A5027238071- Plant Molecular Biology Research
- Plant Gene Expression Analysis
- RNA and protein synthesis mechanisms
- Protein Structure and Dynamics
- Plant Stress Responses and Tolerance
- Enzyme Structure and Function
- Photosynthetic Processes and Mechanisms
- CRISPR and Genetic Engineering
- Growth Hormone and Insulin-like Growth Factors
- Plant responses to water stress
- Soybean genetics and cultivation
- Seed Germination and Physiology
- Plant pathogens and resistance mechanisms
- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Computational Drug Discovery Methods
- RNA modifications and cancer
- Force Microscopy Techniques and Applications
- Estrogen and related hormone effects
- Biochemical and Structural Characterization
- Characterization and Applications of Magnetic Nanoparticles
- Endoplasmic Reticulum Stress and Disease
- Hypothalamic control of reproductive hormones
- 14-3-3 protein interactions
- Redox biology and oxidative stress
University of Copenhagen
2015-2025
TFs (transcription factors) are modular proteins minimally containing a DBD (DNA-binding domain) and TRD regulatory domain). NAC [for NAM (no apical meristem), ATAF, CUC (cup-shaped cotyledon)] comprise one of the largest plant TF families. They key regulators stress perception developmental programmes, most share an N-terminal domain. On basis analyses gene expression data phylogeny Arabidopsis thaliana we systematically decipher structural functional specificities conserved domains...
Transcription factors (TFs) are master regulators of abiotic stress responses in plants. This review focuses on TFs from seven major TF families, known to play functional roles response stresses, including drought, high salinity, osmolarity, temperature extremes and the phytohormone ABA. Although ectopic expression several has improved tolerance plants, fine-tuning protein levels remains a challenge avoid crop yield loss. To further our understanding responses, emerging gene regulatory...
The Arabidopsis thaliana DREB2A transcription factor interacts with the negative regulator RCD1 and ACID domain of subunit 25 transcriptional co-regulator mediator (Med25) to integrate stress signals for gene expression, elusive molecular interplay. Using biophysical structural analyses together high-throughput screening, we reveal a bivalent binding switch in containing an ACID-binding motif (ABS) known RCD1-binding (RIM). RIM is lacking stress-induced splice variant retained activity. ABS...
The variance of the U-box domain in 64 Arabidopsis thaliana (thale cress) E3s (ubiquitin-protein ligases) was used to examine interactions between and E2s (ubiquitin-conjugating enzymes). are components ubiquitin protein degradation pathway. Seven proteins were analysed for their ability ubiquitinate vitro co-operation with different E2s. All domains exhibited ubiquitination activity interacted productively UBC4/5-type Three four mediated addition presence UBC13 UBC7 respectively, but no...
Target gene identification for transcription factors is a prerequisite the systems wide understanding of organismal behaviour. NAM-ATAF1/2-CUC2 (NAC) are amongst largest factor families in plants, yet limited data exist from unbiased approaches to resolve DNA-binding preferences individual members. Here, we present TF-target workflow based on integration novel protein binding microarray with expression and multi-species promoter sequence conservation identify specificities regulatory...
Intrinsically disordered protein regions (IDRs) lack a well defined three-dimensional structure but often facilitate key functions. Some interactions between IDRs and folded domains rely on short linear motifs (SLiMs). These are challenging to identify, once found they can point larger networks of interactions, such as with proteins that serve hubs for essential cellular The stress-associated plant radical-induced cell death1 (RCD1) is one hub, interacting many transcription factors via...
Transcriptional regulation involves interactions between transcription factors, coregulators, and DNA. Intrinsic disorder is a major player in this regulation, but mechanisms driven by remain elusive. Here, we address molecular communication within the stress-regulating Arabidopsis thaliana factor ANAC013. Through high-throughput screening of ANAC013 for transcriptional activation activity, identify three domains its C-terminal intrinsically disordered region. Two these overlap with acidic...
Protein ID (intrinsic disorder) plays a significant, yet relatively unexplored role in transcription factors (TFs). In the present paper, analysis of regulatory domains (TRDs) six phylogenetically representative, plant-specific NAC [no apical meristem, ATAF (Arabidopsis activation factor), cup-shaped cotyledon] TFs shows that are similar average pre-molten or molten globule-like states, but have different patterns order/disorder and MoRFs (molecular recognition features). ANAC046 046) was...
Intrinsic disorder (ID) constitutes a new dimension to the protein structure–function relationship. The ability undergo conformational changes upon binding is key property of intrinsically disordered proteins and remains challenging study using conventional methods. A 1994 paper by R. S. Spolar M. T. Record presented thermodynamic approach for estimating in entropy based on heat capacity changes, allowing quantification residues folding binding. Here, we adapt method studies proteins. We...
The correct levels of deoxyribonucleotide triphosphates and their relative abundance are important to maintain genomic integrity. Ribonucleotide reductase (RNR) regulation is complex multifaceted. RNR regulated allosterically by two nucleotide-binding sites, transcriptional control, small inhibitory proteins that associate with the R1 catalytic subunit. In addition, subcellular localization R2 subunit through cell cycle in response DNA damage. We show fission yeast inhibitor Spd1...
The plant-specific NAC transcription factors have attracted particular attention because of their involvement in stress responses, senescence, and nutrient remobilization. HvNAC005 gene barley encodes a protein belonging to subgroup NAC-a6 the family. This study shows that is associated with developmental senescence. It was significantly up-regulated following ABA treatment, supported by ABA-responsive elements its promoter, but it not during dark-induced C-termini proteins closely related...
Abstract Transcription factors carry long intrinsically disordered regions often containing multiple activation domains. Despite numerous recent high‐throughput identifications and characterizations of domains, the interplay between sequence motifs, regulator binding in transcription factor remains unresolved. Here, we map motifs domains an Arabidopsis thaliana NAC clade, revealing that although coincide, no systematic overlap exists. Biophysical analyses using NMR spectroscopy show region...
Radical-Induced Cell Death1 (RCD1) functions as a cellular hub interacting with intrinsically disordered transcription factor regions, which lack well-defined three-dimensional structure, to regulate plant stress. Here, we address the molecular evolution of RCD1-interactome. Using bioinformatics, its history was traced back more than 480 million years emergence land plants RCD1-binding short linear motif (SLiM) identified from mosses flowering plants. SLiM variants were biophysically...
Protein intrinsic disorder (ID), referring to the lack of a fixed tertiary structure, is significant in signaling and transcription. We recently characterized ID 6 phylogenetically representative Arabidopsis thaliana NAC transcription factors. Their regulatory domains are mostly disordered but contain short, functionally important regions with structure propensities known as molecular recognition features. Here, we analyze for subgroup-specific patterns. Some subgroups, such VND subgroup...
We apply a computational model, global multi-mutant analysis (GMMA), to inform on effects of most amino acid substitutions from randomly mutated gene library. Using high mutation frequency, the method can determine mutations that increase stability even very stable proteins for which conventional selection systems have reached their limit. As demonstration this, we screened mutant library highly and computationally redesigned model protein using an in vivo genetic sensor folding assigned...
Abstract The cytokine hormone prolactin has a vast number of diverse functions. Unfortunately, it also exhibits tumor growth promoting properties, which makes the development receptor antagonists priority. Prolactin binds to its cognate with much lower affinity at low pH than physiological and since extracellular environment around solid tumors often is acidic, desirable develop that have improved binding pH. p K value histidine side chain ∼6.8 making residues obvious candidates for...