Pleiotropic regulatory locus 1 maintains actin cytoskeleton integrity and cellular homeostasis to enable Arabidopsis root growth.

Cell functions are based on the integrity of actin filaments. The actin cytoskeleton is typically the target but also the source of signals. Arabidopsis PRL1 (Pleiotropic Regulatory Locus 1), regulates multiple cellular processes and physiological responses. However, the precise mechanisms underlying PRL1`s multiple functions are unclear. Here, we show that PRL1 maintains actin integrity and concomitant cellular homeostasis. The cortical actin cytoskeleton was de-polymerized in the prl1 mutant, causing the developmental root defect. Actin depolymerization, rather than reactive oxygen species (ROS) imbalance, constituted the fundamental cause of retarded root growth in prl1. ANAC085 upregulation by, and cooperation with, actin depolymerization triggered stele cell death in prl1 roots. Differential gene expression and alternative splicing defects resulting from actin depolymerization occurred independently in prl1. Our work establishes the cause-effect relationships between actin depolymerization and downstream stress-related signals, revealing a novel function of PRL1 and enhancing the understanding of PRL`s functional mechanisms.

Genome-Wide Analysis of DNA Demethylases in Land Plants and Their Expression Pattern in Rice.

DNA demethylation is a very important biochemical pathway regulating a group of biological processes, such as embryo development, fruit ripening, and response to stress. Despite the essential role of DNA demethylases, their evolutionary relationship and detailed biological functions in different land plants remain unclear. In this study, 48 DNA demethylases in 12 land plants were identified and classified. A phylogenetic tree was constructed to demonstrate the evolutionary relationships among these DNA demethylases, indicating how they are related across different species. Conserved domain, protein motif, and gene structure analysis showed that these 48 DNA demethylases fell into the presently identified four classes of DNA demethylases. Amino acid alignment revealed conserved catalytic sites and a previously less-studied protein region (referred to as domain A) within the DNA demethylases. An analysis showed a conserved pattern of gene duplication for DNA demethylases throughout their evolutionary history, suggesting that these genes had been maintained due to their importance. The examination of promoter cis-elements displayed potential signaling and regulating pathways of DNA demethylases. Furthermore, the expression profile was analyzed to investigate the physiological role of rice DNA demethylase in different developmental stages, in tissues, and in response to stress and various phytohormone signals. The findings offer a deeper insight into the functional regions of DNA demethylases and their evolutionary relationships, which can guide future research directions. Understanding the role of DNA demethylases can lead to improved plant stress resistance and contribute to the development of better crop and fruit varieties.

Comparative transcriptome profiling reveals distinct regulatory responses of secondary defensive metabolism in Datura species (Solanaceae) under plant development and herbivory-mediated stress.

Differential expression of genes is key to mediating developmental and stress-related plant responses. Here, we addressed the regulation of plant metabolic responses to biotic stress and the developmental variation of defense-related genes in four species of the genus Datura with variable patterns of metabolite accumulation and development. We combine transcriptome profiling with phylogenomic techniques to analyze gene expression and coexpression in plants subjected to damage by a specialist folivore insect. We found (1) common overall gene expression in species of similar chemical profiles, (2) species-specific responses of proteins involved in specialized metabolism, characterized by constant levels of gene expression coupled with transcriptional rearrangement, and (3) induction of transcriptional rearrangement of major terpene and tropane alkaloid genes upon herbivory. Our results indicate differential modulation of terpene and tropane metabolism linked to jasmonate signaling and specific transcription factors to regulate developmental variation and stress programs, and suggest plastic adaptive responses to cope with herbivory. The transcriptional profiles of specialized metabolism shown here reveal complex genetic control of plant metabolism and contribute to understanding the molecular basis of adaptations and the physiological variation of significant ecological traits.

Integrated physiological analyses, transcriptome, and DNA methylation reveal superiority of pear stigma-style complex development regulation.

Styles and stigmas are crucial components of the fertilization process that allows a pear tree to bear fruit. The information regarding the development mechanism of pear style and stigma is still unclear. Our results demonstrated that IAA, ABA, and BR are significantly increased at 1 DBF, while JA is decreased at 5 DBF. The fructose and starch contents significantly increased at 1 DBF when the style with stigma was ready for pollination. Transcriptome and DNA methylation analysis showed 8087 DEGs and 3771 DMRs were enriched in plant hormones biosynthesis, carbohydrate biosynthesis and metabolism, and TFs in 1 DBF as compared with 7 DBF. The CHH methylation type of DMRs accounts for 84.75%. Most DMRs of CHH upregulated in 1 DBF vs. 7 DBF. This study found for the first time that transcription factor ERFs and DNA methylation are involved in regulating the growth and development of fruit plant style and stigma.

Plant development and reproduction in a changing environment.

Plants face the most diverse climatic conditions throughout their life cycle. As sessile organisms, they are remarkably resilient to adverse environments, which have been exacerbated in the current context of global change. The way in which plants sense and respond to various types of abiotic stresses varies depending on the severity of the stress and the developmental stage of the plant, affecting both vegetative and reproductive aspects. Understanding how plants respond and adapt to a changing environment is crucial for predicting and mitigating the impacts of climate change on ecosystems and ensuring the future survival and reproduction of plant species.

MicroRNA166: Old Players and New Insights into Crop Agronomic Traits Improvement.

MicroRNA (miRNA), a type of non-coding RNA, is crucial for controlling gene expression. Among the various miRNA families, miR166 stands out as a highly conserved group found in both model and crop plants. It plays a key role in regulating a wide range of developmental and environmental responses. In this review, we explore the diverse sequences of MIR166s in major crops and discuss the important regulatory functions of miR166 in plant growth and stress responses. Additionally, we summarize how miR166 interacts with other miRNAs and highlight the potential for enhancing agronomic traits by manipulating the expression of miR166 and its targeted HD-ZIP III genes.

The Biosynthesis Process of Small RNA and Its Pivotal Roles in Plant Development.

In the realm of plant biology, small RNAs (sRNAs) are imperative in the orchestration of gene expression, playing pivotal roles across a spectrum of developmental sequences and responses to environmental stressors. The biosynthetic cascade of sRNAs is characterized by an elaborate network of enzymatic pathways that meticulously process double-stranded RNA (dsRNA) precursors into sRNA molecules, typically 20 to 30 nucleotides in length. These sRNAs, chiefly microRNAs (miRNAs) and small interfering RNAs (siRNAs), are integral in guiding the RNA-induced silencing complex (RISC) to selectively target messenger RNAs (mRNAs) for post-transcriptional modulation. This regulation is achieved either through the targeted cleavage or the suppression of translational efficiency of the mRNAs. In plant development, sRNAs are integral to the modulation of key pathways that govern growth patterns, organ differentiation, and developmental timing. The biogenesis of sRNA itself is a fine-tuned process, beginning with transcription and proceeding through a series of processing steps involving Dicer-like enzymes and RNA-binding proteins. Recent advances in the field have illuminated the complex processes underlying the generation and function of small RNAs (sRNAs), including the identification of new sRNA categories and the clarification of their involvement in the intercommunication among diverse regulatory pathways. This review endeavors to evaluate the contemporary comprehension of sRNA biosynthesis and to underscore the pivotal role these molecules play in directing the intricate performance of plant developmental processes.

Heat-stress-induced ROS in maize silks cause late pollen tube growth arrest and sterility.

The reproductive phase of plants is highly sensitive to ambient temperature stresses. To investigate sensitivity of female reproductive organs in grass crops during the pollination phase, we exposed the elongated stigma (silk) of maize to ambient environment at the silking stage. Moderate heat stress causes cell death of silk hair cells but did not affect early pollen tube growth inside the silk. Late pollen tube growth arrest was observed, leading to sterility. Heat stress causes elevated levels of reactive oxygen species (ROS) in silks, whose levels can be reduced by scavengers partly restoring pollen tube growth and fertility. A number of biological processes including hydrogen peroxide catabolic processes and bHLH transcription factor genes are downregulated by heat stress, while some NAC transcription factor genes are strongly upregulated. In conclusion, this study now provides a basis to select genes for engineering heat-stress-tolerant grass crops during the pollination phase.

A neutral invertase controls cell division besides hydrolysis of sucrose for nutrition during germination and seed setting in rice.

Sucrose is the transport form of carbohydrate in plants serving as signal molecule besides nutrition, but the signaling is elusive. Here, neutral invertase 8 (OsNIN8) mutated at G461R into OsNIN8m, which increased its charge and hydrophobicity, decreased hydrolysis of sucrose to 13% and firmer binding to sucrose than the wildtype. This caused downstream metabolites and energy accumulation forming overnutrition. Paradoxically, division of subinitials in longitudinal cell lineages was only about 15 times but more than 100 times in wildtype, resulting in short radicle. Further, mutation of OsNIN8 into deficiency of hydrolysis but maintenance of sucrose binding allowed cell division until ran out of energy showing the association but not hydrolysis gave the signal. Chemically, sucrose binding to OsNIN8 was exothermic but to OsNIN8m was endothermic. Therefore, OsNIN8m lost the signal function owing to change of thermodynamic state. So, OsNIN8 sensed sucrose for cell division besides hydrolyzed sucrose.

An insight into the roles of ubiquitin-specific proteases in plants: development and growth, morphogenesis, and stress response.

Ubiquitination is a highly conserved and dynamic post-translational modification in which protein substrates are modified by ubiquitin to influence their activity, localization, or stability. Deubiquitination enzymes (DUBs) counter ubiquitin signaling by removing ubiquitin from the substrates. Ubiquitin-specific proteases (UBPs), the largest subfamily of DUBs, are conserved in plants, serving diverse functions across various cellular processes, although members within the same group often exhibit functional redundancy. Here, we briefly review recent advances in understanding the biological roles of UBPs, particularly the molecular mechanism by which UBPs regulate plant development and growth, morphogenesis, and stress response, which sheds light on the mechanistic roles of deubiquitination in plants.

Soybean ethylene response factors GmENS1 and GmENS2 promote nodule senescence.

The final phase in root nodule development is nodule senescence. The mechanism underlying the initiation of nodule senescence requires further elucidation. Here, we investigated the intrinsic signals governing soybean (Glycine max L. Merr.) nodule senescence, uncovering ethylene as a key signal in this intricate mechanism. Two AP2/ERF transcription factor genes, GmENS1 and GmENS2 (Ethylene-responsive transcription factors required for Nodule Senescence), exhibit heightened expression levels in both aged nodules and nodules treated with ethylene. Overexpression of either GmENS1 or GmENS2 accelerated senescence in soybean nodules, whereas the knockout or knockdown of both genes delayed senescence and enhanced nitrogenase activity. Furthermore, our findings indicated that GmENS1 and GmENS2 directly bind to the promoters of GmNAC039, GmNAC018, and GmNAC030, encoding three NAC transcription factors essential for activating soybean nodule senescence. Notably, the nodule senescence process mediated by GmENS1 or GmENS2 overexpression was suppressed in the soybean nac039/018/030 triple mutant compared with the wild-type control. These data indicate GmENS1 and GmENS2 as pivotal transcription factors mediating ethylene-induced nodule senescence through the direct activation of GmNAC039/GmNAC018/GmNAC030 expression in soybean.

Thermopriming Induces Time-Limited Tolerance to Salt Stress.

Implementing sustainable crop protection practices is crucial to protect global harvests and ensure high-quality food supplies. While priming is an established method in seed production for the fortification of plants against various stresses, it is not yet a standard practice in transplant cultivation. Thus, we evaluated the long-term effects of thermopriming-a heat-based priming technique-on the growth, development, and fruit yield of tomato plants. Following a recovery period of about six weeks for thermoprimed plants without stress inducers, we subjected them to subsequent salt stress to ascertain the persistence of the priming effects. Additionally, we compared the efficacy of thermopriming with benzothiadiazole (BTH), a chemical elicitor, in enhancing plant resilience to abiotic stress. While BTH application negatively impacted both plant growth and fruit health, thermopriming showed no such adverse effects on these parameters. Instead, thermopriming initially enhanced the plant defense mechanisms by increasing the accumulation of protective phenols and flavonoids in the leaves. Interestingly, while thermopriming did not alter the response to salt stress, it notably strengthened the overall resilience of the plants. Our findings underscore both the potential and temporal constraints of thermopriming memory. Nonetheless, primed plants exhibited temporarily increased stress tolerance, offering a means to safeguard the offspring.

Involvement of glucosinolates and phenolics in the promotion of broccoli seedling growth through the modulation of primary and secondary metabolism.

Secondary metabolites play an essential role in plant defense. However, the role of glucosinolates and phenols in brassica crop yield in the context of environmentally friendly agricultural practices has not been established. Our study investigated the effects of a Brassica extract, rich in these metabolites, on the physiology and metabolism of broccoli (Brassica oleracea L. var. italica) seedlings and the subsequent development of the plants in adult stages. The results showed an increase in growth in the extract-treated seedlings, which was associated with an alteration of primary and secondary metabolism. In particular, there was an increase in the levels of amino acids, phenolic compounds and hormones, while the levels of glucosinolates decreased. Lipid peroxidation diminished in treated plants, indicating improved membrane integrity. Treated plants subsequently grown in hydroponically showed increased water use efficiency, transpiration, and internal carbon, which contributed to the improved growth of these plants. Overall, our findings underscore the potential of the glucosinolates and phenols ratio as essential to improve crop growth and stress tolerance, as well as revealed the interest of studying the mechanisms involved in the possible uptake and integration of GSLs by broccoli seedlings after external application.

PLETHORA transcription factors promote early embryo development through induction of meristematic potential.

Plants are dependent on divisions of stem cells to establish cell lineages required for growth. During embryogenesis, early division products are considered to be stem cells, whereas during post-embryonic development, stem cells are present in meristems at the root and shoot apex. PLETHORA/AINTEGUMENTA-LIKE (PLT/AIL) transcription factors are regulators of post-embryonic meristem function and are required to maintain stem cell pools. Despite the parallels between embryonic and post-embryonic stem cells, the role of PLTs during early embryogenesis has not been thoroughly investigated. Here, we demonstrate that the PLT regulome in the zygote, and apical and basal cells is in strong congruence with that of post-embryonic meristematic cells. We reveal that out of all six PLTs, only PLT2 and PLT4/BABY BOOM (BBM) are expressed in the zygote, and that these two factors are essential for progression of embryogenesis beyond the zygote stage and first divisions. Finally, we show that other PLTs can rescue plt2 bbm defects when expressed from the PLT2 and BBM promoters, establishing upstream regulation as a key factor in early embryogenesis. Our data indicate that generic PLT factors facilitate early embryo development in Arabidopsis by induction of meristematic potential.

Gibberellin Signaling through RGA Suppresses GCN5 Effects on Arabidopsis Developmental Stages.

Histone acetyltransferases (HATs) modify the amino-terminal tails of the core histone proteins via acetylation, regulating chromatin structure and transcription. GENERAL CONTROL NON-DEREPRESSIBLE 5 (GCN5) is a HAT that specifically acetylates H3K14 residues. GCN5 has been associated with cell division and differentiation, meristem function, root, stem, foliar, and floral development, and plant environmental response. The flowers of gcn5 plants display a reduced stamen length and exhibit male sterility relative to the wild-type plants. We show that these effects may arise from gibberellin (GA)-signaling defects. The signaling pathway of bioactive GAs depends on the proteolysis of their repressors, DELLA proteins. The repressor GA (RGA) DELLA protein represses plant growth, inflorescence, and flower and seed development. Our molecular data indicate that GCN5 is required for the activation and H3K14 acetylation of genes involved in the late stages of GA biosynthesis and catabolism. We studied the genetic interaction of the RGA and GCN5; the RGA can partially suppress GCN5 action during the whole plant life cycle. The reduced elongation of the stamen filament of gcn5-6 mutants is reversed in the rga-t2;gcn5-6 double mutants. RGAs suppress the GCN5 effect on the gene expression and histone acetylation of GA catabolism and GA signaling. Interestingly, the RGA and RGL2 do not suppress ADA2b function, suggesting that ADA2b acts downstream of GA signaling and is distinct from GCN5 activity. In conclusion, we propose that the action of GCN5 on stamen elongation is partially mediated by RGA and GA signaling.

Embryo sac cellularization defects lead to supernumerary egg cells and twin embryos in Arabidopsis thaliana.

Arabidopsis lines with loss-of-function mutation in Embryo sac-specific Pectin MethylEsterase Inhibitor (Atepmei) gene showed seed sterility with embryo sac cellularization defects. Examination of tissue-cleared mature ovules revealed irregularly positioned nuclei/embryos within the embryo sacs. Egg cell-specific marker (DD45) expression analysis confirmed the presence of multiple egg cells in the mutant embryo sacs. These supernumerary egg cells were functional as evident from the production of twin embryos when supernumerary sperm cells were provided. The results of ruthenium red and tannic acid-ferric chloride staining of developing Atepmei mutant ovules showed that cell wall formation and maintenance were altered around embryo sac nuclei, which also coincided with change in the gamete specification. This report implicates the role of cell walls in gamete cell fate determination by altering cell-cell communication. Our analysis of the twin-embryo phenotype of epmei mutants also sheds light on the boundary conditions for double fertilization in plant reproduction.

Update on functional analysis of long non-coding RNAs in common crops.

With the rapid advances in next-generation sequencing technology, numerous non-protein-coding transcripts have been identified, including long noncoding RNAs (lncRNAs), which are functional RNAs comprising more than 200 nucleotides. Although lncRNA-mediated regulatory processes have been extensively investigated in animals, there has been considerably less research on plant lncRNAs. Nevertheless, multiple studies on major crops showed lncRNAs are involved in crucial processes, including growth and development, reproduction, and stress responses. This review summarizes the progress in the research on lncRNA roles in several major crops, presents key strategies for exploring lncRNAs in crops, and discusses current challenges and future prospects. The insights provided in this review will enhance our comprehension of lncRNA functions in crops, with potential implications for improving crop genetics and breeding.