Trithorax-group protein ATX5 mediates the glucose response via impacting the HY1-ABI4 signaling module

Oligosaccharide production and signaling correlate with delayed flowering in an Arabidopsis genotype grown and selected in high [CO2]

Since industrialization began, atmospheric CO2 ([CO2]) has increased from 270 to 415 ppm and is projected to reach 800-1000 ppm this century. Some Arabidopsis thaliana (Arabidopsis) genotypes delayed flowering in elevated [CO2] relative to current [CO2], while others showed no change or accelerations. To predict genotype-specific flowering behaviors, we must understand the mechanisms driving flowering response to rising [CO2]. [CO2] changes alter photosynthesis and carbohydrates in plants. Plants sense carbohydrate levels, and exogenous carbohydrate application influences flowering time and flowering transcript levels. We asked how organismal changes in carbohydrates and transcription correlate with changes in flowering time under elevated [CO2]. We used a genotype (SG) of Arabidopsis that was selected for high fitness at elevated [CO2] (700 ppm). SG delays flowering under elevated [CO2] (700 ppm) relative to current [CO2] (400 ppm). We compared SG to a closely related control genotype (CG) that shows no [CO2]-induced flowering change. We compared metabolomic and transcriptomic profiles in these genotypes at current and elevated [CO2] to assess correlations with flowering in these conditions. While both genotypes altered carbohydrates in response to elevated [CO2], SG had higher levels of sucrose than CG and showed a stronger increase in glucose and fructose in elevated [CO2]. Both genotypes demonstrated transcriptional changes, with CG increasing genes related to fructose 1,6-bisphosphate breakdown, amino acid synthesis, and secondary metabolites; and SG decreasing genes related to starch and sugar metabolism, but increasing genes involved in oligosaccharide production and sugar modifications. Genes associated with flowering regulation within the photoperiod, vernalization, and meristem identity pathways were altered in these genotypes. Elevated [CO2] may alter carbohydrates to influence transcription in both genotypes and delayed flowering in SG. Changes in the oligosaccharide pool may contribute to delayed flowering in SG. This work extends the literature exploring genotypic-specific flowering responses to elevated [CO2].

Dynamics of epigenetic control in plants via SET domain containing proteins: Structural and functional insights

Plants control expression of their genes in a way that involves manipulating the chromatin structural dynamics in order to adapt to environmental changes and carry out developmental processes. Histone modifications like histone methylation are significant epigenetic marks which profoundly and globally modify chromatin, potentially affecting the expression of several genes. Methylation of histones is catalyzed by histone lysine methyltransferases (HKMTs), that features an evolutionary conserved domain known as SET [Su(var)3-9, E(Z), Trithorax]. This methylation is directed at particular lysine (K) residues on H3 or H4 histone. Plant SET domain group (SDG) proteins are categorized into different classes that have been conserved through evolution, and each class have specificity that influences how the chromatin structure operates. The domains discovered in plant SET domain proteins have typically been linked to protein-protein interactions, suggesting that majority of the SDGs function in complexes. Additionally, SDG-mediated histone mark deposition also affects alternative splicing events. In present review, we discussed the diversity of SDGs in plants including their structural properties. Additionally, we have provided comprehensive summary of the functions of the SDG-domain containing proteins in plant developmental processes and response to environmental stimuli have also been highlighted.

Dynamic regulation of DNA methylation and histone modifications in response to abiotic stresses in plants

DNA methylation and histone modification are evolutionarily conserved epigenetic modifications that are crucial for the expression regulation of abiotic stress-responsive genes in plants. Dynamic changes in gene expression levels can result from changes in DNA methylation and histone modifications. In the last two decades, how epigenetic machinery regulates abiotic stress responses in plants has been extensively studied. Here, based on recent publications, we review how DNA methylation and histone modifications impact gene expression regulation in response to abiotic stresses such as drought, abscisic acid, high salt, extreme temperature, nutrient deficiency or toxicity, and ultraviolet B exposure. We also review the roles of epigenetic mechanisms in the formation of transgenerational stress memory. We posit that a better understanding of the epigenetic underpinnings of abiotic stress responses in plants may facilitate the design of more stress-resistant or -resilient crops, which is essential for coping with global warming and extreme environments.

Association mapping for important agronomic traits in wild and cultivated Vigna species using cross-species and cross-genera simple sequence repeat markers

The genus Vigna is an agronomically important taxon, with many of its species inhabiting a wide range of environments and offering numerous useful genes for the improvement of the cultivated types. The present study aimed to detect the genomic regions associated with yield-attributing traits by genome-wide association mapping. A diverse panel of 98 wild and cultivated Vigna accessions (acc.) belonging to 13 different species was evaluated for yield and related traits during the kharif season of 2017 and 2018. The panel was also genotyped using 92 cross-genera and cross-species simple sequence repeat markers to study the population genetic structure and useful market-trait associations. The PCA and trait correlation established relationships amongst the traits during both seasons while 100-seed weight (HSW) had a positive correlation with pod length (PL), and days to first flowering (DFF) with days to maturity (DM). The population genetic structure analysis grouped different acc. into three genetically distinct sub-populations with SP-1 comprising 34 acc., SP-2 (24 acc.), and SP-3 (33 acc.) and one admixture group (7 acc.). Mixed linear model analysis revealed an association of 13 markers, namely, VR018, VR039, VR022, CEDG033, GMES0337, MBSSR008, CEDG220, VM27, CP1225, CP08695, CEDG100, CEDG008, and CEDG096A with nine traits. Seven of the aforementioned markers, namely, VR018 for plant height (PH) and terminal leaflet length (TLL), VR022 for HSW and pod length (PL), CEDG033 for DFF and DM, MBSSR008 for DFF and DM, CP1225 for CC at 30 days (CC30), DFF and DM, CEDG100 for PH and terminal leaflet length (TLL), and CEDG096A for CC30 and chlorophyll content at 45 days were associated with multiple traits. The marker CEDG100, associated with HSW, PH, and TLL, is co-localized in gene-encoding histone-lysine N-methyltransferase ATX5. Similarly, VR22, associated with PL and HSW, is co-located in gene-encoding SHOOT GRAVITROPISM 5 in mungbean. These associations may be highly useful for marker-assisted genetic improvement of mungbean and other related Vigna species.

Methylation hallmarks on the histone tail as a linker of osmotic stress and gene transcription

Plants dynamically manipulate their gene expression in acclimation to the challenging environment. Hereinto, the histone methylation tunes the gene transcription via modulation of the chromatin accessibility to transcription machinery. Osmotic stress, which is caused by water deprivation or high concentration of ions, can trigger remarkable changes in histone methylation landscape and genome-wide reprogramming of transcription. However, the dynamic regulation of genes, especially how stress-inducible genes are timely epi-regulated by histone methylation remains largely unclear. In this review, recent findings on the interaction between histone (de)methylation and osmotic stress were summarized, with emphasis on the effects on histone methylation profiles imposed by stress and how histone methylation works to optimize the performance of plants under stress.

HEXOKINASE1 forms a nuclear complex with the PRC2 subunits CURLY LEAF and SWINGER to regulate glucose signaling

The glucose sensor HEXOKINASE1 (HXK1) integrates myriad external and internal signals to regulate gene expression and development in Arabidopsis thaliana. However, how HXK1 mediates glucose signaling in the nucleus remains unclear. Here, using immunoprecipitation-coupled mass spectrometry, we show that two catalytic subunits of Polycomb Repressive Complex 2, SWINGER (SWN) and CURLY LEAF (CLF), directly interact with catalytically active HXK1 and its inactive forms (HXK1^G104D and HXK1^S177A ) via their evolutionarily conserved SANT domains. HXK1, CLF, and SWN target common glucose-responsive genes to regulate glucose signaling, as revealed by RNA sequencing. The glucose-insensitive phenotypes of the Arabidopsis swn-1 and clf-50 mutants were similar to that of hxk1, and genetic analysis revealed that CLF, SWN, and HXK1 function in the same genetic pathway. Intriguingly, HXK1 is required for CLF- and SWN-mediated histone H3 lysine 27 (H3K27me3) deposition and glucose-mediated gene repression. Moreover, CLF and SWN affect the recruitment of HXK1 to its target chromatin. These findings support a model in which HXK1 and epigenetic modifiers form a nuclear complex to cooperatively mediate glucose signaling, thereby affecting the histone modification and expression of glucose-regulated genes in plants.

Dynamic epigenetic modifications in plant sugar signal transduction

In eukaryotes, dynamic chromatin states are closely related to changes in gene expression. Epigenetic modifications help plants adapt to their ever-changing environment by modulating gene expression via covalent modification at specific sites on DNA or histones. Sugars provide energy, but also function as signaling molecules to control plant growth and development. Various epigenetic modifications participate in sensing and transmitting sugar signals. Here we summarize recent progress in uncovering the epigenetic mechanisms involved in sugar signal transduction, including histone acetylation and deacetylation, histone methylation and demethylation, and DNA methylation. We also highlight changes in chromatin marks when crosstalk occurs between sugar signaling and the light, temperature, and phytohormone signaling pathways, and describe potential questions and approaches for future research.

Multifaceted Signaling Networks Mediated by Abscisic Acid Insensitive 4

Although ABSCISIC ACID INSENSITIVE 4 (ABI4) was initially demonstrated as a key positive regulator in the phytohormone abscisic acid (ABA) signaling cascade, multiple studies have now shown that it is actually involved in the regulation of several other cascades, including diverse phytohormone biogenesis and signaling pathways, various developmental processes (such as seed dormancy and germination, seedling establishment, and root development), disease resistance and lipid metabolism. Consistent with its versatile biological functions, ABI4 either activates or represses transcription of its target genes. The upstream regulators of ABI4 at both the transcription and post-transcription levels have also been documented in recent years. Consequently, a complicated network consisting of the direct target genes and upstream regulators of ABI4, through which ABI4 participates in several phytohormone crosstalk networks, has been generated. In this review, we summarize current understanding of the sophisticated ABI4-mediated molecular networks, mainly focusing on diverse phytohormone (including ABA, gibberellin, cytokinin, ethylene, auxin, and jasmonic acid) crosstalks. We also discuss the potential mechanisms through which ABI4 receives the ABA signal, focusing on protein phosphorylation modification events.

PARP1 Hinders Histone H2B Occupancy at the NFATc1 Promoter to Restrain Osteoclast Differentiation

Induction of nuclear factor of activated T cell cytoplasmic 1 (NFATc1) by macrophage colony-stimulating factor (M-CSF) and receptor activator of NF-κB ligand (RANKL) is essential for macrophage differentiation into osteoclasts (OCs), but the underlying mechanisms remain unclear. The ability of poly(ADP-ribose) polymerase 1 (PARP1) to poly-ADP-ribosylate NFATc1 in T cells prompted us to investigate the PARP1 and NFATc1 interaction during osteoclastogenesis. However, extensive studies failed to directly link PARP1 to NFATc1. A combination of transcriptomics and proteomics studies was then used to identify PARP1 targets under these conditions. These unbiased approaches in conjunction with site-directed mutagenesis studies revealed that PARP1 inhibited NFATc1 expression and OC formation by ADP-ribosylating histone H2B at serine 7 and decreasing the occupancy of this histone variant at the NFATc1 promoter. The anti-osteoclastogenic function of PARP1 was confirmed in vivo in several mouse models of PARP1 loss-of-function or gain-of-function, including a novel model in which PARP1 was conditionally ablated in myeloid cells. Thus, PARP1 ADP-ribosylates H2B to negatively regulate NFATc1 expression and OC differentiation. © 2019 American Society for Bone and Mineral Research.

The Molecular Regulation of Carbon Sink Strength in Grapevine (Vitis vinifera L.)

Sink organs, the net receivers of resources from source tissues, provide food and energy for humans. Crops yield and quality are improved by increased sink strength and source activity, which are affected by many factors, including sugars and hormones. With the growing global population, it is necessary to increase photosynthesis into crop biomass and yield on a per plant basis by enhancing sink strength. Sugar translocation and accumulation are the major determinants of sink strength, so understanding molecular mechanisms and sugar allocation regulation are conducive to develop biotechnology to enhance sink strength. Grapevine (Vitis vinifera L.) is an excellent model to study the sink strength mechanism and regulation for perennial fruit crops, which export sucrose from leaves and accumulates high concentrations of hexoses in the vacuoles of fruit mesocarp cells. Here recent advances of this topic in grape are updated and discussed, including the molecular biology of sink strength, including sugar transportation and accumulation, the genes involved in sugar mobilization and their regulation of sugar and other regulators, and the effects of hormones on sink size and sink activity. Finally, a molecular basis model of the regulation of sugar accumulation in the grape is proposed.