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Genomic DNA methylation patterns play a crucial role in the developmental processes of plants and mammals. In this study, we aimed to investigate the significant effects of epigenetic mechanisms on the development of soybean seedlings and metabolic pathways. Our analyses show that 5‐azaC‐treatment affects radicle development from two Days After Imbibition (DAI), as well as both shoot and root development. We examined the expression levels of key genes related to DNA methylation and demethylation pathways, such as DRM2, which encodes RNA‐directed DNA Methylation (RdDM) pathway, SAM synthase, responsible for methyl group donation, and ROS1, a DNA demethylase. In treated seedling roots, we observed an increase in DRM2 expression and a decrease in ROS1 expression. Additionally, 5‐azaC treatment altered protein accumulation, indicating epigenetic control over stress response while inhibiting nitrogen assimilation, urea cycle, and glycolysis‐related proteins. Furthermore, it influenced the levels of various phytohormones and metabolites crucial for seedling growth, such as ABA, IAA, ethylene, polyamines (PUT and Cad), and free amino acids, suggesting that epigenetic changes may shape soybean responses to pathogens, abiotic stress, and nutrient absorption. Our results assist in understanding how hypomethylation shapes soybean responses to pathogens, abiotic stress, and nutrient absorption crucial for seedling growth, suggesting that the plant's assimilation of carbon and nitrogen, along with hormone pathways, may be influenced by epigenetic changes. [ABSTRACT FROM AUTHOR]

The interactions between plants, beneficial bacteria and their environment are profoundly shaped by various environmental factors, including light, temperature, water availability, and soil quality. Despite efforts to elucidate the molecular mechanisms involved in the association between plants and beneficial bacteria, like Plant Growth-Promoting Bacteria (PGPB), with many studies focusing on the transcriptional reprogramming in the plant, there is no report on the modulation of genetic controls from both plant and associated bacteria standpoints, in response to environment. The main goal of this study was to investigate the relationship between plant-bacteria-environment signaling, using as a model maize plants inoculated with H. seropedicae ZAE94 and cultivated with different doses of N (0.3 and 3 mM). For this purpose, we performed rRNAdepleted RNA-seq to determine the global gene expression of both maize roots and associated H. seropedicae ZAE94. Our results revealed a differential modulation of maize nitrogen metabolism, phytohormone and cell wall responses when associated with H. seropedicae ZAE94 at different N concentrations. In parallel, a modulation of the bacterial metabolism could be observed, by regulating genes involved in transport, secretion system, cell mobility, oxidoreductases, and chemotaxis, when bacteria were associated with maize roots and cultivated at different doses of N. The molecular and phenotypic data of maize plantlets suggested that different doses of N fertilization differentially regulated the beneficial effects of bacterial inoculation, as higher doses (3 mM) favored shoot elongation and lower doses (0.3 mM) favored increase in plant biomass. Our results provide a valuable integrated overview of differentially expressed genes in both maize and associated H. seropedicae ZAE94 in response to different N availability, revealing new insights into pathways involved in grass-PGPB associations. [ABSTRACT FROM AUTHOR]

Summary: The establishment of root‐knot nematode (RKN; Meloidogyne spp.) induced galls in the plant host roots likely involves a wound‐induced regeneration response. Confocal imaging demonstrates physical stress or injury caused by RKN infection during parasitism in the model host Arabidopsis thaliana.The ERF115‐PAT1 heterodimeric transcription factor complex plays a recognized role in wound‐induced regeneration. ERF115 and PAT1 expression flanks injured gall cells likely driving mechanisms of wound healing, implying a local reactivation of cell division which is also hypothetically involved in gall genesis.Herein, functional investigation revealed that ectopic ERF115 expression resulted in premature induction of galls, and callus formation adjacent to the expanding female RKN was seen upon PAT1 upregulation. Smaller galls and less reproduction were observed in ERF115 and PAT1 knockouts. Investigation of components in the ERF115 network upon overexpression and knockdown by qRT‐PCR suggests it contributes to steer gall wound‐sensing and subsequent competence for tissue regeneration. High expression of CYCD6;1 was detected in galls, and WIND1 overexpression resulted in similar ERF115OE gall phenotypes, also showing faster gall induction.Along these lines, we show that the ERF115‐PAT1 complex likely coordinates stress signalling with tissue healing, keeping the gall functional until maturation and nematode reproduction. [ABSTRACT FROM AUTHOR]

Data on cell cycle research in plants indicate that the majority of the fundamental regulators are conserved with other eukaryotes, but the controlling mechanisms imposed on them, and their integration into growth and development is unique to plants. To date, most studies on cell division have been conducted in dicot plants. However, monocot plants have distinct developmental strategies that will affect the regulation of cell division at the meristems. In order to advance our understanding how cell division is integrated with the basic mechanisms controlling cell growth and development in monocots, we took advantage of the sugarcane EST Project (Sucest) to carry an exhaustive data mining to identify components of the cell cycle machinery. Results obtained include the description of distinct classes of cyclin-dependent kinases (CDKs); A, B, D, and H-type cyclins; CDK-interacting proteins, CDK-inhibitory and activating kinases, pRB and E2F transcription factors. Most sugarcane cell cycle genes seem to be member of multigene families. Like in dicot plants, CDKa transcription is not restricted to tissues with elevated meristematic activity, but the vast majority of CDKb-related ESTs are found in regions of high proliferation rates. Expression of CKI genes is far more abundant in regions of less cell division, notably in lateral buds. Shared expression patterns for a group of clusters was unraveled by transcriptional profiling, and we suggest that similar approaches could be used to identify genes that are part of the same regulatory network.

Centrosomes, each containing a pair of centrioles, organize microtubules in animal cells, particularly during mitosis. DNA and centrosomes are normally duplicated once before cell division to maintain optimal genome integrity. We report a new rote for the Orc1 protein, a subunit of the origin recognition complex (ORC) that is a key component of the DNA replication Licensing machinery, in controlling centriole and centrosome copy number in human cells, independent of its rote in DNA replication. Cyclin A promotes Orc1 localization to centrosomes where Orc1 prevents Cyclin E-dependent reduplication of both centrioles and centrosomes in a single cell division cycle. The data suggest that Orc1 is a regulator of centriole and centrosome reduplication as well as the initiation of DNA replication.

Cyc2aAt, cyc2bAt, cyc3aAt and cyc3bAt are four Arabidopsis mitotic-like cyclins that form three separate groups. Reverse transcription-PCR analysis reveals the expression of cyc2aAt and cyc3bAt in all the organs of plants, cyc2bAt in only the roots and no cyc3aAt in leaves and flowers. The localization of cyclin mRNAs to only the mitotically active parts of the roots is observed during whole-mount in situ hybridization on roots, which also suggests unique functions for each group of cyclins.

Abstract Background MicroRNA-regulation of gene expression plays a key role in the development and response to biotic and abiotic stresses. Deep sequencing analyses accelerate the process of small RNA discovery in many plants and expand our understanding of miRNA-regulated processes. We therefore undertook small RNA sequencing of sugarcane miRNAs in order to understand their complexity and to explore their role in sugarcane biology. Results A bioinformatics search was carried out to discover novel miRNAs that can be regulated in sugarcane plants submitted to drought and salt stresses, and under pathogen infection. By means of the presence of miRNA precursors in the related sorghum genome, we identified 623 candidates of new mature miRNAs in sugarcane. Of these, 44 were classified as high confidence miRNAs. The biological function of the new miRNAs candidates was assessed by analyzing their putative targets. The set of bona fide sugarcane miRNA includes those likely targeting serine/threonine kinases, Myb and zinc finger proteins. Additionally, a MADS-box transcription factor and an RPP2B protein, which act in development and disease resistant processes, could be regulated by cleavage (21-nt-species) and DNA methylation (24-nt-species), respectively. Conclusions A large scale investigation of sRNA in sugarcane using a computational approach has identified a substantial number of new miRNAs and provides detailed genotype-tissue-culture miRNA expression profiles. Comparative analysis between monocots was valuable to clarify aspects about conservation of miRNA and their targets in a plant whose genome has not yet been sequenced. Our findings contribute to knowledge of miRNA roles in regulatory pathways in the complex, polyploidy sugarcane genome.

Abstract Background The orderly progression through mitosis is regulated by the Anaphase-Promoting Complex (APC), a large multiprotein E3 ubiquitin ligase that targets key cell-cycle regulators for destruction by the 26 S proteasome. The APC is composed of at least 11 subunits and associates with additional regulatory activators during mitosis and interphase cycles. Despite extensive research on APC and activator functions in the cell cycle, only a few components have been functionally characterized in plants. Results Here, we describe an in-depth search for APC subunits and activator genes in the Arabidopsis, rice and poplar genomes. Also, searches in other genomes that are not completely sequenced were performed. Phylogenetic analyses indicate that some APC subunits and activator genes have experienced gene duplication events in plants, in contrast to animals. Expression patterns of paralog subunits and activators in rice could indicate that this duplication, rather than complete redundancy, could reflect initial specialization steps. The absence of subunit APC7 from the genome of some green algae species and as well as from early metazoan lineages, could mean that APC7 is not required for APC function in unicellular organisms and it may be a result of duplication of another tetratricopeptide (TPR) subunit. Analyses of TPR evolution suggest that duplications of subunits started from the central domains. Conclusions The increased complexity of the APC gene structure, tied to the diversification of expression paths, suggests that land plants developed sophisticated mechanisms of APC regulation to cope with the sedentary life style and its associated environmental exposures.