Histones are positively charged proteins found in the chromatin of eukaryotic cells. They regulate gene expression and are required for the organization and packaging of DNA within the nucleus. Histones are extremely conserved, allowing for transcription, replication, and repair. This review delves into their complex structure and function in DNA assembly, their role in nucleosome assembly, and the higher-order chromatin structures they generate. We look at the five different types of histone proteins: H1, H2A, H2B, H3, H4, and their variations. These histones bind with DNA to produce nucleosomes, the basic units of chromatin that are essential for compacting DNA and controlling its accessibility. Their dynamic control of chromatin accessibility has important implications for genomic stability and cellular activities. We elucidate regulatory mechanisms in both normal and pathological situations by investigating their structural features, diverse interaction mechanisms, and chromatin impact. In addition, we discuss the functions of histone post-translational modifications (PTMs) and their significance in various disorders. These alterations, which include methylation, acetylation, phosphorylation, and ubiquitination, are crucial in regulating histone function and chromatin dynamics. We specifically describe and explore the role of changed histones in the evolution of cancer, neurological disorders, sepsis, autoimmune illnesses, and inflammatory conditions. This comprehensive review emphasizes histone's critical role in genomic integrity and their potential as therapeutic targets in various diseases.
- Klíčová slova
- Chromatin, Disease, Gene expression, Genomic stability, Histones, Nucleosomes, Post-translational modifications (PTMs),
- MeSH
- chromatin metabolismus genetika MeSH
- DNA * genetika metabolismus chemie MeSH
- histony * metabolismus genetika chemie MeSH
- lidé MeSH
- nádory * metabolismus genetika patologie MeSH
- nukleozomy metabolismus genetika MeSH
- posttranslační úpravy proteinů MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- Názvy látek
- chromatin MeSH
- DNA * MeSH
- histony * MeSH
- nukleozomy MeSH
Microtubules (MTs) undergo diverse posttranslational modifications that regulate their structural and functional properties. Among these, polyglutamylation-a dominant and conserved modification targeting unstructured tubulin C-terminal tails-plays a pivotal role in defining the tubulin code. Here, we describe a mechanism by which tubulin tyrosine ligase-like 11 (TTLL11) expands and diversifies the code. Cryo-electron microscopy revealed a unique bipartite MT recognition strategy wherein TTLL11 binding and catalytic domains engage adjacent MT protofilaments. Biochemical and cellular assays identified previously uncharacterized polyglutamylation patterns, showing that TTLL11 directly extends the primary polypeptide chains of α- and β-tubulin in vitro, challenging the prevailing paradigms emphasizing lateral branching. Moreover, cell-based and in vivo data suggest a cross-talk between polyglutamylation and the detyrosination/tyrosination cycle likely linked to the TTLL11-mediated elongation of the primary α-tubulin chain. These findings unveil an unrecognized layer of complexity within the tubulin code and offer mechanistic insights into the molecular basis of functional specialization of MT cytoskeleton.
- MeSH
- elektronová kryomikroskopie MeSH
- lidé MeSH
- mikrotubuly metabolismus MeSH
- molekulární modely MeSH
- peptidsynthasy * metabolismus chemie genetika MeSH
- posttranslační úpravy proteinů MeSH
- tubulin * metabolismus chemie MeSH
- vazba proteinů MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- peptidsynthasy * MeSH
- tubulin polyglutamylase MeSH Prohlížeč
- tubulin * MeSH
Targeting tumor proteostasis has emerged as a promising strategy in anticancer therapy, particularly through Hsp90 inhibition, which has shown clinical potential. However, the efficacy of Hsp90 inhibitors is limited by the activation of HSF1, a master regulator of the heat shock response (HSR), which mitigates proteotoxic stress by inducing protective chaperones. To address this limitation, we investigated the role of HSF1 SUMOylation in modulating its activity and its impact on Hsp90 inhibitor efficacy. We generated HSF1 mutants with lysine-to-arginine substitutions at five SUMOylation sites and studied their function in H1299 lung carcinoma cells with HSF1/HSF2 knockout, which lack a functional HSR. Unexpectedly, these mutants retained full transcriptional activity during the early phase of the heat shock response, mimicking the initial stress response of wild-type HSF1. SUMOylation inhibition using Subasumstat also led to altered nuclear stress bodies morphology but did not impair Hsp70 induction or enhance Hsp90 inhibitor cytotoxicity. Our findings reveal that SUMOylation is dispensable for HSF1 activation and transactivation capacity during the early phase of HSR. These results refine our understanding of HSF1 regulation and suggest that alternative strategies targeting HSF1 stability and degradation may enhance the therapeutic efficacy of proteostasis-targeting cancer therapies.
- Klíčová slova
- Cancer, HSF1, Heat shock response, SUMOylation, Stress, Subasumstat,
- MeSH
- aktivace transkripce * MeSH
- lidé MeSH
- nádorové buněčné linie MeSH
- proteiny tepelného šoku HSP90 metabolismus antagonisté a inhibitory MeSH
- reakce na tepelný šok * genetika MeSH
- sumoylace * MeSH
- transkripční faktory tepelného šoku * metabolismus genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- HSF1 protein, human MeSH Prohlížeč
- proteiny tepelného šoku HSP90 MeSH
- transkripční faktory tepelného šoku * MeSH
Changes in cellular physiology and proteomic homeostasis accompanied the initiation and progression of colorectal cancer. Thus, ubiquitination represents a central regulatory mechanism in proteome dynamics. However, the complexity of the ubiquitinating network involved in carcinogenesis remains unclear. This study revealed the tumor-suppressive role of the ubiquitin ligase Cullin4A (CUL4A) in the intestine. We showed that simultaneous loss of CUL4A and hyperactivation of the Wnt pathway promotes tumor development in the distal colon. This tumor development is caused by an accumulation of the inactive SMAD3, a TGF-β pathway mediator. Depletion of CUL4A resulted in stabilization of HUWE1, which attenuated SMAD3 function. We showed a correlation between the intracellular localization of CUL4A and colorectal cancer progression, where nuclear CUL4A localization correlates with advanced colorectal cancer progression. In summary, we identified CUL4A as an important regulator of SMAD3 signal transduction competence in a HUWE1-dependent manner and demonstrated a critical role for the crosstalk between ubiquitination and the Wnt/TGF-β signaling pathways in gastrointestinal homeostasis.
- Klíčová slova
- CUL4A, Colorectal cancer, HUWE1, Ubiquitination,
- MeSH
- HCT116 buňky MeSH
- kolorektální nádory * patologie genetika metabolismus MeSH
- kulinové proteiny * metabolismus genetika MeSH
- lidé MeSH
- myši MeSH
- nádorové buněčné linie MeSH
- nádorové supresorové proteiny * metabolismus genetika MeSH
- protein Smad3 * metabolismus genetika MeSH
- regulace genové exprese u nádorů MeSH
- signální dráha Wnt MeSH
- ubikvitinace MeSH
- ubikvitinligasy * metabolismus genetika MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- CUL4A protein, human MeSH Prohlížeč
- HUWE1 protein, human MeSH Prohlížeč
- kulinové proteiny * MeSH
- nádorové supresorové proteiny * MeSH
- protein Smad3 * MeSH
- SMAD3 protein, human MeSH Prohlížeč
- ubikvitinligasy * MeSH
Developmental remodeling shapes neural circuits via activity-dependent pruning of synapses and axons. Regulation of the cytoskeleton is critical for this process, as microtubule loss via enzymatic severing is an early step of pruning across many circuits and species. However, how microtubule-severing enzymes, such as spastin, are activated in specific neuronal compartments remains unknown. Here, we reveal that polyglutamylation, a post-translational tubulin modification enriched in neurons, plays an instructive role in developmental remodeling by tagging microtubules for severing. Motor neuron-specific gene deletion of enzymes that add or remove tubulin polyglutamylation-TTLL glutamylases vs. CCP deglutamylases-accelerates or delays neuromuscular synapse remodeling in a neurotransmission-dependent manner. This mechanism is not specific to peripheral synapses but also operates in central circuits, e.g., the hippocampus. Thus, tubulin polyglutamylation acts as a cytoskeletal rheostat of remodeling that shapes neuronal morphology and connectivity.
- MeSH
- hipokampus metabolismus cytologie MeSH
- kyselina polyglutamová * metabolismus MeSH
- mikrotubuly * metabolismus MeSH
- motorické neurony * metabolismus MeSH
- myši MeSH
- nervosvalové spojení metabolismus MeSH
- nervový přenos MeSH
- neurony * metabolismus MeSH
- neuroplasticita * fyziologie MeSH
- peptidsynthasy metabolismus genetika MeSH
- posttranslační úpravy proteinů MeSH
- spastin metabolismus MeSH
- synapse metabolismus MeSH
- tubulin metabolismus MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- kyselina polyglutamová * MeSH
- peptidsynthasy MeSH
- spastin MeSH
- tubulin polyglutamylase MeSH Prohlížeč
- tubulin MeSH
Bottom-up proteomics typically involves enzymatic digestion of proteins, generating a complex peptide mixture. These peptides are separated using reversed-phase ultrahigh-performance liquid chromatography (UHPLC) and analyzed using electrospray ionization (ESI) tandem mass spectrometry (MS/MS) in positive ion mode. Despite its widespread use, this approach has limitations, particularly in ionizing highly acidic or hydrophobic peptides and detecting certain post-translational modifications (PTMs). To overcome these challenges, alternative ionization methods, such as vacuum ultraviolet (VUV) atmospheric pressure photoionization (APPI), have been explored. In this study, we propose peptide analysis using a novel prototype APPI source employing soft X-ray photons. Soft X-ray photons possess orders of magnitude higher energy than VUV photons, enabling additional ionization pathways. Here, we present peptide ionization data using soft X-ray and VUV APPI in both positive and negative ion modes. Notably, soft X-ray photons exhibited a remarkable capacity to generate deprotonated peptides and hydrogen-deficient peptide radical anions ([M - 2H]•-), outperforming conventional VUV photons. Furthermore, collision-induced dissociation (CID) of [M - 2H]•- provided unique structural insight, facilitating PTM characterization. Our findings emphasize the significant potential of soft X-ray APPI in advancing peptide analysis and highlight the utility of negative ion mode for proteomic applications.
- MeSH
- atmosférický tlak MeSH
- fotony MeSH
- hmotnostní spektrometrie s elektrosprejovou ionizací * metody MeSH
- peptidy * analýza chemie MeSH
- posttranslační úpravy proteinů MeSH
- proteomika metody MeSH
- rentgenové záření MeSH
- tandemová hmotnostní spektrometrie * metody MeSH
- ultrafialové záření MeSH
- vysokoúčinná kapalinová chromatografie metody MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- peptidy * MeSH
Membrane contact sites harbor a distinct set of proteins with varying biological functions, thereby emerging as hubs for localized signaling nanodomains underlying adequate cell function. Here, we will focus on mitochondria-associated endoplasmic reticulum membranes (MAMs), which serve as hotspots for Ca2+ signaling, redox regulation, lipid exchange, mitochondrial quality and unfolded protein response pathway. A network of MAM-resident proteins contributes to the structural integrity and adequate function of MAMs. Beyond endoplasmic reticulum (ER)-mitochondrial tethering proteins, MAMs contain several multi-protein complexes that mediate the transfer of or are influenced by Ca2+, reactive oxygen species and lipids. Particularly, IP3 receptors, intracellular Ca2+-release channels, and Sigma-1 receptors (S1Rs), ligand-operated chaperones, serve as important platforms that recruit different accessory proteins and intersect with these local signaling processes. Furthermore, many of these proteins are directly implicated in pathophysiological conditions, where their dysregulation or mutation is not only causing diseases such as cancer and neurodegeneration, but also rare genetic diseases, for example familial Parkinson's disease (PINK1, Parkin, DJ-1), familial Amyotrophic lateral sclerosis (TDP43), Wolfram syndrome1/2 (WFS1 and CISD2), Harel-Yoon syndrome (ATAD3A). In this review, we will discuss the current state-of-the-art regarding the molecular components, protein platforms and signaling networks underlying MAM integrity and function in cell function and how their dysregulation impacts MAMs, thereby driving pathogenesis and/or impacting disease burden. We will highlight how these insights can generate novel, potentially therapeutically relevant, strategies to tackle disease outcomes by improving the integrity of MAMs and the signaling processes occurring at these membrane contact sites.
- Klíčová slova
- ATAD3A related disorders, Amyotrophic lateral sclerosis, Calcium signaling, Cancer, Endoplasmic reticulum stress, Familial Parkinson's disease, Harel-Yoon syndrome, Metabolomics, Mitochondria quality control, Mitochondria-associated endoplasmic reticulum membranes, Rare neurodegenerative diseases, Wolfram syndrome,
- MeSH
- endoplazmatické retikulum * metabolismus patologie MeSH
- intracelulární membrány * metabolismus MeSH
- lidé MeSH
- mitochondriální membrány metabolismus MeSH
- mitochondrie * metabolismus patologie MeSH
- nádory * metabolismus patologie terapie genetika MeSH
- neurodegenerativní nemoci * metabolismus patologie terapie genetika MeSH
- receptor sigma-1 MeSH
- receptory sigma metabolismus MeSH
- signální dráha UPR MeSH
- vápníková signalizace MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
- Názvy látek
- receptor sigma-1 MeSH
- receptory sigma MeSH
Protein misfolding diseases, including α1-antitrypsin deficiency (AATD), pose substantial health challenges, with their cellular progression still poorly understood1-3. We use spatial proteomics by mass spectrometry and machine learning to map AATD in human liver tissue. Combining Deep Visual Proteomics (DVP) with single-cell analysis4,5, we probe intact patient biopsies to resolve molecular events during hepatocyte stress in pseudotime across fibrosis stages. We achieve proteome depth of up to 4,300 proteins from one-third of a single cell in formalin-fixed, paraffin-embedded tissue. This dataset reveals a potentially clinically actionable peroxisomal upregulation that precedes the canonical unfolded protein response. Our single-cell proteomics data show α1-antitrypsin accumulation is largely cell-intrinsic, with minimal stress propagation between hepatocytes. We integrated proteomic data with artificial intelligence-guided image-based phenotyping across several disease stages, revealing a late-stage hepatocyte phenotype characterized by globular protein aggregates and distinct proteomic signatures, notably including elevated TNFSF10 (also known as TRAIL) amounts. This phenotype may represent a critical disease progression stage. Our study offers new insights into AATD pathogenesis and introduces a powerful methodology for high-resolution, in situ proteomic analysis of complex tissues. This approach holds potential to unravel molecular mechanisms in various protein misfolding disorders, setting a new standard for understanding disease progression at the single-cell level in human tissue.
- MeSH
- alfa-1-antitrypsin metabolismus MeSH
- analýza jednotlivých buněk MeSH
- deficit alfa1-antitrypsinu * patologie metabolismus genetika MeSH
- fenotyp MeSH
- hepatocyty metabolismus patologie MeSH
- jaterní cirhóza patologie metabolismus MeSH
- játra patologie metabolismus MeSH
- lidé MeSH
- progrese nemoci MeSH
- proteom * analýza metabolismus MeSH
- proteomika * metody MeSH
- signální dráha UPR MeSH
- strojové učení MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- alfa-1-antitrypsin MeSH
- proteom * MeSH
Nedd4-2 E3 ligase regulates Na+ homeostasis by ubiquitinating various channels and membrane transporters, including the epithelial sodium channel ENaC. In turn, Nedd4-2 dysregulation leads to various conditions, including electrolytic imbalance, respiratory distress, hypertension, and kidney diseases. However, Nedd4-2 regulation remains mostly unclear. The present study aims at elucidating Nedd4-2 regulation by structurally characterizing Nedd4-2 and its complexes using several biophysical techniques. Our cryo-EM reconstruction shows that the C2 domain blocks the E2-binding surface of the HECT domain. This blockage, ubiquitin-binding exosite masking by the WW1 domain, catalytic C922 blockage and HECT domain stabilization provide the structural basis for Nedd4-2 autoinhibition. Furthermore, Ca2+-dependent C2 membrane binding disrupts C2/HECT interactions, but not Ca2+ alone, whereas 14-3-3 protein binds to a flexible region of Nedd4-2 containing the WW2 and WW3 domains, thereby inhibiting its catalytic activity and membrane binding. Overall, our data provide key mechanistic insights into Nedd4-2 regulation toward fostering the development of strategies targeting Nedd4-2 function.
- MeSH
- elektronová kryomikroskopie MeSH
- HEK293 buňky MeSH
- lidé MeSH
- molekulární modely MeSH
- proteinové domény MeSH
- proteiny 14-3-3 * metabolismus chemie MeSH
- ubikvitinace MeSH
- ubikvitinligasy Nedd4 * metabolismus chemie genetika ultrastruktura MeSH
- vápník * metabolismus MeSH
- vazba proteinů MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- Nedd4 protein, human MeSH Prohlížeč
- Nedd4L protein, human MeSH Prohlížeč
- proteiny 14-3-3 * MeSH
- ubikvitinligasy Nedd4 * MeSH
- vápník * MeSH
BACKGROUND: The unfolded protein response (UPR) enables myeloma cells to overcome the stress conditions arising from excessive proteosynthesis and thus provides a survival advantage for myeloma cells. Extramedullary disease is a more aggressive form of multiple myeloma in which myeloma cells lose their dependence on the bone marrow microenvironment and are able to infiltrate other tissues and organs. The pathogenesis of extramedullary disease is not fully elucidated yet. The aim of this study was to determine whether there is a difference in the expression of UPR-related genes between bone marrow plasma cells from multiple myeloma and extramedullary disease patients. MATERIALS AND METHODS: Gene expression of six genes involved in UPR (ERN1, DDIT3, EIF2AK3, TUSC3, XBP1, HSPA5) was analyzed by quantitative reverse transcription polymerase chain reaction. In total, 76 bone marrow plasma cell samples were used, of which 44 were from patients with multiple myeloma and 32 from patients with extramedullary disease. RESULTS: A statistically significant difference was observed between the multiple myeloma and extramedullary disease groups regarding the expression of HSPA5, DDIT3, EIF2AK3, and ERN1 genes. However, in the case of XBP1 and TUSC3 genes, no statistically significant difference in the expression was found. Several statistically significant correlations between the expression levels of the analyzed genes and the clinical data of the patients were observed as well. CONCLUSION: Our results suggest the importance of UPR in the pathogenesis of extramedullary disease. UPR appears to be a promising avenue for further research.
- Klíčová slova
- Kahler-Pick law, Multiple myeloma, Plasma cells, extramedullary disease, unfolded protein response,
- MeSH
- chaperon endoplazmatického retikula BiP MeSH
- endoribonukleasy genetika MeSH
- lidé středního věku MeSH
- lidé MeSH
- mnohočetný myelom * genetika metabolismus patologie MeSH
- plazmatické buňky metabolismus MeSH
- protein-serin-threoninkinasy genetika MeSH
- proteiny teplotního šoku genetika MeSH
- senioři MeSH
- signální dráha UPR * genetika MeSH
- transkripční faktor CHOP genetika MeSH
- transkripční faktory RFX MeSH
- XBP1 genetika MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- chaperon endoplazmatického retikula BiP MeSH
- DDIT3 protein, human MeSH Prohlížeč
- EIF2AK3 protein, human MeSH Prohlížeč
- endoribonukleasy MeSH
- ERN1 protein, human MeSH Prohlížeč
- HSPA5 protein, human MeSH Prohlížeč
- kinasa eIF-2 MeSH
- protein-serin-threoninkinasy MeSH
- proteiny teplotního šoku MeSH
- transkripční faktor CHOP MeSH
- transkripční faktory RFX MeSH
- XBP1 protein, human MeSH Prohlížeč
- XBP1 MeSH
