Isolation and Identification of Nuclear Protein Complexes Using GFP-Tagged Arabidopsis Lines and IP-MS Approach.

Immunoprecipitation coupled with mass spectrometry (IP-MS) is a powerful method that enables the identification of protein-protein interactions and isolation of protein complexes. When optimized to work with plant material, it proved to be suitable for the isolation of different types of nuclear complexes from Arabidopsis. Here, we describe a detailed protocol for the isolation of chromatin remodeling and polycomb repressive complexes using Arabidopsis lines that express GFP-tagged proteins as baits, directly from whole-cell extracts or after nuclei enrichment.

Determining the Identity Nucleotides and the Energy of Binding of tRNAs to Their Aminoacyl-tRNA Synthetases Using a Simple Logistic Model.

This study showed that the predictor in logistic regression can be applied to estimating the Gibbs free energy of tRNAs' recognition of and binding to their aminoacyl-tRNA synthetases. Then, 24 linear logistic regression models predicting different classes of tRNAs loaded with a corresponding amino acid were trained in a machine learning classification method, reducing the misclassification error to zero. The models were based on minimal subsets of Boolean explanatory variables describing the favorite presence of nucleotides or nucleosides localized in the different parts of the tRNA.

Peptide-Based Inhibitors of Protein-Protein Interactions (PPIs): A Case Study on the Interaction Between SARS-CoV-2 Spike Protein and Human Angiotensin-Converting Enzyme 2 (hACE2).

Protein-protein interactions (PPIs) are fundamental to many critical biological processes and are crucial in mediating essential cellular functions across diverse organisms, including bacteria, parasites, and viruses. A notable example is the interaction between the SARS-CoV-2 spike (S) protein and the human angiotensin-converting enzyme 2 (hACE2), which initiates a series of events leading to viral replication. Interrupting this interaction offers a promising strategy for blocking or significantly reducing infection, highlighting its potential as a target for anti-SARS-CoV-2 therapies.

NtZIP5A/B is involved in the regulation of Zn/Cu/Fe/Mn/Cd homeostasis in tobacco.

Plants grow in soils with varying concentrations of microelements, often in the presence of toxic metals e.g. Cd.

Ammonium nutrition modifies cellular calcium distribution influencing ammonium-induced growth inhibition.

Proper plant growth requires balanced nutrient levels. In this study, we analyzed the relationship between ammonium (NH) nutrition and calcium (Ca) homeostasis in the leaf tissues of wild-type and mutant Arabidopsis specimens provided with different nitrogen sources (NH and nitrate, NO). Providing plants with NH as the sole nitrogen source disrupts Ca homeostasis, which is essential for activating signaling pathways and maintaining the cell wall structure.

Ammonium treatment inhibits cell cycle activity and induces nuclei endopolyploidization in Arabidopsis thaliana.

This study determined the effect of ammonium supply on the cell division process and showed that ammonium-dependent elevated reactive oxygen species production could mediate the downregulation of the cell cycle-related gene expression. Plants grown under high-ammonium conditions show stunted growth and other toxicity symptoms, including oxidative stress. However, how ammonium regulates the development of plants remains unknown.

Flexible Pectin Nanopatterning Drives Cell Wall Organization in Plants.

Plant cell walls are abundant sources of materials and energy. Nevertheless, cell wall nanostructure, specifically how pectins interact with cellulose and hemicelluloses to construct a robust and flexible biomaterial, is poorly understood. X-ray scattering measurements are minimally invasive and can reveal ultrastructural, compositional, and physical properties of materials.

Quantum Dots Assembled with Photosynthetic Antennae on a Carbon Nanotube Platform: A Nanohybrid for the Enhancement of Light Energy Harvesting.

The construction of artificial systems for solar energy harvesting is still a challenge. There needs to be a light-harvesting antenna with a broad absorption spectrum and then the possibility to transfer harvested energy to the reaction center, converting photons into a storable form of energy. Bioinspired and bioderivative elements may help in achieving this aim.

A prospective study of short-term apoplastic responses to ammonium treatment.

The integration of external stimuli into plant cells has been extensively studied. Ammonium is a metabolic trigger because it affects plant nutrition status; on the contrary, it is also a stress factor inducing oxidative changes. Plants, upon quick reaction to the presence of ammonium, can avoid the development of toxicity symptoms, but their primary ammonium sensing mechanisms remain unknown.

Metabolically versatile psychrotolerant Antarctic bacterium Pseudomonas sp. ANT_H12B is an efficient producer of siderophores and accompanying metabolites (SAM) useful for agricultural purposes.

Background: Bacterial siderophores are chelating compounds with the potential of application in agriculture, due to their plant growth-promoting (PGP) properties, however, high production and purification costs are limiting factors for their wider application. Cost-efficiency of the production could be increased by omitting purification processes, especially since siderophores accompanying metabolites (SAM) often also possess PGP traits. In this study, the metabolism versatility of Pseudomonas sp.

Identification of candidate genes responsible for chasmogamy in wheat.

Background: The flowering biology of wheat plants favours self-pollination which causes obstacles in wheat hybrid breeding. Wheat flowers can be divided into two groups, the first one is characterized by flowering and pollination within closed flowers (cleistogamy), while the second one possesses the ability to open flowers during processes mentioned above (chasmogamy). The swelling of lodicules is involved in the flowering of cereals and among others their morphology, calcium and potassium content differentiate between cleistogamic and non-cleistogamous flowers.

Wood and bark structure in : anatomical background of stem morphology.

Bark (all tissues outside of the vascular cambium) has been extensively studied in recent years, especially its anatomy and physiology. Macromorphological bark characters can be important taxonomically for many plant groups, including the genus (Scrophulariaceae). However, the relationship between macroscopic bark appearance and its microscopic structure remains obscure, hampering the use and interpretation of bark traits in plant taxonomy and phylogenetics as well as in other fields of botany.

Design of Crotoxin-Based Peptides with Potentiator Activity Targeting the ΔF508NBD1 Cystic Fibrosis Transmembrane Conductance Regulator.

We have previously shown that the CBb subunit of crotoxin, a β-neurotoxin with phospholipase A (PLA) activity, targets the human ΔF508CFTR chloride channel implicated in cystic fibrosis (CF). By direct binding to the nucleotide binding domain 1 (NBD1) of ΔF508CFTR, this neurotoxic PLA acts as a potentiator increasing chloride channel current and corrects the trafficking defect of misfolded ΔF508CFTR inside the cell. Here, for a therapeutics development of new anti-cystic fibrosis agents, we use a structure-based in silico approach to design peptides mimicking the CBb-ΔF508NBD1 interface.

Improvement of native structure-based peptides as efficient inhibitors of protein-protein interactions of SARS-CoV-2 spike protein and human ACE2.

New pathogens responsible for novel human disease outbreaks in the last two decades are mainly the respiratory system viruses. Not different was the last pandemic episode, caused by infection of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). One of the extensively explored targets, in the recent scientific literature, as a possible way for rapid development of COVID-19 specific drug(s) is the interaction between the receptor-binding domain of the virus' spike (S) glycoprotein and human receptor angiotensin-converting enzyme 2 (ACE2).

Glyoxalase I activity affects Arabidopsis sensitivity to ammonium nutrition.

Elevated methylglyoxal levels contribute to ammonium-induced growth disorders in Arabidopsis thaliana. Methylglyoxal detoxification pathway limitation, mainly the glyoxalase I activity, leads to enhanced sensitivity of plants to ammonium nutrition. Ammonium applied to plants as the exclusive source of nitrogen often triggers multiple phenotypic effects, with severe growth inhibition being the most prominent symptom.

Tobacco as an efficient metal accumulator.

Tobacco (Nicotiana tabacum L.) is an important industrial crop plant. However, it efficiently accumulates metals, primarily cadmium (Cd) and also zinc (Zn), in its leaves.

Regulation and Function of Metal Uptake Transporter NtNRAMP3 in Tobacco.

Natural resistance-associated macrophage protein () genes encode proteins with low substrate specificity, important for maintaining metal cross homeostasis in the cell. The role of these proteins in tobacco, an important crop plant with wide application in the tobacco industry as well as in phytoremediation of metal-contaminated soils, remains unknown. Here, we identified NtNRAMP3, the closest homologue to NRAMP3 proteins from other plant species, and functionally characterized it.

New Advances in Short Peptides: Looking Forward.

It is beyond doubt that short peptides hold significant promise in bio-medicine, as the most versatile molecules, both structurally and functionally [...

Respiratory Burst Oxidase Homolog D as a Modulating Component of Oxidative Response under Ammonium Toxicity.

Delayed growth, a visible phenotypic component of the so-called ammonium syndrome, occurs when ammonium is the sole inorganic nitrogen source. Previously, we have shown that modification of apoplastic reactive oxygen species (apROS) metabolism is a key factor contributing to plant growth retardation under ammonium nutrition. Here, we further analyzed the changes in apROS metabolism in transgenic plants with disruption of the D isoform of the respiratory burst oxidase homolog (RBOH) that is responsible for apROS production.

Transcription Factor ChREBP Mediates High Glucose-Evoked Increase in HIF-1α Content in Epithelial Cells of Renal Proximal Tubules.

Hyperglycemia/diabetes appears to be accompanied by the state of hypoxia, which especially affects kidneys. The aim of the study was to elucidate the mechanism of high glucose action on HIF-1α expression in renal proximal tubule epithelial cells. The research hypotheses included: (1) the participation of transcription factor ChREBP; and (2) the involvement of the effects resulting from pseudohypoxia, i.

Bean and Pea Plastoglobules Change in Response to Chilling Stress.

Plastoglobules (PGs) might be characterised as microdomains of the thylakoid membrane that serve as a platform to recruit proteins and metabolites in their spatial proximity in order to facilitate metabolic channelling or signal transduction. This study provides new insight into changes in PGs isolated from two plant species with different responses to chilling stress, namely chilling-tolerant pea () and chilling-sensitive bean (). Using multiple analytical methods, such as high-performance liquid chromatography and visualisation techniques including transmission electron microscopy and atomic force microscopy, we determined changes in PGs' biochemical and biophysical characteristics as a function of chilling stress.

Curvature thylakoid 1 proteins modulate prolamellar body morphology and promote organized thylakoid biogenesis in .

The term "de-etiolation" refers to the light-dependent differentiation of etioplasts to chloroplasts in angiosperms. The underlying process involves reorganization of prolamellar bodies (PLBs) and prothylakoids into thylakoids, with concurrent changes in protein, lipid, and pigment composition, which together lead to the assembly of active photosynthetic complexes. Despite the highly conserved structure of PLBs among land plants, the processes that mediate PLB maintenance and their disassembly during de-etiolation are poorly understood.