes, that associated with the differential biosynthesis of nootkatone and kaempferol in A. oxyphylla fruits from geo-authentic and non-authentic areas. Further investigation highlighted the candidate gene AoFMO1's ability to heterologously biosynthesize nootkatone in Arabidopsis thaliana leaves. This research lays the groundwork for a deeper understanding of the molecular mechanisms behind the authentication of A. oxyphylla's quality synthesis, and presents a comprehensive list of candidate genes for future functional studies to enhance the development of high-quality A. oxyphylla varieties rich in medicinal ingredients.

A novel auxin methyltransferase of the SABATH family for phenylacetic acid methylation is conserved in potato and tomato

The SABATH family of methyltransferases is known for methylating a wide range of substrates, including hormones and secondary metabolites. A notable member of this family is the auxin methyltransferase IAMT which uses indole-3-acetic acid (IAA) as the substrate. This study aims to determine whether methyl phenylacetate (MePAA), the methyl ester of another auxin, phenylacetic acid (PAA), is synthesized by SABATH methyltransferases. Potato (Solanum tuberosum L. cv. Désirée) was chosen as the primary model because it produces MePAA exclusively in flowers. Based on the structural similarity of IAA and PAA, our initial hypothesis was that MePAA is synthesized by an IAMT-like enzyme. The potato genome contains two IAMT-like genes. However, their recombinant enzymes expressed in Escherichia coli were shown to catalyze the methylation of IAA but not PAA, thus rejecting our initial hypothesis. Among the 23 potato SABATH genes, two exhibited flower-specific expression. One was excluded because it had already been identified as an IAMT. In vitro assays of the enzyme encoded by the other gene, StSABATH6, confirmed its catalytic activity against PAA. Consequently, this enzyme was renamed StPAAMT. Notably, StPAAMT has an ortholog in both cultivated and wild tomatoes. The gene from tomato (Solanum lycopersicum), SlPAAMT, was verified to encode PAA methyltransferase. Further genomic and phylogenetic analyses of five Solanum species showed that the PAAMT gene was likely absent in eggplant (Solanum melongena), implying its origin in the common ancestor of potato and tomato. The structural analysis identified key amino acids associated with the substrate specificity of PAAMT. This work provides new insights into the evolution of auxin methyltransferases, particularly PAAMT, as members of the SABATH family.

Damage activates EXG1 and RLP44 to suppress vascular differentiation during regeneration in Arabidopsis

Plants possess remarkable regenerative abilities to form de novo vasculature after damage and in response to pathogens that invade and withdraw nutrients. To identify common factors that affect vascular formation upon stress, we searched for Arabidopsis thaliana genes differentially expressed upon Agrobacterium infection, nematode infection, and plant grafting. One such gene is cell wall-related and highly induced by all three stresses, which we named ENHANCED XYLEM AND GRAFTING1 (EXG1), since its mutations promote ectopic xylem formation in a vascular cell induction system and enhance graft formation. Further observations revealed that exg1 mutants show inhibited cambium development and callus formation but enhanced tissue attachment, syncytium size, phloem reconnection, and xylem formation. Given that brassinosteroids also promote xylem differentiation, we analyzed brassinosteroid-related genes and found that mutations in RLP44 encoding a receptor-like protein cause similar regeneration-related phenotypes as mutations in EXG1. Like EXG1, RLP44 expression is also induced by grafting and wounding. Mutations in EXG1 and RLP44 affect the expression of many genes in common, including those related to cell walls and genes important for vascular regeneration. Our results suggest that EXG1 integrates information from wounding or pathogen stress and functions with RLP44 to suppress vascular differentiation during regeneration and healing.

Characterization of Phosphatidylcholine:Diacylglycerol Cholinephosphotransferases from Soybean (Glycine max)

Plant oils in the form of triacylglycerols (TAGs) have important food and industrial applications. The fatty acid composition of TAGs, especially their degree of unsaturation, affects the oil value and applications. Phosphatidylcholine:Diacylglycerol Cholinephosphotransferase (PDCT) facilitates the exchange of fatty acids between phosphatidylcholine and diacylglycerol, influencing the degree of fatty acid unsaturation. In this study, we identified and characterized two PDCT isoforms from soybean (Glycine max). Phylogenetic and structural analyses revealed that PDCTs are widely conserved across Embryophyta and share key sequence and structural features among species. Subcellular localization assays using transient expression of fluorescent protein-tagged GmPDCTs in Nicotiana benthamiana leaves confirmed their localization to the endoplasmic reticulum. Expression of GmPDCTs in yeast altered lipid unsaturation, while in vitro enzyme assays using yeast microsomal fractions confirmed that both GmPDCTs are catalytically active, preferring unsaturated substrates. Further structural analysis and mutagenesis revealed that the N-terminus and several amino acids within/near the predicted catalytic domains are critical to the PDCT function. Lastly, stable overexpression of GmPDCTs in Arabidopsis thaliana rod1 (pdct) mutant plants successfully restored a wildtype lipid phenotype, providing evidence that these genes encode functional PDCTs. Together, these findings provide new insights into PDCT structure-function relationships, offering potential targets for bioengineering strategies aimed at optimizing oil composition.

The Atypical Pectin Methylesterase Family Member PME31 Promotes Seedling Lipid Droplet Utilization

In plants, the primary form of energy stored in seed lipid droplets, triacylglycerol (TAG), is catabolized during germination to support pre-photosynthetic growth. Although this process is essential for seedling development, it is incompletely understood. In a screen for Arabidopsis thaliana mutants displaying delayed degradation of the lipid droplet coat protein oleosin, five independent mutations in PECTIN METHYLESTERASE31 (PME31) were recovered. In addition to delayed oleosin degradation, pme31 mutant seedlings exhibited sustained lipid droplets and elevated levels of several TAG and diacylglycerol species. Although structural prediction classified PME31 as a pectinesterase, this structural family also includes a putative E. coli lipase, YbhC. Moreover, PME31 lacks an N-terminal signal peptide that would target it to the cell wall, where pectin resides. We found that a fluorescent PME31 reporter was cytosolic and partially associated with peroxisomes, the site of fatty acid catabolism, during lipid mobilization. Our findings suggest that, in contrast to canonical PMEs, which modify cell wall pectin, PME31 functions at peroxisomes to directly or indirectly promote lipid mobilization.

Arabidopsis SGS3 is recruited to chromatin by CHR11 to select RNA that initiate siRNA production

In plants, aberrant RNAs produced by endogenous genes or transgenes are normally degraded by the nuclear and cytosolic RNA quality control (RQC) pathways. Under certain biotic or abiotic stresses, RQC is impaired, and aberrant RNAs are converted into siRNAs that initiate post-transcriptional gene silencing (PTGS) in the cytosol. How aberrant RNAs are selected and brought to the cytoplasm is not known. Here we show that the RNA-binding protein SUPPRESSOR OF GENE SILENCING (SGS)3 shuttles between the cytosol and the nucleus where it associates with the ISWI-like CHROMATIN REMODELER (CHR)11 and with RNAs transcribed from PTGS-sensitive transgene loci binding CHR11. Knocking down CHR11 and its paralog CHR17 strongly reduces transgene PTGS, suggesting that SGS3 recruitment by CHR11/17 facilitates PTGS initiation. CHR11 is also enriched at endogenous protein-coding genes (PCGs) producing nat-siRNAs and va-siRNAs under biotic or abiotic stresses, and this production is reduced in chr11 chr17 double mutants at genome-wide level. Moreover, impairing CHR11 and CHR17 rescues the lethal phenotype caused by the massive production of siRNAs from PCGs in RQC-deficient mutants. We propose that SGS3 recruitment by CHR11/17 allows exporting RNAs to the cytosol to initiate the production of siRNAs.

The Arabidopsis thaliana core splicing factor PORCUPINE/SmE1 requires intron-mediated expression

Plants are prone to genome duplications and tend to preserve multiple gene copies. This is also the case for the genes encoding the Sm proteins of Arabidopsis thaliana (L). The Sm proteins are best known for their roles in RNA processing such as pre-mRNA splicing and nonsense-mediated mRNA decay. In this study, we have taken a closer look at the phylogeny and differential regulation of the SmE-coding genes found in A. thaliana, PCP/SmE1, best known for its cold-sensitive phenotype, and its paralog, PCPL/SmE2. The phylogeny of the PCP homologs in the green lineage shows that SmE duplications happened multiple times independently in different plant clades and that the duplication that gave rise to PCP and PCPL occurred only in the Brassicaceae family. Our analysis revealed that A. thaliana PCP and PCPL proteins, which only differ in two amino acids, exhibit a very high level of functional conservation and can perform the same function in the cell. However, our results indicate that PCP is the prevailing copy of the two SmE genes in A. thaliana as it is more highly expressed and that the main difference between PCP and PCPL resides in their transcriptional regulation, which is strongly linked to intronic sequences. Our results provide insight into the complex mechanisms that underlie the differentiation of the paralogous gene expression as an adaptation to stress.

The aerial epidermis is a major site of quinolizidine alkaloid biosynthesis in narrow-leafed lupin

Lupins are promising protein crops that accumulate toxic quinolizidine alkaloids (QAs) in the seeds, complicating their end-use. QAs are synthesized in green organs (leaves, stems, and pods) and a subset of them is transported to the seeds during fruit development. The exact sites of biosynthesis and accumulation remain unknown; however, mesophyll cells have been proposed as sources, and epidermal cells as sinks. We investigated the exact sites of QA biosynthesis and accumulation in biosynthetic organs of narrow-leafed lupin (Lupinus angustifolius) using mass spectrometry-based imaging (MSI), laser-capture microdissection coupled to RNA-Seq, and precursor feeding studies coupled to LC-MS and MSI. We found that the QAs that accumulate in seeds ('core' QAs) were evenly distributed across tissues; however, their esterified versions accumulated primarily in the epidermis. Surprisingly, RNA-Seq revealed strong biosynthetic gene expression in the epidermis, which was confirmed in leaves by quantitative real-time polymerase chain reaction. Finally, feeding studies using a stably labeled precursor showed that the lower leaf epidermis is highly biosynthetic. Our results indicate that the epidermis is a major site of QA biosynthesis in narrow-leafed lupin, challenging the current assumptions. Our work has direct implications for the elucidation of the QA biosynthesis pathway and the long-distance transport network from source to seed.

Transcription factors PHR1 and PHR1-like 1 regulate ABA-mediated inhibition of seed germination and stomatal opening in Arabidopsis

Low phosphate (LP) availability significantly impacts crop yield and quality. PHOSPHATE STARVATION RESPONSE1 (PHR1) along with PHR1-like 1 (PHL1) act as a key transcriptional regulator in a plant's adaptive response to LP conditions. Abscisic acid (ABA) plays an important role in how plants respond to environmental stresses like salinity and drought. However, the involvement of PHR1 and PHL1 in ABA response and signalling mechanisms remains to be fully understood. Our findings reveal that PHR1 and PHR1/PHL1 knockout mutations enhance the responsiveness of seed germination, early seedling growth, and stomatal opening to ABA in Arabidopsis. Furthermore, these mutations increase sensitivity to combined LP and ABA stress. In contrast, overexpression of PHR1 or PHL1 reduces this sensitivity in Arabidopsis. Knockout mutations of PHR1 and PHR1/PHL1 also increase sensitivity to salt and osmotic stresses, as well as to combined LP and salinity/osmotic stress, while overexpression of PHR1 or PHL1 reduces their sensitivity in seed germination and early seedling development. Knockout mutations of SPX1 and SPX2, negative regulators of PHR1 and PHL1, decrease sensitivity to ABA and salt/osmotic stresses in Arabidopsis. A group of genes related to ABA metabolism and signalling is significantly affected by the knockout or overexpression of PHR1 and PHL1, with a large proportion of these genes containing PHR1 binding site (P1BS) in their promoters. Moreover, the ABA-sensitive phenotype of phr1 or phr1 phl1 mutants can be rescued by PHR1 homologs from chlorophyte algae, liverwort and rice, suggesting their conserved roles in ABA signalling. These results indicate that PHR1 and its homologs negatively regulate plant responses to ABA in seed germination and stomatal aperture. This study provides new insights into the interplay between Pi homeostasis, abiotic stress and ABA signaling. Moderately increasing the expression of PHR1 or its homologs in crops could be a potential strategy to enhance plant resistance to combined LP and osmotic stress.

Suppression of Chorismate Mutase 1 in Hybrid Poplar to Investigate Potential Redundancy in the Supply of Lignin Precursors

Chorismate is an important branchpoint metabolite in the biosynthesis of lignin and a wide array of metabolites in plants. Chorismate mutase (CM), the enzyme responsible for transforming chorismate into prephenate, is a key regulator of metabolic flux towards the synthesis of aromatic amino acids and onwards to lignin. We examined three CM genes in hybrid poplar (Populus alba × grandidentata; P39, abbreviated as Pa×g) and used RNA interference (RNAi) to suppress the expression of Pa×gCM1, the most highly expressed isoform found in xylem tissue. Although this strategy was successful in disrupting Pa×gCM1 transcripts, there was also an unanticipated increase in lignin content, a shift towards guaiacyl lignin units, and more xylem vessels with smaller lumen areas, at least in the most severely affected transgenic line. This was accompanied by compensatory expression of the other two CM isoforms, Pa×gCM2 and Pa×gCM3, as well as widespread changes in gene expression and metabolism. This study investigates potential redundancy within the CM gene family in the developing xylem of poplar and highlights the pivotal role of chorismate in plant metabolism, development, and physiology.

CYP722A1-mediated 16-hydroxylation of carlactonoic acid regulates the floral transition in Arabidopsis

Strigolactones (SLs) are multifunctional plant hormones and rhizosphere signals with diverse structures, roughly classified into two categories: canonical and noncanonical SLs. In Arabidopsis thaliana, SL biosynthesis mutants exhibit increased shoot branching and early flowering, underscoring their roles in developmental regulation. Shoot branching inhibition in Arabidopsis is associated with the methylation of a noncanonical SL, carlactonoic acid (CLA), catalyzed by CLA methyltransferase (CLAMT). Canonical SLs primarily function as rhizosphere signals, with their biosynthesis in dicots mediated by CYP722C enzymes. It is hypothesized that Arabidopsis does not produce canonical SL because of the lack of the CYP722C genes in its genome. Instead, Arabidopsis possesses CYP722A1, a member of the previously uncharacterized CYP722A subfamily, distinct from the CYP722C subfamily. This study demonstrates that Arabidopsis cyp722a1 mutants exhibit an earlier floral transition without excessive shoot branching. Biochemical analysis revealed that CYP722A1 catalyzes the hydroxylation of CLA to produce 16-hydroxy-CLA (16-HO-CLA), which is subsequently methylated by CLAMT to form 16-HO-MeCLA. 16-HO-CLA and 16-HO-MeCLA were detected in the wildtype; however, these compounds were absent in max1-4 mutant, deficient in CLA synthesis, and in cyp722a1 mutant. These findings show CYP722A1-dependent 16-hydroxylation activity of CLA in Arabidopsis. Moreover, they suggest that hydroxylated CLA specifically regulates floral transition, distinct from branching inhibition. Through the identification of CYP722A1 affecting floral transition, which is the distinct role of the CYP722A subfamily, this work provides insights into the structural diversification of SLs for specialized biological functions in plant development.

Lung seven transmembrane receptors are involved in Arabidopsis root growth mediated by Danger-associated peptide Pep1

Lung seven transmembrane receptor family is a small part of Arabidopsis gene family. So far, the function of some members of the this family is unknown. Plant elicitor peptide1 (Pep1) is one of damage-associated molecular patterns (DAMPs), which could trigger root growth inhibition and plant immunity responses. Here, we identified members of the Lung seven transmembrane family, and proved they are important for Pep1-induced root growth and development. We found that the expression levels of 7TM2 and 7TM6 were elevated in wild-type treated with Pep1. Phenotypic analysis showed that the growth phenotypes of 7tm2 and 7tm6 were similar to the wild-type under Pep1 treatment, but the 7tm2 7tm6 had a Pep1 hypersensitivity phenotype compared to wild-type. Furthermore, the complementation lines were able to restore the Pep1 phenotype of 7tm2 7tm6 to that similar to wild-type. These results suggest that 7TM2 and 7TM6 are involved in the regulation of root growth by Pep1. This study revealed the new functions of the Lung seven transmembrane receptor family and provided new ideas for further revealing the molecular mechanism of Pep1-regulated root growth and development.

Evolutionary signatures of the erosion of sexual reproduction genes in domesticated cassava (Manihot esculenta)

Centuries of clonal propagation in cassava (Manihot esculenta) have reduced sexual recombination, leading to the accumulation of deleterious mutations. This has resulted in both inbreeding depression affecting yield and a significant decrease in reproductive performance, creating hurdles for contemporary breeding programs. Cassava is a member of the Euphorbiaceae family, including notable species such as rubber tree (Hevea brasiliensis) and poinsettia (Euphorbia pulcherrima). Expanding upon preliminary draft genomes, we annotated 7 long-read genome assemblies and aligned a total of 52 genomes, to analyze selection across the genome and the phylogeny. Through this comparative genomic approach, we identified 48 genes under relaxed selection in cassava. Notably, we discovered an overrepresentation of floral expressed genes, especially focused at 6 pollen-related genes. Our results indicate that domestication and a transition to clonal propagation have reduced selection pressures on sexually reproductive functions in cassava leading to an accumulation of mutations in pollen-related genes. This relaxed selection and the genome-wide deleterious mutations responsible for inbreeding depression are potential targets for improving cassava breeding, where the generation of new varieties relies on recombining favorable alleles through sexual reproduction.

20 years of the Bio-Analytic Resource for Plant Biology

The Bio-Analytic Resource for Plant Biology ('the BAR', at https://bar.utoronto.ca) is celebrating its 20th year in operation in 2025. The BAR encompasses and provides visualization tools for large 'omics data sets from plants. The BAR covers data from Arabidopsis, tomato, wheat, barley and 29 other plant species (with data for 2 others to be released soon). These data include nucleotide and protein sequence data, gene expression data, protein-protein and protein-DNA interactions, protein structures, subcellular localizations, and polymorphisms. The data are stored in more than 200 relational databases holding 186 GB of data and are presented to the researchers via web apps. These web apps provide data analysis and visualization tools. Some of the most popular tools are eFP ('electronic fluorescent pictograph') Browsers, ePlants and ThaleMine (an Arabidopsis-specific instance of InterMine). The BAR was designated a Global Core Biodata Resource in 2023. Like other GCBRs, the BAR has excellent operational stability, provides access without login requirement, and provides an API for researchers to be able to access BAR data programmatically. We present in this update a new overarching search tool called Gaia that permits easy access to all BAR data, powered by machine learning and artificial intelligence.

The cytokinin efflux transporter ABCC4 participates in Arabidopsis root system development

The directional and sequential flow of cytokinin in plants is organized by a complex network of transporters. Genes involved in several aspects of cytokinin transport have been characterized; however, much of the elaborate system remains elusive. In this study, we used a transient expression system in tobacco (Nicotiana benthamiana) leaves to screen Arabidopsis (Arabidopsis thaliana) transporter genes and isolated ATP-BINDING CASSETTE TRANSPORTER C4 (ABCC4). Validation through drug-induced expression in Arabidopsis and heterologous expression in budding yeast revealed that ABCC4 effluxes the active form of cytokinins. During the seedling stage, ABCC4 was highly expressed in roots, and its expression was upregulated in response to cytokinin application. Loss-of-function mutants of ABCC4 displayed enhanced primary root elongation, similar to mutants impaired in cytokinin biosynthesis or signaling, that was suppressed by exogenous trans-zeatin treatment. In contrast, overexpression of the gene led to suppression of root elongation. These results suggest that ABCC4 plays a role in the efflux of active cytokinin, thereby contributing to root growth regulation. Additionally, cytokinin-dependent enlargement of stomatal aperture was impaired in the loss-of-function and overexpression lines. Our findings contribute to unraveling the many complexities of cytokinin flow and enhance our understanding of the regulatory mechanisms underlying root system development and stomatal opening in plants.

OsIAA19, an Aux/IAA Family Gene, Involved in the Regulation of Seed-Specific Traits in Rice

The Aux/IAA family proteins, key components of the auxin signaling pathway, are plant-specific transcription factors with important roles in regulating a wide range of plant growth and developmental events. The Aux/IAA family genes have been extensively studied in Arabidopsis. However, most of the Aux/IAA family genes in rice have not been functionally studied. Only two IAA genes have been reported to be involved in the regulation of rice grain size. Grain size is a key factor affecting both rice yield and quality. Therefore, we selected an unreported IAA member, OsIAA19, based on bioinformatics analysis to investigate its potential role in grain size control. Our study showed that OsIAA19 was constitutively expressed in all tissues tested and that the encoding protein was nuclear localized. The osiaa19 mutants were then generated using CRISPR/Cas9 gene editing. Agronomic trait analyses showed that the OsIAA19 mutation significantly increased rice grain length and weight, but had no significant effect on plant height, number of tillers, flag leaf length and width. In addition, the chalkiness of the osiaa19 mutant seeds also increased, but their eating and cooking quality (ECQ) was not altered. Finally, seed germination analysis showed that knocking out OsIAA19 slightly suppressed rice seed germination. These results suggest that OsIAA19 may specifically regulate rice seed-related traits, such as grain shape, rice chalkiness and seed germination. This study not only enriched the functional study of the Aux/IAA genes and the auxin signaling pathway in rice, but also provided valuable genetic resources for breeding elite rice varieties.

At2-MMP Is Required for Attenuation of Cell Proliferation during Wound Healing in Incised Arabidopsis Inflorescence Stems

Wound healing of partially incised Arabidopsis inflorescence stems constitutes cell proliferation that initiates mainly in pith tissues about 3 d after incision and the healing process that completes in about 7 d. Although the initiation mechanisms of cell proliferation have been well documented, the suppression mechanisms remain elusive. Matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases well known as proteolytic enzymes in animal system functioning in extracellular matrix remodeling during physiological and pathological processes, including tissue differentiation, growth, defense, wound healing and control of cancer growth. In this study, we report that At2-MMP might contribute to the suppression mechanism for cell proliferation during the tissue-repair process of incised inflorescence stems. At2-MMP transcript was gradually upregulated from day 0 to 5 after incision and slightly decreased on day 7. Morphological analysis of incised stem of defected mutant at2-mmp revealed significantly enhanced cell proliferation around the incision site. Consistent with this, semi-quantitative analysis of dividing cells displayed a significant increment in the number of dividing cells in at2-mmp as compared to wild type. These results showed that the upregulation of At2-MMP at a later stage of the wound-healing process is likely to be involved in the completion of the process by attenuating cell proliferation.

Arabidopsis KNS3 and its two homologs mediate endoplasmic reticulum-to-plasma membrane traffic of boric acid channels

Membrane proteins targeted to the plasma membrane are first transported from the endoplasmic reticulum (ER) to the Golgi apparatus. This study explored the mechanisms controlling plasma membrane trafficking of the boric acid channel AtNIP5;1 from the ER. Imaging-based screening using transgenic Arabidopsis identified six mutants in which GFP-NIP5;1 was localized in the ER in addition to the plasma membrane. Genetic mapping and whole-genome resequencing identified the responsible gene in four among the six mutants as KAONASHI3 (KNS3)/SPOTTY1/IMPERFECTIVE EXINE FORMATION. Among the plasma membrane-localized proteins tested, NIP5;1 and its homolog NIP6;1 were retained in the ER of the kns3 mutants. Our genetic analysis further discovered that two homologs of KNS3, KNSTH1 and KNSTH2, were also involved in the ER exit of NIP5;1. In Arabidopsis protoplasts and tobacco leaves, mCherry-fused KNS3 localized to the ER and Golgi, whereas KNSTH2 localized to the ER. The cytosolic C-terminal tail of KNS3 contains amino acids important for Golgi-to-ER trafficking. Furthermore, the ER-to-Golgi trafficking of KNS3 depended on KNSTH1 and KNSTH2, and the accumulation of these three proteins in Arabidopsis roots depended on each other. We propose that KNS3, KNSTH1, and KNSTH2 function as a cargo-receptor complex mediating the ER exit of NIP5;1.

Soybean genomics research community strategic plan: A vision for 2024-2028

This strategic plan summarizes the major accomplishments achieved in the last quinquennial by the soybean [Glycine max (L.) Merr.] genetics and genomics research community and outlines key priorities for the next 5 years (2024-2028). This work is the result of deliberations among over 50 soybean researchers during a 2-day workshop in St Louis, MO, USA, at the end of 2022. The plan is divided into seven traditional areas/disciplines: Breeding, Biotic Interactions, Physiology and Abiotic Stress, Functional Genomics, Biotechnology, Genomic Resources and Datasets, and Computational Resources. One additional section was added, Training the Next Generation of Soybean Researchers, when it was identified as a pressing issue during the workshop. This installment of the soybean genomics strategic plan provides a snapshot of recent progress while looking at future goals that will improve resources and enable innovation among the community of basic and applied soybean researchers. We hope that this work will inform our community and increase support for soybean research.

AutoXAI4Omics: an automated explainable AI tool for omics and tabular data

Machine learning (ML) methods offer opportunities for gaining insights into the intricate workings of complex biological systems, and their applications are increasingly prominent in the analysis of omics data to facilitate tasks, such as the identification of novel biomarkers and predictive modeling of phenotypes. For scientists and domain experts, leveraging user-friendly ML pipelines can be incredibly valuable, enabling them to run sophisticated, robust, and interpretable models without requiring in-depth expertise in coding or algorithmic optimization. By streamlining the process of model development and training, researchers can devote their time and energies to the critical tasks of biological interpretation and validation, thereby maximizing the scientific impact of ML-driven insights. Here, we present an entirely automated open-source explainable AI tool, AutoXAI4Omics, that performs classification and regression tasks from omics and tabular numerical data. AutoXAI4Omics accelerates scientific discovery by automating processes and decisions made by AI experts, e.g. selection of the best feature set, hyper-tuning of different ML algorithms and selection of the best ML model for a specific task and dataset. Prior to ML analysis AutoXAI4Omics incorporates feature filtering options that are tailored to specific omic data types. Moreover, the insights into the predictions that are provided by the tool through explainability analysis highlight associations between omic feature values and the targets under investigation, e.g. predicted phenotypes, facilitating the identification of novel actionable insights. AutoXAI4Omics is available at: https://github.com/IBM/AutoXAI4Omics.

The Roles of RNA Modifications in Regulating Chloroplast Performance and Photosynthesis Efficiency

The regulation of gene expression is crucial for maintaining cellular activities and responding to environmental stimuli. RNA molecules are central to this regulatory network, influencing transcription, post-transcriptional processing, and translation. Recent advancements have expanded our understanding of RNA modifications beyond the nucleus, highlighting their impact on chloroplast function and photosynthesis efficiency. Chloroplasts, essential for photosynthesis, rely on precise genetic regulation to adapt to environmental changes. RNA modifications, such as methylation and pseudouridylation, are critical in regulating chloroplast RNA stability, processing, and translation. This review summarizes current knowledge of how RNA modifications affect chloroplast function and photosynthesis. It discusses the roles of specific RNA modifications occurring in chloroplast RNA, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), and pseudouridylation, as well as the enzymes which are known to be involved in these processes. This review also explores extrachloroplastic RNA modifications that influence chloroplast function, emphasizing the importance of m6A and m5C modifications and their associated enzymes.

Shade-induced ROS/NO reinforce COP1-mediated diffuse cell growth

Canopy shade enhances the activity of PHYTOCHROME INTERACTING FACTORs (PIFs) to boost auxin synthesis in the cotyledons. Auxin, together with local PIFs and their positive regulator CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1), promotes hypocotyl growth to facilitate access to light. Whether shade alters the cellular redox status thereby affecting growth responses, remains unexplored. Here, we show that, under shade, high auxin levels increased reactive oxygen species and nitric oxide accumulation in the hypocotyl of Arabidopsis. This nitroxidative environment favored the promotion of hypocotyl growth by COP1 under shade. We demonstrate that COP1 is S-nitrosylated, particularly under shade. Impairing this redox regulation enhanced COP1 degradation by the proteasome and diminished the capacity of COP1 to interact with target proteins and to promote hypocotyl growth. Disabling this regulation also generated transversal asymmetries in hypocotyl growth, indicating poor coordination among different cells, which resulted in random hypocotyl bending and predictably low ability to compete with neighbors. These findings highlight the significance of redox signaling in the control of diffuse growth during shade avoidance.

THI1 Gene Evolutionary Trends: A Comprehensive Plant-Focused Assessment via Data Mining and Large-Scale Analysis

Molecular evolution analysis typically involves identifying selection pressure and reconstructing evolutionary trends. This process usually requires access to specific data related to a target gene or gene family within a particular group of organisms. While recent advancements in high-throughput sequencing techniques have resulted in the rapid accumulation of extensive genomics and transcriptomics data and the creation of new databases in public repositories, extracting valuable insights from such vast data sets remains a significant challenge for researchers. Here, we elucidated the evolutionary history of THI1, a gene responsible for encoding thiamine thiazole synthase. The thiazole ring is a precursor for vitamin B1 and a crucial cofactor in primary metabolic pathways. A thorough search of complete genomes available within public repositories reveals 702 THI1 homologs of Archaea and Eukarya. Throughout its diversification, the plant lineage has preserved the THI1 gene by incorporating the N-terminus and targeting the chloroplasts. Likewise, evolutionary pressures and lifestyle appear to be associated with retention of TPP riboswitch sites and consequent dual posttranscriptional regulation of the de novo biosynthesis pathway in basal groups. Multicopy retention of THI1 is not a typical plant pattern, even after successive genome duplications. Examining cis-regulatory sites in plants uncovers two shared motifs across all plant lineages. A data mining of 484 transcriptome data sets supports the THI1 homolog expression under a light/dark cycle response and a tissue-specific pattern. Finally, the work presented brings a new look at public repositories as an opportunity to explore evolutionary trends to THI1.

Analysis of Ion Transport Properties of Glycine max HKT Transporters and Identifying a Regulation of GmHKT1;1 by the Non-Functional GmHKT1;4

High-affinity potassium transporters (HKTs) play an important role in plants responding to salt stress, but the transport properties of the soybean HKT transporters at the molecular level are still unclear. Here, using Xenopus oocyte as a heterologous expression system and two-electrode voltage-clamp technique, we identified four HKT transporters, GmHKT1;1, GmHKT1;2, GmHKT1;3 and GmHKT1;4, all of which belong to type I subfamily, but have distinct ion transport properties. While GmHKT1;1, GmHKT1;2 and GmHKT1;3 function as Na+ transporters, GmHKT1;1 is less selective against K+ than the two other transporters. Astonishingly, GmHKT1;4, which lacks transmembrane segments and has no ion permeability, is significantly expressed, and its gene expression pattern is different from the other three GmHKTs under salt stress. Interestingly, GmHKT1;4 reduced the Na+/K+ currents mediated by GmHKT1;1. Further study showed that the transport ability of GmHKT1;1 regulated by GmHKT1;4 was related to the structural differences in the first intracellular domain and the fourth repeat domain. Overall, we have identified one unique GmHKT member, GmHKT1;4, which modulates the Na+ and K+ transport ability of GmHKT1;1 via direct interaction. Thus, we have revealed a new type of HKT interaction model for altering their ion transport properties.

Evolutionary analysis of tonoplast intrinsic proteins (TIPs) unraveling the role of TIP3s in plant seed development

Tonoplast intrinsic proteins (TIPs) are crucial in facilitating the transportation of water and various small solutes across biological membranes. The evolutionary path and functional roles of TIPs is poorly understood in plants. In the present study, a total of 976 TIPs were identified in 104 diverse species and subsequently studied to trace their lineage-specific evolutionary path and tissue-specific function. Interestingly, TIPs were found to be absent in lower forms such as algae and fungi and they evolved later in primitive plants like bryophytes. Bryophytes possess a distant class of TIPs, denoted as TIP6, which is not found in higher plants. The aromatic/arginine (ar/R) selectivity filter found in TIP6 of certain liverworts share similarity with hybrid intrinsic protein (HIP), suggesting an evolutionary kinship. As plants evolved to more advanced forms, TIPs diversified into five different sub-groups (TIP1 to TIP5). Notably, TIP5 is a sub-group unique to angiosperms. The evolutionary history of the TIP subfamily reveals an interesting observation that the TIP3 subgroup has evolved within seed-bearing Spermatophyta. Further, TIPs exhibit tissue-specific expression that is conserved within various plant species. Specifically, the TIP3s were found to be exclusively expressed in seeds. Quantitative PCR analysis of TIP3s showed gradually increasing expression in soybean seed developmental stages. The expression of TIP3s in different plant species was also found to be gradually increasing during seed maturation. The results presented here address the knowledge gap concerning the evolutionary background of TIPs, specifically TIP3 in plants, and provide valuable insights for a deeper comprehension of the functions of TIPs in plants.

Molecular simulation reveals that pathogenic mutations in BTB/ANK domains of Arabidopsis thaliana NPR1 circumscribe the EDS1-mediated immune regulation

The NPR1 (nonexpressor of pathogenesis-related genes 1) is a key regulator of the salicylic-acid-mediated immune response caused by pathogens in Arabidopsis thaliana. Mutations C150Y and H334Y in the BTB/ANK domains of NPR1 inhibit the defense response, and transcriptional co-activity with enhanced disease susceptibility 1 (EDS1) has been revealed experimentally. This study examined the conformational changes and reduced NPR1-EDS1 interaction upon mutation using a molecular dynamics simulation. Initially, BTBC150YNPR1 and ANKH334YNPR1 were categorized as pathological mutations rather than others based on sequence conservation. A distant ortholog was used to map the common residues shared among the wild-type because the mutations were highly conserved. Overall, 179 of 373 residues were determining the secondary structures and fold versatility of conformations. In addition, the mutational hotspots Cys150, Asp152, Glu153, Cys155, His157, Cys160, His334, Arg339 and Lys370 were crucial for oligomer-to-monomer exchange. Subsequently, the atomistic simulations with free energy (MM/PB(GB)SA) calculations predicted structural displacements engaging in the N-termini α5133-178α7 linker connecting the central ANK regions (α13260-290α14 and α18320-390α22), where prominent long helices (α516) and short helices (α310) replaced with β-turns and loops disrupting hydrogen bonds and salt bridges in both mutants implicating functional regulation and activation. Furthermore, the mutation repositions the intact stability of multiple regions (L13C149-N356α20BTB/ANK-α17W301-E357α21N-ter/coiled-coil) compromising a dynamic interaction of NPR1-EDS1. By unveiling the transitions between the distinct functions of mutational perception, this study paves the way for future investigation to orchestrate additive host-adapted transcriptional reprogramming that controls defense-related regulatory mechanisms of NPR1s in plants.

ggPlantmap: an open-source R package for the creation of informative and quantitative ggplot maps derived from plant images

As plant research generates an ever-growing volume of spatial quantitative data, the need for decentralized and user-friendly visualization tools to explore large and complex datasets becomes crucial. Existing resources, such as the Plant eFP (electronic Fluorescent Pictograph) viewer, have played a pivotal role on the communication of gene expression data across many plant species. However, although widely used by the plant research community, the Plant eFP viewer lacks open and user-friendly tools for the creation of customized expression maps independently. Plant biologists with less coding experience can often encounter challenges when attempting to explore ways to communicate their own spatial quantitative data. We present 'ggPlantmap' an open-source R package designed to address this challenge by providing an easy and user-friendly method for the creation of ggplot representative maps from plant images. ggPlantmap is built in R, one of the most used languages in biology, to empower plant scientists to create and customize eFP-like viewers tailored to their experimental data. Here, we provide an overview of the package and tutorials that are accessible even to users with minimal R programming experience. We hope that ggPlantmap can assist the plant science community, fostering innovation, and improving our understanding of plant development and function.

Sugar signaling modulates SHOOT MERISTEMLESS expression and meristem function in Arabidopsis

In plants, development of all above-ground tissues relies on the shoot apical meristem (SAM) which balances cell proliferation and differentiation to allow life-long growth. To maximize fitness and survival, meristem activity is adjusted to the prevailing conditions through a poorly understood integration of developmental signals with environmental and nutritional information. Here, we show that sugar signals influence SAM function by altering the protein levels of SHOOT MERISTEMLESS (STM), a key regulator of meristem maintenance. STM is less abundant in inflorescence meristems with lower sugar content, resulting from plants being grown or treated under limiting light conditions. Additionally, sucrose but not light is sufficient to sustain STM accumulation in excised inflorescences. Plants overexpressing the α1-subunit of SUCROSE-NON-FERMENTING1-RELATED KINASE 1 (SnRK1) accumulate less STM protein under optimal light conditions, despite higher sugar accumulation in the meristem. Furthermore, SnRK1α1 interacts physically with STM and inhibits its activity in reporter assays, suggesting that SnRK1 represses STM protein function. Contrasting the absence of growth defects in SnRK1α1 overexpressors, silencing SnRK1α in the SAM leads to meristem dysfunction and severe developmental phenotypes. This is accompanied by reduced STM transcript levels, suggesting indirect effects on STM. Altogether, we demonstrate that sugars promote STM accumulation and that the SnRK1 sugar sensor plays a dual role in the SAM, limiting STM function under unfavorable conditions but being required for overall meristem organization and integrity under favorable conditions. This highlights the importance of sugars and SnRK1 signaling for the proper coordination of meristem activities.

HIGH PLOIDY2-mediated SUMOylation of transcription factor ARR1 controls two-component signaling in Arabidopsis

Cytokinins regulate plant growth, development, and responses to environmental stresses such as cold via phosphorelay from cytokinin receptors to the ARABIDOPSIS RESPONSE REGULATORs (ARRs). However, the molecular mechanisms underlying the activation of type-B ARR transcriptional activity in Arabidopsis (Arabidopsis thaliana) remain unclear. Here, we show that the E3 SUMO ligase HIGH PLOIDY2 SUMOylates ARR1, a type-B ARR, at K236, triggering its activation. Cold- or cytokinin-induced phosphorylation of ARR1 at D89 is crucial for its interaction with HPY2. Lysine 236 is critical for ARR1's transactivation without compromising its DNA-binding ability, while D89 is crucial for ARR1's binding to target gene promoters. Cytokinin enhances ARR1's chromatin binding, but cold does not. ARR1 K236 plays a critical role in promoting histone H3 acetylation in response to both cytokinin and cold without affecting chromatin binding. The K236R mutation in ARR1 reduces target gene expression and alters cytokinin and cold response phenotypes. This study unveils a mechanism of ARR1 activation wherein phosphorylated ARR1 interacts with HPY2 and binds to chromatin in response to cytokinin. Cold triggers a phosphorelay targeting chromatin-bound ARR1. HPY2 then catalyzes ARR1 SUMOylation at K236, enhancing histone H3 acetylation and leading to transcriptional activation of ARR1 in response to both cold and cytokinin.

Model-based inference of a dual role for HOPS in regulating guard cell vacuole fusion

Guard cell movements depend, in part, on the remodelling of vacuoles from a highly fragmented state to a fused morphology during stomata opening. Indeed, full opening of plant stomata requires vacuole fusion to occur. Fusion of vacuole membranes is a highly conserved process in eukaryotes, with key roles played by two multi-subunit complexes: HOPS (homotypic fusion and vacuolar protein sorting) and SNARE (soluble NSF attachment protein receptor). HOPS is a vacuole tethering factor that is thought to chaperone SNAREs from apposing vacuole membranes into a fusion-competent complex capable of rearranging membranes. In plants, recruitment of HOPS subunits to the tonoplast has been shown to require the presence of the phosphoinositide phosphatidylinositol 3-phosphate. However, chemically depleting this lipid induces vacuole fusion. To resolve this counter-intuitive observation regarding the role of HOPS in regulating plant vacuole morphology, we defined a quantitative model of vacuole fusion dynamics and used it to generate testable predictions about HOPS-SNARE interactions. We derived our model by using simulation-based inference to integrate prior knowledge about molecular interactions with limited, qualitative observations of emergent vacuole phenotypes. By constraining the model parameters to yield the emergent outcomes observed for stoma opening-as induced by two distinct chemical treatments-we predicted a dual role for HOPS and identified a stalled form of the SNARE complex that differs from phenomena reported in yeast. We predict that HOPS has contradictory actions at different points in the fusion signalling pathway, promoting the formation of SNARE complexes, but limiting their activity.

Characterization of Arabidopsis aldolases AtFBA4, AtFBA5, and their inhibition by morin and interaction with calmodulin

Fructose bisphosphate aldolases (FBAs) catalyze the reversible cleavage of fructose 1,6-bisphosphate into dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. We analyzed two previously uncharacterized cytosolic Arabidopsis FBAs, AtFBA4 and AtFBA5. Based on a recent report, we examined the interaction of AtFBA4 with calmodulin (CaM)-like protein 11 (AtCML11). AtFBA4 did not bind AtCML11; however, we found that CaM bound AtFBA5 in a Ca2+-dependent manner with high specificity and affinity (KD ~ 190 nm) and enhanced its stability. AtFBA4 and AtFBA5 exhibited Michaelis-Menten kinetics with Km and Vmax values of 180 μm and 4.9 U·mg-1 for AtFBA4, and 6.0 μm and 0.30 U·mg-1 for AtFBA5, respectively. The flavonoid morin inhibited both isozymes. Our study suggests that Ca2+ signaling and flavanols may influence plant glycolysis/gluconeogenesis.

Characterization of the small Arabidopsis thaliana GTPase and ADP-ribosylation factor-like 2 protein TITAN 5

Small GTPases switch between GDP- and GTP-bound states during cell signaling. The ADP-ribosylation factor (ARF) family of small GTPases is involved in vesicle trafficking. Although evolutionarily well conserved, little is known about ARF and ARF-like GTPases in plants. We characterized biochemical properties and cellular localization of the essential small ARF-like GTPase TITAN 5 (TTN5; also known as HALLIMASCH, ARL2 and ARLC1) from Arabidopsis thaliana, and two TTN5 proteins with point mutants in conserved residues, TTN5T30N and TTN5Q70L, that were expected to be unable to perform nucleotide exchange and GTP hydrolysis, respectively. TTN5 exhibited very rapid intrinsic nucleotide exchange and remarkably low GTP hydrolysis activity, functioning as a non-classical small GTPase being likely present in a GTP-loaded active form. We analyzed signals from YFP-TTN5 and HA3-TTN5 by in situ immunolocalization in Arabidopsis seedlings and through use of a transient expression system. Colocalization with endomembrane markers and pharmacological treatments suggests that TTN5 can be present at the plasma membrane and that it dynamically associates with membranes of vesicles, Golgi stacks and multivesicular bodies. Although TTN5Q70L mirrored wild-type TTN5 behavior, the TTN5T30N mutant differed in some aspects. Hence, the unusual rapid nucleotide exchange activity of TTN5 is linked with its membrane dynamics, and TTN5 likely has a role in vesicle transport within the endomembrane system.

Sugar sensing in C4 source leaves: a gap that needs to be filled

Plant growth depends on sugar production and export by photosynthesizing source leaves and sugar allocation and import by sink tissues (grains, roots, stems, and young leaves). Photosynthesis and sink demand are tightly coordinated through metabolic (substrate, allosteric) feedback and signalling (sugar, hormones) mechanisms. Sugar signalling integrates sugar production with plant development and environmental cues. In C3 plants (e.g. wheat and rice), it is well documented that sugar accumulation in source leaves, due to source-sink imbalance, negatively feeds back on photosynthesis and plant productivity. However, we have a limited understanding about the molecular mechanisms underlying those feedback regulations, especially in C4 plants (e.g. maize, sorghum, and sugarcane). Recent work with the C4 model plant Setaria viridis suggested that C4 leaves have different sugar sensing thresholds and behaviours relative to C3 counterparts. Addressing this research priority is critical because improving crop yield requires a better understanding of how plants coordinate source activity with sink demand. Here we review the literature, present a model of action for sugar sensing in C4 source leaves, and suggest ways forward.

Application of orthology and network biology to infer gene functions in non-model plants

Approximately 60% of the genes and gene products in the model species Arabidopsis thaliana have been functionally characterized. In non-model plant species, the functional annotation of the gene space is largely based on homology, with the assumption that genes with shared common ancestry have conserved functions. However, the wide variety in possible morphological, physiological, and ecological differences between plant species gives rise to many species- and clade-specific genes, for which this transfer of knowledge is not possible. Other complications, such as difficulties with genetic transformation, the absence of large-scale mutagenesis methods, and long generation times, further lead to the slow characterization of genes in non-model species. Here, we discuss different resources that integrate plant gene function information. Different approaches that support the functional annotation of gene products, based on orthology or network biology, are described. While sequence-based tools to characterize the functional landscape in non-model species are maturing and becoming more readily available, easy-to-use network-based methods inferring plant gene functions are not as prevalent and have limited functionality.

P-type calcium ATPases play important roles in biotic and abiotic stress signaling

MAIN CONCLUSION

Knowledge of Ca2+-ATPases is imperative for improving crop quality/ food security, highly threatened due to global warming. Ca2+-ATPases modulates calcium, essential for stress signaling and modulating growth, development, and immune activities. Calcium is considered a versatile secondary messenger and essential for short- and long-term responses to biotic and abiotic stresses in plants. Coordinated transport activities from both calcium influx and efflux channels are required to generate cellular calcium signals. Various extracellular stimuli cause an induction in cytosolic calcium levels. To cope with such stresses, it is important to maintain intracellular Ca2+ levels. Plants need to evolve efficient efflux mechanisms to maintain Ca2+ ion homeostasis. Plant Ca2+-ATPases are members of the P-type ATPase superfamily and localized in the plasma membrane and endoplasmic reticulum (ER). They are required for various cellular processes, including plant growth, development, calcium signaling, and even retorts to environmental stress. These ATPases play an essential role in Ca2+ homeostasis and are actively involved in Ca2+ transport. Plant Ca2+-ATPases are categorized into two major classes: type IIA and type IIB. Although these two classes of ATPases share similarities in protein sequence, they differ in their structure, cellular localization, and sensitivity to inhibitors. Due to the emerging role of Ca2+-ATPase in abiotic and biotic plant stress, members of this family may help promote agricultural improvement under stress conditions. This review provides a comprehensive overview of P-type Ca2+-ATPase, and their role in Ca2+ transport, stress signaling, and cellular homeostasis focusing on their classification, evolution, ion specificities, and catalytic mechanisms. It also describes the main aspects of the role of Ca2+-ATPase in transducing signals during plant biotic and abiotic stress responses and its role in plant development and physiology.

Arabidopsis CaLB1 undergoes phase separation with the ESCRT protein ALIX and modulates autophagosome maturation

Autophagy is relevant for diverse processes in eukaryotic cells, making its regulation of fundamental importance. The formation and maturation of autophagosomes require a complex choreography of numerous factors. The endosomal sorting complex required for transport (ESCRT) is implicated in the final step of autophagosomal maturation by sealing of the phagophore membrane. ESCRT-III components were shown to mediate membrane scission by forming filaments that interact with cellular membranes. However, the molecular mechanisms underlying the recruitment of ESCRTs to non-endosomal membranes remain largely unknown. Here we focus on the ESCRT-associated protein ALG2-interacting protein X (ALIX) and identify Ca2+-dependent lipid binding protein 1 (CaLB1) as its interactor. Our findings demonstrate that CaLB1 interacts with AUTOPHAGY8 (ATG8) and PI(3)P, a phospholipid found in autophagosomal membranes. Moreover, CaLB1 and ALIX localize with ATG8 on autophagosomes upon salt treatment and assemble together into condensates. The depletion of CaLB1 impacts the maturation of salt-induced autophagosomes and leads to reduced delivery of autophagosomes to the vacuole. Here, we propose a crucial role of CaLB1 in augmenting phase separation of ALIX, facilitating the recruitment of ESCRT-III to the site of phagophore closure thereby ensuring efficient maturation of autophagosomes.

Localization of four class I glutaredoxins in the cytosol and the secretory pathway and characterization of their biochemical diversification

Class I glutaredoxins (GRXs) are catalytically active oxidoreductases and considered key proteins mediating reversible glutathionylation and deglutathionylation of protein thiols during development and stress responses. To narrow in on putative target proteins, it is mandatory to know the subcellular localization of the respective GRXs and to understand their catalytic activities and putative redundancy between isoforms in the same compartment. We show that in Arabidopsis thaliana, GRXC1 and GRXC2 are cytosolic proteins with GRXC1 being attached to membranes through myristoylation. GRXC3 and GRXC4 are identified as type II membrane proteins along the early secretory pathway with their enzymatic function on the luminal side. Unexpectedly, neither single nor double mutants lacking both GRXs isoforms in the cytosol or the ER show phenotypes that differ from wild-type controls. Analysis of electrostatic surface potentials and clustering of GRXs based on their electrostatic interaction with roGFP2 mirrors the phylogenetic classification of class I GRXs, which clearly separates the cytosolic GRXC1 and GRXC2 from the luminal GRXC3 and GRXC4. Comparison of all four studied GRXs for their oxidoreductase function highlights biochemical diversification with GRXC3 and GRXC4 being better catalysts than GRXC1 and GRXC2 for the reduction of bis(2-hydroxyethyl) disulfide. With oxidized roGFP2 as an alternative substrate, GRXC1 and GRXC2 catalyze the reduction faster than GRXC3 and GRXC4, which suggests that catalytic efficiency of GRXs in reductive reactions depends on the respective substrate. Vice versa, GRXC3 and GRXC4 are faster than GRXC1 and GRXC2 in catalyzing the oxidation of pre-reduced roGFP2 in the reverse reaction.

Class I TCP in fruit development: much more than growth

Fruit development can be viewed as the succession of three main steps consisting of the fruit initiation, growth and ripening. These processes are orchestrated by different factors, notably the successful fertilization of flowers, the environmental conditions and the hormones whose action is coordinated by a large variety of transcription factors. Among the different transcription factor families, TEOSINTE BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTOR (TCP) family has received little attention in the frame of fruit biology despite its large effects on several developmental processes and its action as modulator of different hormonal pathways. In this respect, the comprehension of TCP functions in fruit development remains an incomplete puzzle that needs to be assembled. Building on the abundance of genomic and transcriptomic data, this review aims at collecting available TCP expression data to allow their integration in the light of the different functional genetic studies reported so far. This reveals that several Class I TCP genes, already known for their involvement in the cell proliferation and growth, display significant expression levels in developing fruit, although clear evidence supporting their functional significance in this process remains scarce. The extensive expression data compiled in our study provide convincing elements that shed light on the specific involvement of Class I TCP genes in fruit ripening, once these reproductive organs acquire their mature size. They also emphasize their putative role in the control of specific biological processes such as fruit metabolism and hormonal dialogue.

Characterization of the small Arabidopsis thaliana GTPase and ADP-ribosylation factor-like 2 protein TITAN 5

Small GTPases function by conformational switching ability between GDP- and GTP-bound states in rapid cell signaling events. The ADP-ribosylation factor (ARF) family is involved in vesicle trafficking. Though evolutionarily well conserved, little is known about ARF and ARF-like GTPases in plants. Here, we characterized biochemical properties and cellular localization of the essential small ARF-like GTPase TITAN 5/HALLIMASCH/ARL2/ARLC1 (hereafter termed TTN5) from Arabidopsis thaliana. Two TTN5 variants were included in the study with point mutations at conserved residues, suspected to be functional for nucleotide exchange and GTP hydrolysis, TTN5T30N and TTN5Q70L. We found that TTN5 had a very rapid intrinsic nucleotide exchange capacity with a conserved nucleotide switching mechanism. TTN5 acted as a non-classical small GTPase with a remarkably low GTP hydrolysis activity, suggesting it is likely present in GTP-loaded active form in the cell. We analyzed signals from yellow fluorescent protein (YFP)-tagged TTN5 and from in situ immunolocalization of hemagglutine-tagged HA3-TTN5 in Arabidopsis seedlings and in a transient expression system. Together with colocalization using endomembrane markers and pharmacological treatments the microscopic analysis suggests that TTN5 can be present at the plasma membrane and dynamically associated with membranes of vesicles, Golgi stacks and multivesicular bodies. While the TTN5Q70L variant showed similar GTPase activities and localization behavior as wild-type TTN5, the TTN5T30N mutant differed in some aspects. Hence, the unusual capacity of rapid nucleotide exchange activity of TTN5 is linked with cell membrane dynamics, likely associated with vesicle transport pathways in the endomembrane system.

A method for mining condition-specific co-expressed genes in Camellia sinensis based on k-means clustering

BACKGROUND

As one of the world's most important beverage crops, tea plants (Camellia sinensis) are renowned for their unique flavors and numerous beneficial secondary metabolites, attracting researchers to investigate the formation of tea quality. With the increasing availability of transcriptome data on tea plants in public databases, conducting large-scale co-expression analyses has become feasible to meet the demand for functional characterization of tea plant genes. However, as the multidimensional noise increases, larger-scale co-expression analyses are not always effective. Analyzing a subset of samples generated by effectively downsampling and reorganizing the global sample set often leads to more accurate results in co-expression analysis. Meanwhile, global-based co-expression analyses are more likely to overlook condition-specific gene interactions, which may be more important and worthy of exploration and research.

RESULTS

Here, we employed the k-means clustering method to organize and classify the global samples of tea plants, resulting in clustered samples. Metadata annotations were then performed on these clustered samples to determine the "conditions" represented by each cluster. Subsequently, we conducted gene co-expression network analysis (WGCNA) separately on the global samples and the clustered samples, resulting in global modules and cluster-specific modules. Comparative analyses of global modules and cluster-specific modules have demonstrated that cluster-specific modules exhibit higher accuracy in co-expression analysis. To measure the degree of condition specificity of genes within condition-specific clusters, we introduced the correlation difference value (CDV). By incorporating the CDV into co-expression analyses, we can assess the condition specificity of genes. This approach proved instrumental in identifying a series of high CDV transcription factor encoding genes upregulated during sustained cold treatment in Camellia sinensis leaves and buds, and pinpointing a pair of genes that participate in the antioxidant defense system of tea plants under sustained cold stress.

CONCLUSIONS

To summarize, downsampling and reorganizing the sample set improved the accuracy of co-expression analysis. Cluster-specific modules were more accurate in capturing condition-specific gene interactions. The introduction of CDV allowed for the assessment of condition specificity in gene co-expression analyses. Using this approach, we identified a series of high CDV transcription factor encoding genes related to sustained cold stress in Camellia sinensis. This study highlights the importance of considering condition specificity in co-expression analysis and provides insights into the regulation of the cold stress in Camellia sinensis.

Nuclear lamina component KAKU4 regulates chromatin states and transcriptional regulation in the Arabidopsis genome

BACKGROUND

The nuclear lamina links the nuclear membrane to chromosomes and plays a crucial role in regulating chromatin states and gene expression. However, current knowledge of nuclear lamina in plants is limited compared to animals and humans.

RESULTS

This study mainly focused on elucidating the mechanism through which the putative nuclear lamina component protein KAKU4 regulates chromatin states and gene expression in Arabidopsis leaves. Thus, we constructed a network using the association proteins of lamin-like proteins, revealing that KAKU4 is strongly associated with chromatin or epigenetic modifiers. Then, we conducted ChIP-seq technology to generate global epigenomic profiles of H3K4me3, H3K27me3, and H3K9me2 in Arabidopsis leaves for mutant (kaku4-2) and wild-type (WT) plants alongside RNA-seq method to generate gene expression profiles. The comprehensive chromatin state-based analyses indicate that the knockdown of KAKU4 has the strongest effect on H3K27me3, followed by H3K9me2, and the least impact on H3K4me3, leading to significant changes in chromatin states in the Arabidopsis genome. We discovered that the knockdown of the KAKU4 gene caused a transition between two types of repressive epigenetics marks, H3K9me2 and H3K27me3, in some specific PLAD regions. The combination analyses of epigenomic and transcriptomic data between the kaku4-2 mutant and WT suggested that KAKU4 may regulate key biological processes, such as programmed cell death and hormone signaling pathways, by affecting H3K27me3 modification in Arabidopsis leaves.

CONCLUSIONS

In summary, our results indicated that KAKU4 is directly and/or indirectly associated with chromatin/epigenetic modifiers and demonstrated the essential roles of KAKU4 in regulating chromatin states, transcriptional regulation, and diverse biological processes in Arabidopsis.

NKS1/ELMO4 is an integral protein of a pectin synthesis protein complex and maintains Golgi morphology and cell adhesion in Arabidopsis

Adjacent plant cells are connected by specialized cell wall regions, called middle lamellae, which influence critical agricultural characteristics, including fruit ripening and organ abscission. Middle lamellae are enriched in pectin polysaccharides, specifically homogalacturonan (HG). Here, we identify a plant-specific Arabidopsis DUF1068 protein, called NKS1/ELMO4, that is required for middle lamellae integrity and cell adhesion. NKS1 localizes to the Golgi apparatus and loss of NKS1 results in changes to Golgi structure and function. The nks1 mutants also display HG deficient phenotypes, including reduced seedling growth, changes to cell wall composition, and tissue integrity defects. These phenotypes are comparable to qua1 and qua2 mutants, which are defective in HG biosynthesis. Notably, genetic interactions indicate that NKS1 and the QUAs work in a common pathway. Protein interaction analyses and modeling corroborate that they work together in a stable protein complex with other pectin-related proteins. We propose that NKS1 is an integral part of a large pectin synthesis protein complex and that proper function of this complex is important to support Golgi structure and function.

Profiling of the gene expression and alternative splicing landscapes of Eucalyptus grandis

Eucalyptus is a widely planted hardwood tree species due to its fast growth, superior wood properties and adaptability. However, the post-transcriptional regulatory mechanisms controlling tissue development and stress responses in Eucalyptus remain poorly understood. In this study, we performed a comprehensive analysis of the gene expression profile and the alternative splicing (AS) landscape of E. grandis using strand-specific RNA-Seq, which encompassed 201 libraries including different organs, developmental stages, and environmental stresses. We identified 10 416 genes (33.49%) that underwent AS, and numerous differentially expressed and/or differential AS genes involved in critical biological processes, such as primary-to-secondary growth transition of stems, adventitious root formation, aging and responses to phosphorus- or boron-deficiency. Co-expression analysis of AS events and gene expression patterns highlighted the potential upstream regulatory role of AS events in multiple processes. Additionally, we highlighted the lignin biosynthetic pathway to showcase the potential regulatory functions of AS events in the KNAT3 and IRL3 genes within this pathway. Our high-quality expression atlas and AS landscape serve as valuable resources for unravelling the genetic control of woody plant development, long-term adaptation, and understanding transcriptional diversity in Eucalyptus. Researchers can conveniently access these resources through the interactive ePlant browser (https://bar.utoronto.ca/eplant_eucalyptus).

Rice requires a chromatin remodeler for Polymerase IV-small interfering RNA production and genomic immunity

Transgenes are often spontaneously silenced, which hinders the application of genetic modifications to crop breeding. While gene silencing has been extensively studied in Arabidopsis (Arabidopsis thaliana), the molecular mechanism of transgene silencing remains elusive in crop plants. We used rice (Oryza sativa) plants silenced for a 35S::OsGA2ox1 (Gibberellin 2-oxidase 1) transgene to isolate five elements mountain (fem) mutants showing restoration of transgene expression. In this study, we isolated multiple fem2 mutants defective in a homolog of Required to Maintain Repression 1 (RMR1) of maize (Zea mays) and CLASSY (CLSY) of Arabidopsis. In addition to failing to maintain transgene silencing, as occurs in fem3, in which mutation occurs in NUCLEAR RNA POLYMERASE E1 (OsNRPE1), the fem2 mutant failed to establish transgene silencing of 35S::OsGA2ox1. Mutation in FEM2 eliminated all RNA POLYMERASE IV (Pol-IV)-FEM1/OsRDR2 (RNA-DEPENDENT RNA POLYMERASE 2)-dependent small interfering RNAs (siRNAs), reduced DNA methylation on genome-wide scale in rice seedlings, caused pleiotropic developmental defects, and increased disease resistance. Simultaneous mutation in 2 FEM2 homologous genes, FEM2-Like 1 (FEL1) and FEL2, however, did not affect DNA methylation and rice development and disease resistance. The predominant expression of FEM2 over FEL1 and FEL2 in various tissues was likely caused by epigenetic states. Overexpression of FEL1 but not FEL2 partially rescued hypomethylation of fem2, indicating that FEL1 maintains the cryptic function. In summary, FEM2 is essential for establishing and maintaining gene silencing; moreover, FEM2 is solely required for Pol IV-FEM1 siRNA biosynthesis and de novo DNA methylation.

Rice OseIF6.1 encodes a eukaryotic translation initiation factor and is essential for the development of grain and anther

The eIF6 proteins are distributed extensively in eukaryotes and play diverse and essential roles. The bona fide eIF6 protein in Arabidopsis, At-eIF6;1, is essential for embryogenesis. However, the role of eIF6 proteins in rice growth and development remains elusive and requires further investigation. Here, we characterized the functions of OseIF6.1, which is homologous to At-eIF6;1. OseIF6.1 encodes an eukaryotic translation initiation factor with a conserved eIF6 domain. The knockdown of OseIF6.1 resulted in a decrease in grain length and pollen sterility, whereas the overexpression of OseIF6.1 displayed opposite phenotypes. Further studies revealed that OseIF6.1 regulates grain shape by influencing cell expansion and proliferation. In addition, OseIF6.1 interacts with OsNMD3, which is a nuclear export adaptor for the 60S ribosomal subunit. The knockdown of OsNMD3 in plants exhibited reduced fertility and seed setting. Therefore, our findings have significantly enriched the current understanding of the role of OseIF6.1 in rice growth and development.