[This corrects the article DOI: 10.1371/journal.pone.0044361.].

The epigenetic mechanisms that regulate the DNA–histone contacts and the chromatin-based control of transcription provide an essential link between various signaling pathways in plants. The developmental process controlling the transition from vegetative to reproductive meristem and flowering time in plants represents a crucial and complex interlinked module and is governed by various environmental cues and signaling cascades. Research in Arabidopsis has elucidated the core components of principal flowering pathways that converge to activate floral meristem identity genes, thereby integrating environmental and developmental cues to promote flowering. Under the scenario of a changing climate, the epigenetic mechanism seems to emerge as a pivotal regulatory module in controlling gene expression and developmental responses in plants, including flowering. Based on these, the current review mainly highlights the interplay between epigenetic modifiers and key players of flowering pathways, showcasing the co-expression analysis of genes related to specific as well as overlapping epigenetic regulation in the flowering transition pathway of Arabidopsis. Here, we addressed how the intricate interplay and the relationships among the various epigenetic mechanisms, such as chromatin remodeling, histone modifications, microRNAs, and long non-coding RNAs, control the expression of genes involved in major flowering pathways to regulate flowering. The fundamental concepts offer a contemporary perspective on the crosstalk between epigenetic regulation and flowering in the context of plant growth, development, and crop yield.

Translating the nitrogen-fixing ability of legume-rhizobia symbiosis to other crops has long been a dream for molecular biologists. Over the past two decades, several crucial genes involved in the pathway have been identified, that prevails as an intricate network governing root nodule symbiosis (RNS). RNS signaling employs the common symbiotic signaling pathway required for Arbuscular Mycorrhizal (AM) symbiosis (plant-fungal symbiosis) that is widely known in several crop plants. Therefore, understanding the similarities and divergence between the two signaling pathways has always been a hotspot for research. The major adjuvants in the RNS pathway are the Nod Factor Receptors (NFRs - that perceive Nod Factors released by rhizobia), and a Nodule-INception protein (NIN - a transcription factor that activates cortical cell division), which direct the pathway from AMS towards RNS. Therefore, understanding the structure and the signaling mechanism(s) of NFRs and NIN is crucial for the success of translational approaches. In this article, we will be highlighting the most recent discoveries pertaining to the functionality of NFRs, which have taken us a few steps closer towards receptor engineering into non-nodulating plants.

Signaling in root nodule symbiosis is initiated by the perception of rhizobial Nod factors (NFs) by two plant Lysin motif (LysM)-containing Nod factor receptors (NFR1 and NFR5). Here, we identified the NFR1 homolog from chickpea (Cicer arietinum) and functionally established its role by a gene silencing approach. To achieve insights into the molecular mechanisms of CaNFR1, we evaluated a highly conserved residue in its activation loop and a specific region of the juxtamembrane (ΔJM) domain. The replacement of threonine with alanine at position 476 had significant implications, causing the loss of a phosphorylation event and disrupting the interaction with NFR5. The elimination of the ΔJM domain of CaNFR1 also weakened the interaction strength with CaNFR5. Based on molecular docking and simulation studies, these structural alterations aligned with our yeast-based and in planta protein-protein interaction data, as well as a significant reduction in nodule number, size, and infection cell abundance after overexpression of CaNFR1 variants. Cross-species genetic complementation in the lyk3 mutant of Medicago truncatula highlighted the critical role of the evolutionarily conserved T476 in the activation loop and ΔJM domain of NFR1, in its interaction with NFR5, underscoring a crucial step in the receptor-mediated activation mechanism leading to root nodulation in legumes.

This article has been retracted by the Editor-in-Chief following concerns raised after publication. Specifically, duplication of two lanes within the same blot was identified in Figure 1b, where different samples were represented using the same data. The authors were unable to provide a satisfactory explanation or a suitable replacement figure. As a result, the editor has lost confidence in the data and conclusions presented in the study. One author (Swarup Roy Choudhury) disagreed with the retraction. The remaining authors did not respond to correspondence from the publisher regarding this issue.

The RWP-RK domain is a key DNA-binding domain found in all NIN (Nodule Inception)/NLP (NIN-like proteins) and RKD (RWP-RK Domain Containing) transcription factors (TFs). The RWP-RK domain in NINs/NLPs contains a highly evolutionarily conserved sequence, RWPSRK, while in RKDs, the fourth serine (S) amino acid is substituted with either tyrosine (Y) or histidine (H). To regulate autoregulation of nodulation, the RWP-RK domain of NIN TF binds to the promoter region of CLE peptides but not RKDs. Therefore, investigating the protein-DNA interaction from a structural perspective is essential to understand the evolutionary significance of the serine (S) residue of the RWP-RK domain. Herein, we have modelled both the wild type (WT) and the variant RWP-RK domains containing substitutions like glutamic acid (E), tyrosine (Y), and histidine (H) and docked them with the modelled pCLE13 cis-element. Our docking results revealed that a helix-turn-helix (HTH) motif of the RWP-RK domain interacts with pCLE13. The WT HTH-DNA complex exhibited the most negative binding free energy, indicating a strong interaction, particularly hydrogen bonds acting between them. Simulation analysis of WT and variant models provided deeper insights into protein-DNA binding dynamics. The hydrogen bond occupancy percentage indicated that the fourth serine (S) residue is vital for maintaining a significant percentage of hydrogen bonds with DNA. The variants substituting this conserved serine (S) residue displayed energetic frustration upon binding to DNA and lost correlation among their residues. Overall, it suggested that serine (S) residue of the RWP-RK domain of all NINs/NLPs is crucial for appropriate protein-DNA interaction, which might be required for their biological relevance.

The accumulation of the livestock-harming cyanogenic glucoside dhurrin in the vegetative tissues limits the use of sorghum as a major pasture crop. This study integrates transcriptomics and metabolomics data from the ICSV 93046, CSH 24-MF and ICSR 14001 genotypes, which differ in drought tolerance and cyanide potential (HCNp), to understand the molecular processes of cyanogenesis under drought stress conditions. While ICSV 93046 showed drought adaptation and reduced HCNp, ICSR 14001 and CSH 24-MF exhibited decreased drought stress tolerance with HCN accumulation. The differentially expressed gene (DEG) data showed drought-related genes were significantly upregulated in ICSV 93046 but downregulated in ICSR 14001. KEGG pathway analysis revealed enriched dhurrin biosynthesis and cyanoamino acid metabolism genes, with higher expression in ICSR 14001 than in ICSV 93046. WGCNA analysis revealed that hub genes are involved in drought-induced signalling components, such as phospholipases (PLPs) and lipoxygenases (LOXs), which are implicated in membrane protection. In drought-sensitive genotypes, stress-induced membrane damages lead to the release of dhurrin into the cytoplasm, thus elevating HCN content and activating defence responses. Conversely, the drought-adapted genotype could mitigate HCN production by averting membrane injury, thereby effectively modulating the oxidative stress and preventing the release of dhurrin into the cytoplasm.

Heterotrimeric GTP-binding protein alpha subunit (Gα) and its cognate regulator of G-protein signaling (RGS) protein transduce signals in eukaryotes spanning protists, amoeba, animals, fungi, and plants. The core catalytic mechanisms of the GTPase activity of Gα and the interaction interface with RGS for acceleration of GTP hydrolysis seem to be conserved across these groups; however, the RGS gene is under low selective pressure in plants, resulting in its frequent loss. Our current understanding of the structural basis of Gα:RGS regulation in plants has been shaped by Arabidopsis Gα, (AtGPA1), which has a cognate RGS protein. To gain a comprehensive understanding of this regulation beyond Arabidopsis, we obtained the x-ray crystal structures of Oryza sativa Gα, which has no RGS, and Selaginella moellendorffi Gα, a lycophyte Gα that has low sequence similarity with AtGPA1 but has an RGS. We show that the three-dimensional structure, protein-protein interaction with RGS, and the dynamic features of these Gα are similar to AtGPA1 and metazoan Gα. Molecular dynamic simulation of the Gα-RGS interaction identifies the contacts established by specific residues of the switch regions of GTP-bound Gα, crucial for this interaction, but finds no significant difference due to specific amino acid substitutions. Together, our data provide valuable insights into the regulatory mechanisms of plant G-proteins, but do not support the hypothesis of adaptive co-evolution of Gα:RGS proteins in plants.

Desiccation tolerance is a complex biological phenomenon that allows certain plants to survive extreme dehydration and revive upon rehydration. Although significant progress has been made in understanding the physiological and molecular mechanisms involved in desiccation tolerance, recovery mechanisms after prolonged desiccation periods are enigmatic. Combining physiological, biochemical, transcriptomic and metabolomic approaches, we investigated the role of prolonged desiccation on recovery of Selaginella bryopteris. Prolonged desiccation causes a decline in the antioxidant system, leading to accumulation of ROS that hinder recovery by inducing cellular damage. Transcriptome and WGCNA analysis revealed the significance of protective proteins, alternative respiration and protein homeostasis in cellular protection and recovery after short and long-term desiccation. Metabolomic analysis exhibited an increased accumulation of antioxidant compounds, which can be substituted for antioxidant enzymes to maintain cellular protection during prolonged desiccation. The significant role of autophagy and autophagic components was evaluated by H2O2 treatment and phylogenetic analysis of ATG4 and ATG8, which unveiled their substantial role in desiccation tolerance and remarkable conservation of the autophagy-related genes across plant species. Our data demonstrated that prolonged desiccation leads to ROS-induced cell death by extensive autophagy due to enormous loss of protective proteins, antioxidant enzymes and energy resources during desiccation.

Plants accumulate flavonoids as part of UV-B acclimation, while a high level of UV-B irradiation induces DNA damage and leads to genome instability. Here, we show that MYB4, a member of the R2R3-subfamily of MYB transcription factor plays important role in regulating plant response to UV-B exposure through the direct repression of the key genes involved in flavonoids biosynthesis and repair of DNA double-strand breaks (DSBs). Our results demonstrate that MYB4 inhibits seed germination and seedling establishment in Arabidopsis following UV-B exposure. Phenotype analyses of atmyb4-1 single mutant line along with uvr8-6/atmyb4-1, cop1-6/atmyb4-1, and hy5-215/atmyb4-1 double mutants indicate that MYB4 functions downstream of UVR8 mediated signaling pathway and negatively affects UV-B acclimation and cotyledon expansion. Our results indicate that MYB4 acts as transcriptional repressor of two key flavonoid biosynthesis genes, including 4CL and FLS, via directly binding to their promoter, thus reducing flavonoid accumulation. On the other hand, AtMYB4 overexpression leads to higher accumulation level of DSBs along with repressed expression of several key DSB repair genes, including AtATM, AtKU70, AtLIG4, AtXRCC4, AtBRCA1, AtSOG1, AtRAD51, and AtRAD54, respectively. Our results further suggest that MYB4 protein represses the expression of two crucial DSB repair genes, AtKU70 and AtXRCC4 through direct binding with their promoters. Together, our results indicate that MYB4 functions as an important coordinator to regulate plant response to UV-B through transcriptional regulation of key genes involved in flavonoids biosynthesis and repair of UV-B induced DNA damage.

MYB4, a member of the R2R3-type subfamily of MYB transcription factor plays a crucial role in regulating the accumulation of UV-B absorbing phenylpropanoids in plants. UV-B exposure for a longer duration down-regulates the expression of MYB4 gene in Arabidopsis. MYB4 protein represses its own expression by binding to its own promoter. However, at present practically nothing is known about the post-translational regulation of MYB4 protein in vivo. Here, we provide evidence that in Arabidopsis MYB4 protein is phosphorylated in vivo and is targeted by the ubiquitin-26S proteasome-dependent pathway. Immunoprecipitation, immunoblotting, and phosphoprotein staining experiments have revealed that both the accumulation pattern and phosphorylation of MYB4 increase in the light condition during the 24hours time span under long-day conditions. Yeast two-hybrid and bimolecular fluorescence complementation assays have shown that MYB4 directly interacts with a nuclear WD40 repeat protein, PRL1 in vivo. Cell-free protein degradation assay in the absence and presence of proteasome inhibitor indicates that MYB4 is degraded in a ubiquitin proteasome-dependent manner. Furthermore, analyses of MYB4 protein accumulation levels in transgenic atmyb4-1 mutant line expressing 35S:AtMYB4 (35S:AtMYB4-atmyb4-1) and atprl1-1 mutant line indicate that PRL1 regulate stability of MYB4 in Arabidopsis. Overall, our results provide important information on the possible mechanism of post-translational modification and regulation of stability of MYB4 protein in Arabidopsis in vivo.

The MYB gene superfamily encompasses a group of related genes found in all eukaryotes. In contrast to animals, higher plants contain large numbers of two-repeat MYB genes, which have been established in regulating crucial developmental, biotic, and abiotic stress responses that profoundly affect the plant's yield. However, a comprehensive analysis of the two-repeat MYB gene family in groundnut and its progenitors, especially the role of two-repeat MYB genes in response to drought stress, and the effect of those genes in nodulation have not been reported so far. Our recent analysis of the groundnut genome has identified 79 (Arachis duranensis), 84 (Arachis ipaensis), and 161 (Arachis hypogaea) two-repeat MYB genes, which belong to multiple distinct subgroups based on their architecture. Here, we provided a complete overview of the gene structure, protein motif organization, chromosome localization, gene duplication events, and synteny analysis to clarify evolutionary perspectives. Members of the same subgroup showed highly conserved structure and motif compositions. The whole-genome duplication and segmental duplication likely contributed to the expansion of two-repeat MYB genes in Arachis hypogaea. The upstream sequences of most genes contained phytohormone-responsive, stress-responsive, lightresponsive, and plant growth-related elements. The genes not only have diverse expression profiles across different development stages but as shown in our experimental findings, most of them were induced by ABA and drought-related stress. Further gene silencing experiments demonstrated that two drought-inducible MYB genes, homologs of Arabidopsis MYB96 and MYB94, function as a negative regulator of root nodulation. The results of this study can serve as a strong foundation for further elucidation of the physiological and molecular function of two-repeat MYB genes in groundnut.

Molecular interspecies dialogue between leguminous plants and nitrogen-fixing rhizobia results in the development of symbiotic root nodules. This is initiated by several nodulation-related receptors present on the surface of root hair epidermal cells. We have shown previously that specific subunits of heterotrimeric G-proteins and their associated regulator of G-protein signaling (RGS) proteins act as molecular links between the receptors and downstream components during nodule formation in soybeans. Nod factor receptor 1 (NFR1) interacts with and phosphorylates RGS proteins to regulate the G-protein cycle. Symbiosis receptor-like kinases (SymRK) phosphorylate Gα to make it inactive and unavailable for Gβγ. We now show that like NFR1, SymRK also interacts with the RGS proteins to phosphorylate them. Phosphorylated RGS has higher activity for accelerating guanosine triphosphate (GTP) hydrolysis by Gα, which favors conversion of active Gα to its inactive form. Phosphorylation of RGS proteins is physiologically relevant, as overexpression of a phospho-mimic version of the RGS protein enhances nodule formation in soybean. These results reveal an intricate fine-tuning of the G-protein signaling during nodulation, where a negative regulator (Gα) is effectively deactivated by RGS due to the concerted efforts of several receptor proteins to ensure adequate nodulation. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Biological nitrogen fixation (BNF) enables plants to cope with nitrogen-deficient soils and enhances the protein content of legumes. Root nodule symbiosis (RNS) is a complex molecular communication between the plant and microbe and is crucial for the BNF of legumes. Rhizobia, a group of nitrogen-fixing soil bacteria, can establish a mutualistic association with legumes by secretion of NOD factors (NF), which is perceived by LysM (lysin motif) domain receptor-like kinases (LysM-RLKs). Apart from LysM-RLKs, a few leucine-rich repeat receptor-like protein kinases (LRR-RLKs) play a significant role in RNS by rhizobial invasion and nodule organogenesis and autoregulation of nodulation (AON). Studies on phosphorylation-dependent modulation of RLKs and their interactors have largely contributed to a better understanding of the fundamental signaling mechanisms of root nodule formation. This chapter accommodates critical discussions on the importance of phosphorylation of various RLKs during RNS in legumes.

In recent years, foliar applications of nanoparticles are increasingly being employed in agricultural fields as fertilizers to enhance crop yields. However, limited studies are available on the foliar uptake of nanoscale nutrients and their interaction with plants. In this study, we reported the effects of foliar spray with varied concentrations of nanoscale silica (N-SiO2) and bulk tetraethyl orthosilicate (TEOS at 2000 ppm) on the growth and yield of groundnut. Nanosilica was prepared by a sol-gel method and characterized by transmission electron microscopy, dynamic light scattering, and X-ray diffraction. The size and zeta potential of N-SiO2 were found to be 28.7 nm and 32 mV, respectively. The plant height, number of branches, total dry weight, SPAD chlorophyll meter reading, photosynthetic rate, water use efficiency, number of nodules, and ascorbic acid content were increased significantly with the N-SiO2 foliar application at 400 ppm over control. The number of filled pods increased significantly by 38.78 and 58.60% with N-SiO2 at 400 ppm application over TEOS and control, respectively. The pod yield per plant in N-SiO2 at 400 ppm increased by 25.52 and 31.7% higher over TEOS and control, respectively. Antioxidant enzyme activities enhanced significantly in N-SiO2 at 200 and 400 ppm over control, indicating a stimulatory effect on the plant growth. In addition, confocal microscopy revealed that fluorescein isothiocyanate (FITC)-N-SiO2 entered through stomata and then transported to vascular bundles via apoplastic movement. Our study for the first time demonstrated that N-SiO2 can significantly modulate multiple complex traits in groundnut through an eco-friendly and sustainable approach.

Abstract Background Cyclin-dependent kinases (CDKs) are a predominant group of serine/threonine protein kinases that have multi-faceted functions in eukaryotes. The plant CDK members have well-known roles in cell cycle progression, transcriptional regulation, DNA repair, abiotic stress and defense responses, making them promising targets for developing stress adaptable high-yielding crops. There is relatively sparse information available on the CDK family genes of cultivated oilseed crop peanut and its diploid progenitors. Results We have identified 52 putative cyclin-dependent kinases (CDKs) and CDK-like (CDKLs) genes in Arachis hypogaea (cultivated peanut) and total 26 genes in each diploid parent of cultivated peanut (Arachis duranensis and Arachis ipaensis). Both CDK and CDKL genes were classified into eight groups based on their cyclin binding motifs and their phylogenetic relationship with Arabidopsis counterparts. Genes in the same subgroup displayed similar exon–intron structure and conserved motifs. Further, gene duplication analysis suggested that segmental duplication events played major roles in the expansion and evolution of CDK and CDKL genes in cultivated peanuts. Identification of diverse cis-acting response elements in CDK and CDKL genes promoter indicated their potential fundamental roles in multiple biological processes. Various gene expression patterns of CDKs and CDKLs in different peanut tissues suggested their involvement during growth and development. In addition, qRT-PCR analysis demonstrated that most representing CDK and CDKL gene family members were significantly down-regulated under ABA, PEG and mannitol treatments. Conclusions Genome-wide analysis offers a comprehensive understanding of the classification, evolution, gene structure, and gene expression profiles of CDK and CDKL genes in cultivated peanut and their diploid progenitors. Additionally, it also provides cell cycle regulatory gene resources for further functional characterization to enhance growth, development and abiotic stress tolerance.

Additional file 1: Table S1. Physico chemical and subcellular localizations of CDKs and CDKLs.

The present study determined the extent to which object and letter recognition recruit similar or dissociated neural resources. Participants passively viewed and silently named line drawings of objects, single letters, and visual noise patterns and centrally fixated an asterisk. We used whole-brain functional MRI and a very conservative approach to hypothesis testing that distinguished among brain regions that were selectively activated by different experimental conditions and those that were conjointly activated. The left fusiform gyrus (BA 19 & 37) and left inferior frontal cortex BA(44/6) showed a greater degree of conjoined activation for objects and letters than selective activation for either category, whereas left inferior parietal cortex (BA 40) and the left insula showed a strong letter-selective response. Equal recruitment of left fusiform and inferior frontal regions by objects and letters reflects similar demands on cognitive processing by these two categories and argues against category-specific modules in these regions. However, cortical systems for object and letter processing are not completely shared given the exclusive activation of left inferior parietal cortex by letters.