Anterior gradient 2 (AGR2) is an endoplasmic reticulum (ER)-resident protein disulfide isomerase (PDI) known to be overexpressed in many human epithelial cancers and is involved in cell migration, cellular transformation, angiogenesis, and metastasis. This protein inhibits the activity of the tumor suppressor p53, and its expression levels can be used to predict cancer patient outcome. However, the precise network of AGR2-interacting partners and clients remains to be fully characterized. Herein, we used label-free quantification and also stable isotope labeling with amino acids in cell culture-based LC-MS/MS analyses to identify proteins interacting with AGR2. Functional annotation confirmed that AGR2 and its interaction partners are associated with processes in the ER that maintain intracellular metabolic homeostasis and participate in the unfolded protein response, including those associated with changes in cellular metabolism, energy, and redox states in response to ER stress. As a proof of concept, the interaction between AGR2 and PDIA3, another ER-resident PDI, was studied in more detail. Pathway analysis revealed that AGR2 and PDIA3 play roles in protein folding in ER, including post-translational modification and in cellular response to stress. We confirmed the AGR2-PDIA3 complex formation in cancer cells, which was enhanced in response to ER stress. Accordingly, molecular docking characterized potential quaternary structure of this complex; however, it remains to be elucidated whether AGR2 rather contributes to PDIA3 maturation in ER, the complex directly acts in cellular signaling, or mediates AGR2 secretion. Our study provides a comprehensive insight into the protein-protein interaction network of AGR2 by identifying functionally relevant proteins and related cellular and biochemical pathways associated with the role of AGR2 in cancer cells.

• MeSH
• chromatografie kapalinová MeSH
• lidé MeSH
• mapy interakcí proteinů MeSH
• mukoproteiny * metabolismus   MeSH
• nádory * MeSH
• onkogenní proteiny * metabolismus   MeSH
• proteindisulfidisomerasy * MeSH
• simulace molekulového dockingu MeSH
• tandemová hmotnostní spektrometrie MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

[Figure: see text].

• MeSH
• adaptorové proteiny signální transdukční chemie   metabolismus   MeSH
• DNA vazebné proteiny chemie   metabolismus   MeSH
• elongace genetické transkripce * MeSH
• exprese genu MeSH
• interakční proteinové domény a motivy genetika   MeSH
• lidé MeSH
• mapy interakcí proteinů MeSH
• molekulární modely MeSH
• mutace MeSH
• nádorové buněčné linie MeSH
• proteinové domény MeSH
• proteiny vázající RNA chemie   genetika   metabolismus   MeSH
• RNA-polymerasa II chemie   metabolismus   MeSH
• transkripční elongační faktory chemie   metabolismus   MeSH
• transkripční faktory chemie   genetika   metabolismus   MeSH
• vazba proteinů MeSH
• vnitřně neuspořádané proteiny chemie   metabolismus   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH

Cardiovascular disease is the main cause of death worldwide, making it crucial to search for new therapies to mitigate major adverse cardiac events (MACEs) after a cardiac ischemic episode. Drugs in the class of the glucagon-like peptide-1 receptor agonists (GLP1Ra) have demonstrated benefits for heart function and reduced the incidence of MACE in patients with diabetes. Previously, we demonstrated that a short-acting GLP1Ra known as DMB (2-quinoxalinamine, 6,7-dichloro-N-[1,1-dimethylethyl]-3-[methylsulfonyl]-,6,7-dichloro-2-methylsulfonyl-3-N-tert-butylaminoquinoxaline or compound 2, Sigma) also mitigates adverse postinfarction left ventricular remodeling and cardiac dysfunction in lean mice through activation of parkin-mediated mitophagy following infarction. Here, we combined proteomics with in silico analysis to characterize the range of effects of DMB in vivo throughout the course of early postinfarction remodeling. We demonstrate that the mitochondrion is a key target of DMB and mitochondrial respiration, oxidative phosphorylation and metabolic processes such as glycolysis and fatty acid beta-oxidation are the main biological processes being regulated by this compound in the heart. Moreover, the overexpression of proteins with hub properties identified by protein-protein interaction networks, such as Atp2a2, may also be important to the mechanism of action of DMB. Data are available via ProteomeXchange with identifier PXD027867.

• MeSH
• chinoxaliny aplikace a dávkování   farmakologie   MeSH
• glykolýza MeSH
• mapy interakcí proteinů MeSH
• modely nemocí na zvířatech MeSH
• myši MeSH
• oxidativní fosforylace MeSH
• proteomika metody   MeSH
• receptor pro glukagonu podobný peptid 1 agonisté   MeSH
• remodelace komor účinky léků   MeSH
• sarkoplazmatická Ca2+-ATPáza metabolismus   MeSH
• srdeční komory metabolismus   MeSH
• srdeční mitochondrie metabolismus   MeSH
• výpočetní biologie MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Although human nucleoporin Tpr is frequently deregulated in cancer, its roles are poorly understood. Here we show that Tpr depletion generates transcription-dependent replication stress, DNA breaks, and genomic instability. DNA fiber assays and electron microscopy visualization of replication intermediates show that Tpr deficient cells exhibit slow and asymmetric replication forks under replication stress. Tpr deficiency evokes enhanced levels of DNA-RNA hybrids. Additionally, complementary proteomic strategies identify a network of Tpr-interacting proteins mediating RNA processing, such as MATR3 and SUGP2, and functional experiments confirm that their depletion trigger cellular phenotypes shared with Tpr deficiency. Mechanistic studies reveal the interplay of Tpr with GANP, a component of the TREX-2 complex. The Tpr-GANP interaction is supported by their shared protein level alterations in a cohort of ovarian carcinomas. Our results reveal links between nucleoporins, DNA transcription and replication, and the existence of a network physically connecting replication forks with transcription, splicing, and mRNA export machinery.

• MeSH
• acetyltransferasy genetika   metabolismus   MeSH
• HeLa buňky MeSH
• intracelulární signální peptidy a proteiny genetika   metabolismus   MeSH
• komplex proteinů jaderného póru genetika   metabolismus   MeSH
• lidé MeSH
• mapy interakcí proteinů MeSH
• nádory genetika   MeSH
• nestabilita genomu MeSH
• poškození DNA MeSH
• protoonkogenní proteiny genetika   metabolismus   MeSH
• replikace DNA * MeSH
• transport RNA MeSH
• viabilita buněk MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

In vitro models are often used for studying macrophage functions, including the process of phagocytosis. The application of primary macrophages has limitations associated with the individual characteristics of animals, which can lead to insufficient standardization and higher variability of the obtained results. Immortalized cell lines do not have these disadvantages, but their responses to various signals can differ from those of the living organism. In the present study, a comparative proteomic analysis of immortalized PMJ2-R cell line and primary peritoneal macrophages isolated from C57BL/6 mice was performed. A total of 4005 proteins were identified, of which 797 were quantified. Obtained results indicate significant differences in the abundances of many proteins, including essential proteins associated with the process of phagocytosis, such as Elmo1, Gsn, Hspa8, Itgb1, Ncf2, Rac2, Rack1, Sirpa, Sod1, C3, and Msr1. These findings indicate that outcomes of studies utilizing PMJ2-R cells as a model of peritoneal macrophages should be carefully validated. All MS data are deposited in ProteomeXchange with the identifier PXD022133.

• MeSH
• down regulace MeSH
• fagocytóza MeSH
• genová ontologie MeSH
• kultivované buňky MeSH
• mapy interakcí proteinů MeSH
• myši inbrední C57BL MeSH
• peritoneální makrofágy metabolismus   MeSH
• proteom metabolismus   MeSH
• proteomika * MeSH
• upregulace MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored data from 3,823 mutant mouse strains for BMD, a measure that is frequently altered in a range of bone pathologies, including osteoporosis. A total of 200 genes were found to significantly affect BMD. This pool of BMD genes comprised 141 genes with previously unknown functions in bone biology and was complementary to pools derived from recent human studies. Nineteen of the 141 genes also caused skeletal abnormalities. Examination of the BMD genes in osteoclasts and osteoblasts underscored BMD pathways, including vesicle transport, in these cells and together with in silico bone turnover studies resulted in the prioritization of candidate genes for further investigation. Overall, the results add novel pathophysiological and molecular insight into bone health and disease.

• MeSH
• celogenomová asociační studie MeSH
• fenotyp MeSH
• genetická pleiotropie MeSH
• genotyp MeSH
• genová ontologie MeSH
• kostní denzita genetika   MeSH
• mapy interakcí proteinů MeSH
• mutace MeSH
• myši transgenní MeSH
• myši MeSH
• osteoblasty metabolismus   patologie   MeSH
• osteoklasty metabolismus   patologie   MeSH
• osteoporóza genetika   metabolismus   MeSH
• pohlavní dimorfismus MeSH
• promotorové oblasti (genetika) MeSH
• regulace genové exprese genetika   MeSH
• transkriptom MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• myši MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH

Ca2+/calmodulin-dependent protein kinase kinase 2 (CaMKK2) regulates several key physiological and pathophysiological processes, and its dysregulation has been implicated in obesity, diabetes, and cancer. CaMKK2 is inhibited through phosphorylation in a process involving binding to the scaffolding 14-3-3 protein, which maintains CaMKK2 in the phosphorylation-mediated inhibited state. The previously reported structure of the N-terminal CaMKK2 14-3-3-binding motif bound to 14-3-3 suggested that the interaction between 14-3-3 and CaMKK2 could be stabilized by small-molecule compounds. Thus, we investigated the stabilization of interactions between CaMKK2 and 14-3-3γ by Fusicoccin A and other fusicoccanes-diterpene glycosides that bind at the interface between the 14-3-3 ligand binding groove and the 14-3-3 binding motif of the client protein. Our data reveal that two of five tested fusicoccanes considerably increase the binding of phosphopeptide representing the 14-3-3 binding motif of CaMKK2 to 14-3-3γ. Crystal structures of two ternary complexes suggest that the steric contacts between the C-terminal part of the CaMKK2 14-3-3 binding motif and the adjacent fusicoccane molecule are responsible for differences in stabilization potency between the study compounds. Moreover, our data also show that fusicoccanes enhance the binding affinity of phosphorylated full-length CaMKK2 to 14-3-3γ, which in turn slows down CaMKK2 dephosphorylation, thus keeping this protein in its phosphorylation-mediated inhibited state. Therefore, targeting the fusicoccin binding cavity of 14-3-3 by small-molecule compounds may offer an alternative strategy to suppress CaMKK2 activity by stabilizing its phosphorylation-mediated inhibited state.

• MeSH
• fosforylace účinky léků   MeSH
• glykosidy chemie   farmakologie   MeSH
• kinasa proteinkinasy závislé na vápníku a kalmodulinu chemie   metabolismus   MeSH
• krystalografie rentgenová MeSH
• lidé MeSH
• mapy interakcí proteinů účinky léků   MeSH
• proteiny 14-3-3 chemie   metabolismus   MeSH
• simulace molekulového dockingu MeSH
• vazba proteinů účinky léků   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

De-etiolation is the first developmental process under light control allowing the heterotrophic seedling to become autotrophic. The phytohormones cytokinins (CKs) largely contribute to this process. Reversible phosphorylation is a key event of cell signaling, allowing proteins to become active or generating a binding site for specific protein interaction. 14-3-3 proteins regulate a variety of plant responses. The expression, hormonal regulation, and proteomic network under the control of 14-3-3s were addressed in tomato (Solanum lycopersicum L.) during blue light-induced photomorphogenesis. Two isoforms were specifically investigated due to their high expression during tomato de-etiolation. The multidisciplinary approach demonstrated that TFT9 expression, but not TFT6, was regulated by CKs and identified cis-regulating elements required for this response. Our study revealed >130 potential TFT6/9 interactors. Their functional annotation predicted that TFTs might regulate the activity of proteins involved notably in cell wall strengthening or primary metabolism. Several potential interactors were also predicted to be CK-responsive. For the first time, the 14-3-3 interactome linked to de-etiolation was investigated and evidenced that 14-3-3s might be involved in CK signaling pathway, cell expansion inhibition and steady-state growth rate establishment, and reprograming from heterotrophy to autotrophy. BIOLOGICAL SIGNIFICANCE: Tomato (Solanum lycopersicum L.) is one of the most important vegetables consumed all around the world and represents probably the most preferred garden crop. Regulation of hypocotyl growth by light plays an important role in the early development of a seedling, and consequently the homogeneity of the culture. The present study focuses on the importance of tomato 14-3-3/TFT proteins in this process. We provide here the first report of 14-3-3 interactome in the regulation of light-induced de-etiolation and subsequent photomorphogenesis. Our data provide new insights into light-induced de-etiolation and open new horizons for dissecting the post-transcriptional regulations.

• MeSH
• chromatografie afinitní MeSH
• mapy interakcí proteinů * MeSH
• proteiny 14-3-3 metabolismus   MeSH
• proteomika * MeSH
• rostlinné proteiny metabolismus   MeSH
• semenáček růst a vývoj   MeSH
• Solanum lycopersicum růst a vývoj   MeSH
• světlo * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Chronic myeloid leukemia (CML) is a clonal myeloproliferative disorder arising from chromosomal translocation producing a chimeric BCR-ABL protein with unregulated tyrosine kinase (TK) activity. Targeting of the BCR-ABL activity by the TK inhibitors (TKIs) is a frontline in treatment of the CML. While majority of the CML patients positively respond to the TKIs, their use does not cure the disease. The facts that the CML patients often acquire BCR-ABL mutations causing resistance to TKIs, that slowly proliferating cancer stem cells are poorly targeted with TKIs, and that other oncogenic pathways cooperate with the BCR-ABL in the CML development are all responsible for disease relapse. Main goal of the proposed project is to characterise the BCR-ABL interactome comprising of stably and transiently associated proteins in different clinical stages of CML along with identification of protein-protein interactions responsible for survival of the BCR-ABL positive cells. The results are to identify novel treatment strategies in CML.

Chronická myeloidní leukémie (CML) je klonální myeloproliferativní onemocnění vznikající v důsledku chromosomální translokace, jež vede k produkci chimerického BCR-ABL proteinu s neregulovanou tyrosin kinázovou (TK) aktivitou. Inhibice BCR-ABL aktivity pomocí TK inhibitorů (TKI) představuje standard v léčbě CML. Ačkoliv většina pacientů pozitivně reaguje na administraci TKI, jejich použití nevede k eradikaci choroby. Skutečnost, že: i) pacienti s CML vyvinou resistenci vůči TKI v důsledku mutací v BCR-ABL, ii) TKI jsou neefektivní pro pomalu proliferující rakovinné kmenové buňky, a iii) řada dalších onkogenických signálních drah se spolupodílí na propagaci CML, vede k relapsu onemocnění. Hlavním cílem tohoto projektu je charakterizace interaktomu BCR-ABL zahrnujícího stabilně a transientně asociované proteiny v různých klinických fázích CML a identifikace protein-proteinových interakcí zodpovědných za přežívání buněk pozitivních na BCR-ABL. Výsledky tohoto projektu umožní identifikaci nových přístupů k léčbě CML.

• MeSH
• bcr-abl fúzové proteiny MeSH
• chronická myeloidní leukemie terapie   MeSH
• klinický obraz nemoci MeSH
• mapování interakce mezi proteiny MeSH
• mapy interakcí proteinů MeSH
• proteinkinasa BTK MeSH
• signální transdukce MeSH

• Konspekt
• Patologie. Klinická medicína
• NLK Obory
• onkologie
• hematologie a transfuzní lékařství
• biochemie
• NLK Publikační typ
• závěrečné zprávy o řešení grantu AZV MZ ČR

Analysis of protein-protein interactions (PPI) is key for the understanding of most protein assemblies including structural maintenance of chromosomes (SMC) complexes. SMC complexes are composed of SMC proteins, kleisin, and kleisin-interacting subunits. These subunits interact in specific ways to constitute and regulate the closed structure of the complexes. Specifically, kleisin molecules bridge the SMC dimers and the kleisin-interacting subunits modulate stability of the bridge. Here we describe a multicomponent version of a yeast two-hybrid (Y2H) method and its application for analysis of the bridging role of the Nse4 kleisin in the SMC5/6 complex. Using this technique, we also show a stabilizing effect of KITE (kleisin-interacting tandem winged-helix element) proteins on SMC5/6.

• MeSH
• chromozomy hub fyziologie   MeSH
• mapy interakcí proteinů fyziologie   MeSH
• multiproteinové komplexy metabolismus   MeSH
• podjednotky proteinů metabolismus   MeSH
• proteiny buněčného cyklu metabolismus   MeSH
• Saccharomyces cerevisiae - proteiny metabolismus   MeSH
• Saccharomyces cerevisiae metabolismus   MeSH
• techniky dvojhybridového systému MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH