Molecular mechanisms underlying phytochrome-controlled morphogenesis in plants

AbstractPhytochromes are bilin-binding photosensory receptors which control development over a broad range of environmental conditions and throughout the whole plant life cycle. Light-induced conformational changes enable phytochromes to interact with signaling partners, in particular transcription factors or proteins that regulate them, resulting in large-scale transcriptional reprograming. Phytochromes also regulate promoter usage, mRNA splicing and translation through less defined routes. In this review we summarize our current understanding of plant phytochrome signaling, emphasizing recent work performed in Arabidopsis. We compare and contrast phytochrome responses and signaling mechanisms among land plants and highlight open questions in phytochrome research.

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A combined approach to characterize ligand-induced solid–solid phase transitions in biomacromolecular crystals

Journal of Applied Crystallography ◽

10.1107/s1600576721003137 ◽

2021 ◽

Vol 54 (3) ◽

Author(s):

Saminathan Ramakrishnan ◽

Jason R. Stagno ◽

Valentin Magidson ◽

William F. Heinz ◽

Yun-Xing Wang

Keyword(s):

Phase Transitions ◽

Conformational Changes ◽

Large Scale ◽

Molecular Mechanisms ◽

Solid Phase ◽

Control Element ◽

Time Resolved ◽

Crystalline Materials ◽

Force Microscopy ◽

Glass Surfaces

Solid–solid phase transitions (SSPTs) are widespread naturally occurring phenomena. Understanding the molecular mechanisms and kinetics of SSPTs in various crystalline materials, however, has been challenging due to technical limitations. In particular, SSPTs in biomacromolecular crystals, which may involve large-scale changes and particularly complex sets of interactions, are largely unexplored, yet may have important implications for time-resolved crystallography and for developing synthetic biomaterials. The adenine riboswitch (riboA) is an RNA control element that uses ligand-induced conformational changes to regulate gene expression. Crystals of riboA, upon the addition of a ligand, undergo an SSPT from monoclinic to triclinic to orthorhombic. Here, solution atomic force microscopy (AFM) and polarized video microscopy (PVM) are used to characterize the multiple transition states throughout the SSPT in both the forward and the reverse directions. This contribution describes detailed protocols for growing crystals directly on mica or glass surfaces for AFM and PVM characterization, respectively, as well as methods for image processing and phase-transition kinetics analysis.

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Reprogramming of 24nt siRNAs in rice gametes

10.1101/670463 ◽

2019 ◽

Author(s):

Chenxin Li ◽

Hengping Xu ◽

Fang-Fang Fu ◽

Scott D. Russell ◽

Venkatesan Sundaresan ◽

...

Keyword(s):

Small Rna ◽

Small Rnas ◽

Large Scale ◽

Dna Methyltransferases ◽

Critical Stage ◽

Vegetative Tissues ◽

Plant Life ◽

Genome Wide ◽

Strong Indicator ◽

Plant Life Cycle

ABSTRACTGametes constitute a critical stage of the plant life cycle, during which the genome undergoes reprogramming in preparation for embryogenesis. Here we characterized the small RNA transcriptomes of egg cells and sperm cells from rice to elucidate genome-wide distributions of 24nt siRNAs, which are a hallmark of RNA-directed DNA methylation (RdDM) in plants and are typically concentrated at boundaries of heterochromatin. We found that 24nt siRNAs were depleted from heterochromatin boundaries in both gametes, reminiscent of siRNA patterns in DDM1-type nucleosome remodeler mutants. In sperm, 24nt siRNAs were spread across broad heterochromatic regions, while in eggs, 24nt siRNAs were concentrated at a smaller number of heterochromatic loci throughout the genome, which were shared with vegetative tissues and sperm. In both gametes, patterns of CHH methylation, typically a strong indicator of RdDM, were similar to vegetative tissues, although lower in magnitude. These findings indicate that the small RNA transcriptome undergoes large-scale re-programming in both male and female gametes, which is not correlated with recruitment of DNA methyltransferases in gametes and suggestive of unexplored regulatory activities of gamete small RNAs in seeds after fertilization.

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Large-scale ratcheting in a bacterial DEAH/RHA-type RNA helicase that modulates antibiotics susceptibility

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2100370118 ◽

2021 ◽

Vol 118 (30) ◽

pp. e2100370118

Author(s):

Lena M. Grass ◽

Jan Wollenhaupt ◽

Tatjana Barthel ◽

Iwan Parfentev ◽

Henning Urlaub ◽

...

Keyword(s):

Conformational Changes ◽

Bound States ◽

Large Scale ◽

Molecular Mechanisms ◽

Limited Proteolysis ◽

Rna Helicase ◽

Crystal Structure Analysis ◽

Helicase Activity ◽

Bacterial Survival ◽

Antibiotics Susceptibility

Many bacteria harbor RNA-dependent nucleoside-triphosphatases of the DEAH/RHA family, whose molecular mechanisms and cellular functions are poorly understood. Here, we show that the Escherichia coli DEAH/RHA protein, HrpA, is an ATP-dependent 3 to 5′ RNA helicase and that the RNA helicase activity of HrpA influences bacterial survival under antibiotics treatment. Limited proteolysis, crystal structure analysis, and functional assays showed that HrpA contains an N-terminal DEAH/RHA helicase cassette preceded by a unique N-terminal domain and followed by a large C-terminal region that modulates the helicase activity. Structures of an expanded HrpA helicase cassette in the apo and RNA-bound states in combination with cross-linking/mass spectrometry revealed ratchet-like domain movements upon RNA engagement, much more pronounced than hitherto observed in related eukaryotic DEAH/RHA enzymes. Structure-based functional analyses delineated transient interdomain contact sites that support substrate loading and unwinding, suggesting that similar conformational changes support RNA translocation. Consistently, modeling studies showed that analogous dynamic intramolecular contacts are not possible in the related but helicase-inactive RNA-dependent nucleoside-triphosphatase, HrpB. Our results indicate that HrpA may be an interesting target to interfere with bacterial tolerance toward certain antibiotics and suggest possible interfering strategies.

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The complexity of PRC2 catalysts CLF and SWN in plants

Biochemical Society Transactions ◽

10.1042/bst20200660 ◽

2020 ◽

Vol 48 (6) ◽

pp. 2779-2789

Author(s):

Jie Shu ◽

Chen Chen ◽

Chenlong Li ◽

Yuhai Cui

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Molecular Mechanisms ◽

Histone H3 ◽

Catalytic Subunits ◽

Trithorax Group ◽

Polycomb Repressive Complex 2 ◽

Plant Life ◽

Plant Life Cycle ◽

Curly Leaf

Polycomb repressive complex 2 (PRC2) is an evolutionally conserved multisubunit complex essential for the development of eukaryotes. In Arabidopsis thaliana (Arabidopsis), CURLY LEAF (CLF) and SWINGER (SWN) are PRC2 catalytic subunits that repress gene expression through trimethylating histone H3 at lysine 27 (H3K27me3). CLF and SWN function to safeguard the appropriate expression of key developmental regulators throughout the plant life cycle. Recent researches have advanced our knowledge of the biological roles and the regulation of the activity of CLF and SWN. In this review, we summarize these recent findings and highlight the redundant and differential roles of CLF and SWN in plant development. Further, we discuss the molecular mechanisms underlying CLF and SWN recruitment to specific genomic loci, as well as their interplays with Trithorax-group (TrxG) proteins in plants.

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Anaphylactic Degranulation of Mast Cells: Focus on Compound Exocytosis

Journal of Immunology Research ◽

10.1155/2019/9542656 ◽

2019 ◽

Vol 2019 ◽

pp. 1-12 ◽

Cited By ~ 9

Author(s):

Ofir Klein ◽

Ronit Sagi-Eisenberg

Keyword(s):

Mast Cell ◽

Mast Cells ◽

Molecular Mechanisms ◽

Secretory Granules ◽

Cell Types ◽

Secretory Cells ◽

Regulated Exocytosis ◽

Open Questions ◽

Conflicting Evidence ◽

Compound Exocytosis

Anaphylaxis is a notorious type 2 immune response which may result in a systemic response and lead to death. A precondition for the unfolding of the anaphylactic shock is the secretion of inflammatory mediators from mast cells in response to an allergen, mostly through activation of the cells via the IgE-dependent pathway. While mast cells are specialized secretory cells that can secrete through a variety of exocytic modes, the most predominant mode exerted by the mast cell during anaphylaxis is compound exocytosis—a specialized form of regulated exocytosis where secretory granules fuse to one another. Here, we review the modes of regulated exocytosis in the mast cell and focus on compound exocytosis. We review historical landmarks in the research of compound exocytosis in mast cells and the methods available for investigating compound exocytosis. We also review the molecular mechanisms reported to underlie compound exocytosis in mast cells and expand further with reviewing key findings from other cell types. Finally, we discuss the possible reasons for the mast cell to utilize compound exocytosis during anaphylaxis, the conflicting evidence in different mast cell models, and the open questions in the field which remain to be answered.

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EGCG binds intrinsically disordered N-terminal domain of p53 and disrupts p53-MDM2 interaction

Nature Communications ◽

10.1038/s41467-021-21258-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Jing Zhao ◽

Alan Blayney ◽

Xiaorong Liu ◽

Lauren Gandy ◽

Weihua Jin ◽

...

Keyword(s):

Large Scale ◽

Molecular Mechanisms ◽

Epigallocatechin Gallate ◽

Cancer Drug ◽

Dynamic Interactions ◽

Cancer Drug Discovery ◽

Intrinsically Disordered ◽

Terminal Domain ◽

Cancerous Cells

AbstractEpigallocatechin gallate (EGCG) from green tea can induce apoptosis in cancerous cells, but the underlying molecular mechanisms remain poorly understood. Using SPR and NMR, here we report a direct, μM interaction between EGCG and the tumor suppressor p53 (KD = 1.6 ± 1.4 μM), with the disordered N-terminal domain (NTD) identified as the major binding site (KD = 4 ± 2 μM). Large scale atomistic simulations (>100 μs), SAXS and AUC demonstrate that EGCG-NTD interaction is dynamic and EGCG causes the emergence of a subpopulation of compact bound conformations. The EGCG-p53 interaction disrupts p53 interaction with its regulatory E3 ligase MDM2 and inhibits ubiquitination of p53 by MDM2 in an in vitro ubiquitination assay, likely stabilizing p53 for anti-tumor activity. Our work provides insights into the mechanisms for EGCG’s anticancer activity and identifies p53 NTD as a target for cancer drug discovery through dynamic interactions with small molecules.

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H2S action in plant life cycle

Plant Growth Regulation ◽

10.1007/s10725-021-00693-w ◽

2021 ◽

Author(s):

Mingjian Zhou ◽

Heng Zhou ◽

Jie Shen ◽

Zhirong Zhang ◽

Cecilia Gotor ◽

...

Keyword(s):

Life Cycle ◽

Plant Life ◽

Plant Life Cycle

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Transport, functions, and interaction of calcium and manganese in plant organellar compartments

Plant Physiology ◽

10.1093/plphys/kiab122 ◽

2021 ◽

Author(s):

Jie He ◽

Nico Rössner ◽

Minh T T Hoang ◽

Santiago Alejandro ◽

Edgar Peiter

Keyword(s):

Molecular Mechanisms ◽

Metal Tolerance ◽

Essential Elements ◽

Natural Resistance ◽

Ionic Radii ◽

Bivalent Cation ◽

Cyclic Nucleotide Gated Channels ◽

Complex Processes ◽

Open Questions ◽

Golgi Network

Abstract Calcium (Ca2+) and manganese (Mn2+) are essential elements for plants and have similar ionic radii and binding coordination. They are assigned specific functions within organelles, but share many transport mechanisms to cross organellar membranes. Despite their points of interaction, those elements are usually investigated and reviewed separately. This review takes them out of this isolation. It highlights our current mechanistic understanding and points to open questions of their functions, their transport, and their interplay in the endoplasmic reticulum (ER), vesicular compartments [Golgi apparatus, trans-Golgi Network (TGN), prevacuolar compartment (PVC)], vacuoles, chloroplasts, mitochondria, and peroxisomes. Complex processes demanding these cations, such as Mn2+-dependent glycosylation or systemic Ca2+ signaling, are covered in some detail if they have not been reviewed recently or if recent findings add to current models. The function of Ca2+ as signaling agent released from organelles into the cytosol and within the organelles themselves is a recurrent theme of this review, again keeping the interference by Mn2+ in mind. The involvement of organellar channels [e.g., Glutamate-Receptor-Likes (GLRs), Cyclic-Nucleotide-Gated Channels (CNGCs), Mitochondrial Conductivity Units (MCUs), Two-Pore Channel1 (TPC1)], transporters [e.g., Natural-Resistance-Associated Macrophage Proteins (NRAMPs), Calcium Exchangers (CAXs), Metal-Tolerance Proteins (MTPs), Bivalent-Cation Transporters (BICATs)] and pumps [Autoinhibited Ca2+-ATPases (ACAs), ER Ca2+-ATPases (ECAs)] in the import and export of organellar Ca2+ and Mn2+ is scrutinized, whereby current controversial issues are pointed out. Mechanisms in animals and yeast are taken into account where they may provide a blueprint for processes in plants, in particular with respect to tunable molecular mechanisms of Ca2+-versus-Mn2+ selectivity.

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Integrative cBioPortal Analysis Revealed Molecular Mechanisms That Regulate EGFR-PI3K-AKT-mTOR Pathway in Diffuse Gliomas of the Brain

Cancers ◽

10.3390/cancers13133247 ◽

2021 ◽

Vol 13 (13) ◽

pp. 3247

Author(s):

Petar Brlek ◽

Anja Kafka ◽

Anja Bukovac ◽

Nives Pećina-Šlaus

Keyword(s):

Large Scale ◽

Molecular Mechanisms ◽

In Silico Analysis ◽

Total Sample ◽

Mtor Signaling ◽

Biological Behavior ◽

Mrna Transcription ◽

Diffuse Gliomas ◽

New Treatment ◽

Using Data

Diffuse gliomas are a heterogeneous group of tumors with aggressive biological behavior and a lack of effective treatment methods. Despite new molecular findings, the differences between pathohistological types still require better understanding. In this in silico analysis, we investigated AKT1, AKT2, AKT3, CHUK, GSK3β, EGFR, PTEN, and PIK3AP1 as participants of EGFR-PI3K-AKT-mTOR signaling using data from the publicly available cBioPortal platform. Integrative large-scale analyses investigated changes in copy number aberrations (CNA), methylation, mRNA transcription and protein expression within 751 samples of diffuse astrocytomas, anaplastic astrocytomas and glioblastomas. The study showed a significant percentage of CNA in PTEN (76%), PIK3AP1 and CHUK (75% each), EGFR (74%), AKT2 (39%), AKT1 (32%), AKT3 (19%) and GSK3β (18%) in the total sample. Comprehensive statistical analyses show how genomics and epigenomics affect the expression of examined genes differently across various pathohistological types and grades, suggesting that genes AKT3, CHUK and PTEN behave like tumor suppressors, while AKT1, AKT2, EGFR, and PIK3AP1 show oncogenic behavior and are involved in enhanced activity of the EGFR-PI3K-AKT-mTOR signaling pathway. Our findings contribute to the knowledge of the molecular differences between pathohistological types and ultimately offer the possibility of new treatment targets and personalized therapies in patients with diffuse gliomas.

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Insights into the roles of charged residues in substrate binding and mode of action of mannuronan C-5 epimerase AlgE4

Glycobiology ◽

10.1093/glycob/cwab025 ◽

2021 ◽

Author(s):

Margrethe Gaardløs ◽

Sergey A Samsonov ◽

Marit Sletmoen ◽

Maya Hjørnevik ◽

Gerd Inger Sætrom ◽

...

Keyword(s):

Optical Tweezers ◽

Conformational Changes ◽

Molecular Mechanisms ◽

Hydrophobic Interactions ◽

Substrate Binding ◽

Interdisciplinary Approach ◽

Product Formation ◽

Titration Calorimetry ◽

Binding Groove ◽

Dynamics Simulations

Abstract Mannuronan C-5 epimerases catalyse the epimerization of monomer residues in the polysaccharide alginate, changing the physical properties of the biopolymer. The enzymes are utilized to tailor alginate to numerous biological functions by alginate-producing organisms. The underlying molecular mechanisms that control the processive movement of the epimerase along the substrate chain is still elusive. To study this, we have used an interdisciplinary approach combining molecular dynamics simulations with experimental methods from mutant studies of AlgE4, where initial epimerase activity and product formation were addressed with NMR spectroscopy, and characteristics of enzyme-substrate interactions were obtained with isothermal titration calorimetry and optical tweezers. Positive charges lining the substrate-binding groove of AlgE4 appear to control the initial binding of poly-mannuronate, and binding also seems to be mediated by both electrostatic and hydrophobic interactions. After the catalytic reaction, negatively charged enzyme residues might facilitate dissociation of alginate from the positive residues, working like electrostatic switches, allowing the substrate to translocate in the binding groove. Molecular simulations show translocation increments of two monosaccharide units before the next productive binding event resulting in MG-block formation, with the epimerase moving with its N-terminus towards the reducing end of the alginate chain. Our results indicate that the charge pair R343-D345 might be directly involved in conformational changes of a loop that can be important for binding and dissociation. The computational and experimental approaches used in this study complement each other, allowing for a better understanding of individual residues’ roles in binding and movement along the alginate chains.

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