Aromatic ring-hydroxylating dioxygenases (ARHDs) play a crucial role in the aerobic biodegradation of both natural and anthropogenic aromatic compounds. Although their ability to process contaminants is not entirely understood, it is thought to have evolved from the transformation of structurally similar secondary plant metabolites (SPMs). Hence, to investigate this connection, we tested a variety of SPMs from the monoterpene and flavonoid classes as carbon sources and transcriptional effectors of several phylogenetically distant ARHD genes involved in the degradation of aromatic pollutants. Specifically, we focused on bphA1, nahA1 and phtA1 in Rhodococcus opacus C1, whose genomic analysis is also presented hereinafter, and bphA1a, nahA1-bphA1b and etbA1ab in Rhodococcus sp. WAY2. Whilst induction was only observed with (R)-carvone for bphA1a and nahA1-bphA1b of strain WAY2, and with p-cymene for nahA1 and nahA1-bphA1b of strains C1 and WAY2, respectively, an extensive inhibition by flavonoids was observed for most of the genes in both strains. To the best of our knowledge, our study is the first to report the effect of flavonoids and monoterpenes on the transcription of nahA1, etbA1 and phtA1 genes. In addition, we show that, in contrast to pseudomonads, many flavonoids inhibit the transcription of the ARHD genes in rhodococci. Thus, our work provides a new perspective on flavonoids as the transcriptional effectors of ARHDs, highlighting the significant variability of these enzymes and the divergent responses that they elicit. Moreover, our results contribute to understanding the complex interactions between microorganisms and SPMs and provide insights into the molecular basis of a number of them.

• Klíčová slova
• Rhodococcus, aromatic pollutants, aromatic ring-hydroxylating dioxygenases, biodegradation, flavonoids, monoterpenes,
• MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• biodegradace MeSH
• dioxygenasy * genetika   metabolismus   MeSH
• flavonoidy * farmakologie   metabolismus   MeSH
• fylogeneze MeSH
• genetická transkripce účinky léků   MeSH
• monoterpeny * farmakologie   metabolismus   MeSH
• regulace genové exprese u bakterií účinky léků   MeSH
• Rhodococcus * genetika   účinky léků   enzymologie   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• bakteriální proteiny MeSH
• dioxygenasy * MeSH
• flavonoidy * MeSH
• monoterpeny * MeSH

Cytokinins (CKs) are known to regulate the biogenesis of chloroplasts under changing environmental conditions and at different stages of plant ontogenesis. However, the underlying mechanisms are still poorly understood. Apparently, the mechanisms can be duplicated in several ways, including the influence of nuclear genes that determine the expression of plastome through the two-component CK regulatory circuit. In this study, we evaluated the role of cytokinins and CK signaling pathway on the expression of nuclear genes for plastid RNA polymerase-associated proteins (PAPs). Cytokinin induced the expression of all twelve Arabidopsis thalianaPAP genes irrespective of their functions via canonical CK signaling pathway but this regulation might be indirect taking into consideration their different functions and versatile structure of promoter regions. The disruption of PAP genes contributed to the abolishment of positive CK effect on the accumulation of the chloroplast gene transcripts and transcripts of the nuclear genes for plastid transcription machinery as can be judged from the analysis of pap1 and pap6 mutants. However, the CK regulatory circuit in the mutants remained practically unperturbed. Knock-out of PAP genes resulted in cytokinin overproduction as a consequence of the strong up-regulation of the genes for CK synthesis.

• Klíčová slova
• Arabidopsis thaliana, PEP-associated proteins, chloroplast biogenesis, cytokinin, plastid transcription machinery,
• MeSH
• Arabidopsis účinky léků   genetika   MeSH
• buněčné jádro účinky léků   genetika   MeSH
• chloroplasty účinky léků   genetika   MeSH
• cytokininy farmakologie   MeSH
• fotosyntéza účinky léků   MeSH
• genetická transkripce účinky léků   MeSH
• geny chloroplastů * MeSH
• messenger RNA genetika   metabolismus   MeSH
• mutace genetika   MeSH
• regulace genové exprese u rostlin účinky léků   MeSH
• signální transdukce účinky léků   MeSH
• zeatin farmakologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• cytokininy MeSH
• messenger RNA MeSH
• zeatin MeSH

Titanium dioxide nanoparticles (TiO2NPs) are revolutionizing biomedicine due to their potential application as diagnostic and therapeutic agents. However, the TiO2NP immune-compatibility remains an open issue, even for ethical reasons. In this work, we investigated the immunomodulatory effects of TiO2NPs in an emergent proxy to human non-mammalian model for in vitro basic and translational immunology: the sea urchin Paracentrotus lividus. To highlight on the new insights into the evolutionarily conserved intracellular signaling and metabolism pathways involved in immune-TiO2NP recognition/interaction we applied a wide-ranging approach, including electron microscopy, biochemistry, transcriptomics and metabolomics. Findings highlight that TiO2NPs interact with immune cells suppressing the expression of genes encoding for proteins involved in immune response and apoptosis (e.g. NF-κB, FGFR2, JUN, MAPK14, FAS, VEGFR, Casp8), and boosting the immune cell antioxidant metabolic activity (e.g. pentose phosphate, cysteine-methionine, glycine-serine metabolism pathways). TiO2NP uptake was circumscribed to phagosomes/phagolysosomes, depicting harmless vesicular internalization. Our findings underlined that under TiO2NP-exposure sea urchin innate immune system is able to control inflammatory signaling, excite antioxidant metabolic activity and acquire immunological tolerance, providing a new level of understanding of the TiO2NP immune-compatibility that could be useful for the development in Nano medicines.

• Klíčová slova
• Homeostasis restoring, Human gene networks, Innate immunity, Metabolic rewiring, TiO(2)NP-responsive genes,
• MeSH
• antioxidancia metabolismus   MeSH
• chemické látky znečišťující vodu toxicita   MeSH
• fagocytóza účinky léků   MeSH
• genetická transkripce účinky léků   MeSH
• kultivované buňky MeSH
• nanočástice toxicita   MeSH
• Paracentrotus cytologie   účinky léků   imunologie   metabolismus   MeSH
• přirozená imunita účinky léků   genetika   MeSH
• titan toxicita   MeSH
• viabilita buněk účinky léků   imunologie   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• antioxidancia MeSH
• chemické látky znečišťující vodu MeSH
• titan MeSH
• titanium dioxide MeSH Prohlížeč

Reprogramming of non-endocrine pancreatic cells into insulin-producing cells represents a promising therapeutic approach for the restoration of endogenous insulin production in diabetic patients. In this paper, we report that human organoid cells derived from the pancreatic tissue can be reprogrammed into the insulin-producing cells (IPCs) by the combination of in vitro transcribed modified mRNA encoding transcription factor neurogenin 3 and small molecules modulating the epigenetic state and signalling pathways. Upon the reprogramming, IPCs formed 4.6 ± 1.2 % of the total cells and expressed typical markers (insulin, glucokinase, ABCC8, KCNJ11, SLC2A2, SLC30A8) and transcription factors (PDX1, NEUROD1, MAFA, NKX2.2, NKX6.1, PAX4, PAX6) needed for the proper function of pancreatic β-cells. Additionally, we have revealed a positive effect of ALK5 inhibitor RepSox on the overall reprogramming efficiency. However, the reprogrammed IPCs possessed only a partial insulin-secretory capacity, as they were not able to respond to the changes in the extracellular glucose concentration by increasing insulin secretion. Based on the achieved results we conclude that due to the incomplete reprogramming, the IPCs have immature character and only partial properties of native human β-cells.

• MeSH
• antigen AC133 metabolismus   MeSH
• beta-buňky cytologie   účinky léků   MeSH
• dospělí MeSH
• genetická transkripce účinky léků   MeSH
• homeoboxový protein Nkx-2.2 MeSH
• homeodoménové proteiny MeSH
• inzulin biosyntéza   MeSH
• jaderné proteiny MeSH
• knihovny malých molekul farmakologie   MeSH
• lidé MeSH
• messenger RNA genetika   metabolismus   MeSH
• organoidy cytologie   MeSH
• přeprogramování buněk účinky léků   genetika   MeSH
• proliferace buněk MeSH
• proteiny nervové tkáně genetika   metabolismus   MeSH
• transkripční faktory bHLH genetika   metabolismus   MeSH
• transkripční faktory MeSH
• Check Tag
• dospělí MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• antigen AC133 MeSH
• homeoboxový protein Nkx-2.2 MeSH
• homeodoménové proteiny MeSH
• inzulin MeSH
• jaderné proteiny MeSH
• knihovny malých molekul MeSH
• messenger RNA MeSH
• NEUROG3 protein, human MeSH Prohlížeč
• NKX2-2 protein, human MeSH Prohlížeč
• proteiny nervové tkáně MeSH
• transkripční faktory bHLH MeSH
• transkripční faktory MeSH

FOXO transcription factors are critical regulators of cell homeostasis and steer cell death, differentiation and longevity in mammalian cells. By combined pharmacophore-modeling-based in silico and fluorescence polarization-based screening we identified small molecules that physically interact with the DNA-binding domain (DBD) of FOXO3 and modulate the FOXO3 transcriptional program in human cells. The mode of interaction between compounds and the FOXO3-DBD was assessed via NMR spectroscopy and docking studies. We demonstrate that compounds S9 and its oxalate salt S9OX interfere with FOXO3 target promoter binding, gene transcription and modulate the physiologic program activated by FOXO3 in cancer cells. These small molecules prove the druggability of the FOXO-DBD and provide a structural basis for modulating these important homeostasis regulators in normal and malignant cells.

• Klíčová slova
• FOXO transcription factors, biochemistry, cancer biology, chemical biology, docking, drug targeting, human, molecular biophysics, pharmacophore modelling, small compounds, structural biology,
• MeSH
• DNA chemie   genetika   metabolismus   MeSH
• genetická transkripce účinky léků   MeSH
• genový knockdown MeSH
• HEK293 buňky MeSH
• knihovny malých molekul chemie   metabolismus   farmakologie   MeSH
• konformace nukleové kyseliny MeSH
• lidé MeSH
• magnetická rezonanční spektroskopie MeSH
• molekulární modely MeSH
• nádorové buněčné linie MeSH
• promotorové oblasti (genetika) genetika   MeSH
• protein FOXO3 chemie   genetika   metabolismus   MeSH
• proteinové domény MeSH
• simulace molekulového dockingu MeSH
• stanovení celkové genové exprese metody   MeSH
• vazba proteinů MeSH
• vazebná místa genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA MeSH
• FOXO3 protein, human MeSH Prohlížeč
• knihovny malých molekul MeSH
• protein FOXO3 MeSH

Recognition of pathogen-associated molecular patterns (PAMPs) is crucial for plant defence against pathogen attack. The best characterized PAMP is flg22, a 22 amino acid conserved peptide from flagellin protein. In Arabidopsis thaliana, flg22 is recognized by the flagellin sensing 2 (FLS2) receptor. In this study, we focused on biotic stress responses triggered by flg22 after exposure to temporary heat stress (HS). It is important to study the reactions of plants to multiple stress conditions because plants are often exposed simultaneously to a combination of both abiotic and biotic stresses. Transient early production of reactive oxygen species (ROS) is a well-characterized response to PAMP recognition. We demonstrate the strong reduction of flg22-induced ROS production in A. thaliana after HS treatment. In addition, a decrease in FLS2 transcription and a decrease of the FLS2 presence at the plasma membrane are shown after HS. In summary, our data show the strong inhibitory effect of HS on flg22-triggered events in A. thaliana. Subsequently, temporary HS strongly decreases the resistance of A. thaliana to Pseudomonas syringae. We propose that short exposure to high temperature is a crucial abiotic stress factor that suppresses PAMP-triggered immunity, which subsequently leads to the higher susceptibility of plants to pathogens.

• Klíčová slova
• Arabidopsis thaliana, Pseudomonas syringae, PAMP-triggered immunity, flagellin sensing 2 receptor, flg22, heat stress, reactive oxygen species,
• MeSH
• alarminy metabolismus   MeSH
• Arabidopsis účinky léků   genetika   imunologie   mikrobiologie   MeSH
• flagelin farmakologie   MeSH
• genetická transkripce účinky léků   MeSH
• imunita rostlin * účinky léků   MeSH
• nemoci rostlin imunologie   mikrobiologie   MeSH
• odolnost vůči nemocem imunologie   MeSH
• proteiny huseníčku genetika   metabolismus   MeSH
• Pseudomonas syringae účinky léků   fyziologie   MeSH
• reakce na tepelný šok * účinky léků   MeSH
• regulace genové exprese u rostlin účinky léků   MeSH
• respirační vzplanutí účinky léků   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• alarminy MeSH
• flagelin MeSH
• proteiny huseníčku MeSH

Protein-DNA interactions are important in replication, transcription, repair, as well as epigenetic modifications of DNA, which involve methylation and demethylation of DNA resulting in regulation of gene expression. Understanding of these processes and chemical tools for studying and perhaps even modulating them could be of great relevance and importance not only in chemical biology but also in real diagnostics and treatment of diseases. In the past decade, we have been working on development of synthesis of base-modified 2'-deoxyribo- or ribonucleoside triphosphates (dNTPs or NTPs) and their use in enzymatic synthesis of modified nucleic acids using DNA or RNA polymerases. These synthetic and enzymatic methods are briefly summarized with focus on recent development and outlining of scope, limitations, and further challenges. The main focus of this Account is on applications of base-modified nucleic acids in sensing of protein-DNA interactions, in covalent cross-linking to DNA-binding proteins ,and in modulation of protein-DNA binding and transcription. Several environment-sensitive fluorescent nucleotides were incorporated to DNA probes which responded to protein binding by light-up, changing of color, or lifetime of fluorescence. Using a cyclodextrin-peptide transporter, fluorescent nucleotides can be transported through the cell membrane and incorporated to genomic DNA. Several dNTPs bearing reactive groups (i.e., vinylsulfonamide or chloroacetamide) were used for polymerase synthesis of DNA reactive probes which cross-link to Cys, His, or Lys in peptides or proteins. An attractive challenge is to use DNA modifications and bioorthogonal reactions in the major groove of DNA for modulation and switching of protein-DNA interactions. We have systematically explored the influence of major-groove modifications on recognition and cleavage of DNA by restriction endonucleases and constructed simple chemical switches of DNA cleavage. Systematic study of the influence of major-groove modifications on transcription with bacterial RNA polymerases revealed not only that some modified bases are tolerated, but also that the presence of 5-hydroxymethyluracil or -cytosine can even enhance the transcription (350 or 250% compared to native DNA). Based on these results, we have constructed the first chemical switch of transcription based on photocaging of hydroxymethylpyrimidines in DNA by 2-nitrobenzyl protection (transcription off), photochemical deprotection of the DNA (transcription on), and enzymatic phosphorylation (only for 5-hydroxymethyluracil, transcription off). Although it has been so far demonstrated only in vitro, it is the proof-of-principle first step toward chemical epigenetics.

• MeSH
• DNA řízené RNA-polymerasy chemie   MeSH
• DNA sondy chemická syntéza   chemie   účinky záření   MeSH
• DNA vazebné proteiny chemie   metabolismus   MeSH
• DNA-dependentní DNA-polymerasy chemie   MeSH
• DNA chemická syntéza   metabolismus   MeSH
• genetická transkripce účinky léků   účinky záření   MeSH
• ribonukleotidy chemie   MeSH
• světlo MeSH
• vazba proteinů účinky léků   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA řízené RNA-polymerasy MeSH
• DNA sondy MeSH
• DNA vazebné proteiny MeSH
• DNA-dependentní DNA-polymerasy MeSH
• DNA MeSH
• ribonukleotidy MeSH

Macrophages play key roles in the immune systems of humans and other mammals. Here, we performed single-cell analyses of the mRNAs and proteins of human macrophages to compare their responses to the signaling molecules lipopolysaccharide (LPS), a component of Gram-negative bacteria, and palmitate (PAL), a free fatty acid. We found that, although both molecules signal through the cell surface protein Toll-like receptor 4 (TLR4), they stimulated the expression of different genes, resulting in specific pro- and anti-inflammatory cellular states for each signal. The effects of the glucocorticoid receptor, which antagonizes LPS signaling, and cyclic AMP-dependent transcription factor 3, which inhibits PAL-induced inflammation, on inflammatory response seemed largely determined by digital on-off events. Furthermore, the quantification of transcriptional variance and signaling entropy enabled the identification of cell state-specific deregulated molecular pathways. These data suggest that the preservation of signaling in distinct cells might confer diversity on macrophage populations essential to maintaining major cellular functions.

• MeSH
• analýza jednotlivých buněk metody   MeSH
• genetická transkripce účinky léků   genetika   MeSH
• genetická variace genetika   MeSH
• homeostáza genetika   MeSH
• interleukin-1beta genetika   MeSH
• interleukin-8 genetika   MeSH
• lidé MeSH
• lipopolysacharidy farmakologie   MeSH
• makrofágy cytologie   účinky léků   metabolismus   MeSH
• palmitany farmakologie   MeSH
• regulace genové exprese účinky léků   MeSH
• signální transdukce účinky léků   genetika   MeSH
• THP-1 buňky MeSH
• toll-like receptor 4 genetika   MeSH
• transkripční faktor ATF3 genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• interleukin-1beta MeSH
• interleukin-8 MeSH
• lipopolysacharidy MeSH
• palmitany MeSH
• toll-like receptor 4 MeSH
• transkripční faktor ATF3 MeSH

Auxin phytohormones control most aspects of plant development through a complex and interconnected signaling network. In the presence of auxin, AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors are targeted for degradation by the SKP1-CULLIN1-F-BOX (SCF) ubiquitin-protein ligases containing TRANSPORT INHIBITOR RESISTANT 1/AUXIN SIGNALING F-BOX (TIR1/AFB). CULLIN1-neddylation is required for SCFTIR1/AFB functionality, as exemplified by mutants deficient in the NEDD8-activating enzyme subunit AUXIN-RESISTANT 1 (AXR1). Here, we report a chemical biology screen that identifies small molecules requiring AXR1 to modulate plant development. We selected four molecules of interest, RubNeddin 1 to 4 (RN1 to -4), among which RN3 and RN4 trigger selective auxin responses at transcriptional, biochemical, and morphological levels. This selective activity is explained by their ability to consistently promote the interaction between TIR1 and a specific subset of AUX/IAA proteins, stimulating the degradation of particular AUX/IAA combinations. Finally, we performed a genetic screen using RN4, the RN with the greatest potential for dissecting auxin perception, which revealed that the chromatin remodeling ATPase BRAHMA is implicated in auxin-mediated apical hook development. These results demonstrate the power of selective auxin agonists to dissect auxin perception for plant developmental functions, as well as offering opportunities to discover new molecular players involved in auxin responses.

• Klíčová slova
• auxin, chemical biology, hormone perception, prohormone, selective agonist,
• MeSH
• Arabidopsis genetika   metabolismus   MeSH
• F-box proteiny metabolismus   MeSH
• genetická transkripce účinky léků   MeSH
• geneticky modifikované rostliny genetika   MeSH
• kyseliny indoloctové metabolismus   MeSH
• protein NEDD8 genetika   MeSH
• proteinligasy komplexu SCF metabolismus   MeSH
• proteiny huseníčku genetika   metabolismus   MeSH
• proteolýza * MeSH
• receptory buněčného povrchu metabolismus   MeSH
• regulace genové exprese u rostlin MeSH
• regulátory růstu rostlin genetika   metabolismus   MeSH
• semenáček metabolismus   MeSH
• signální transdukce MeSH
• transkripční faktory metabolismus   MeSH
• vývoj rostlin genetika   fyziologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Názvy látek
• F-box proteiny MeSH
• indoleacetic acid MeSH Prohlížeč
• kyseliny indoloctové MeSH
• protein NEDD8 MeSH
• proteinligasy komplexu SCF MeSH
• proteiny huseníčku MeSH
• receptory buněčného povrchu MeSH
• regulátory růstu rostlin MeSH
• transkripční faktory MeSH

The aim of current study was to evaluate the effect of the most common anthocyanidins (cyanidin, delphinidin, malvidin, pelargonidin, and peonidin) on the transcriptional activity of steroid and nuclear receptors. The activities of steroid receptors - progesterone receptor (PR), estrogen receptor (ER), androgen receptor (AR), glucocorticoid receptor (GR), and nuclear receptors - vitamin D receptor (VDR), retinoid X receptor (RXR), retinoic acid receptor (RAR), pregnane X receptor (PXR), and thyroid receptor (TR) were assessed using either stable transfected luciferase gene reporter cell lines or transiently transfected cell lines. The cytotoxicity assays and gene reporter assays were performed after the 24-h treatment of cells with increasing range of concentrations (10 nM to 50 µM) of selected anthocyanidins. The results of experiments indicate that none of the examined anthocyanidins in all tested concentrations caused remarkable changes of transcriptional activity of studied steroid receptors, but their increasing concentrations slightly inhibited transcriptional activity of nuclear receptors induced by model agonists.

• Klíčová slova
• Anthocyanidins, nuclear receptors, steroid receptors, transcriptional activity,
• MeSH
• anthokyaniny farmakologie   MeSH
• genetická transkripce účinky léků   MeSH
• lidé MeSH
• nádorové buňky kultivované MeSH
• receptory cytoplazmatické a nukleární genetika   MeSH
• steroidní receptory genetika   MeSH
• viabilita buněk účinky léků   MeSH
• vztah mezi dávkou a účinkem léčiva MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• anthokyaniny MeSH
• receptory cytoplazmatické a nukleární MeSH
• steroidní receptory MeSH