Most antibiotics are natural compounds or their derivatives, and bacteria have evolved defensive mechanisms to resist them. Many of these mechanisms are still poorly understood or unknown. This study reveals that in Bacillus subtilis, the transcription factor HelD increases resistance to rifampicin by protecting its target, RNA polymerase (RNAP). This protection is mediated by the HelD N-terminal domain that penetrates into RNAP to the close vicinity of the rifampicin binding pocket. Importantly, the bacterium detects low rifampicin levels using a unique regulatory system involving two convergent promoters with finely tuned kinetic properties. In the absence of rifampicin, the stronger antisense promoter inhibits transcription from the sense promoter. In the presence of subinhibitory rifampicin concentration, the antisense promoter is more likely to encounter rifampicin-bound RNAP. This relieves the repression from the sense promoter, increasing its transcription by almost two orders of magnitude, boosting helD expression. A similar two-promoter arrangement also controls the pps gene, which encodes a rifampicin-modifying enzyme. These findings define a widespread bacterial response system sensitive to rifampicin, as this dual-promoter architecture is conserved across many bacterial species and found upstream of genes potentially involved in rifampicin resistance, such as those for hydrolases, transporters, and transferases.

Astringency is a multimodal sensory experience resulting from complex interactions between chemical compounds and the oral environment, involving tactile, chemosensory and thermosensory pathways. Recent human studies have examined the role of the polymodal transient receptor potential (TRP) channels TRPV1 and TRPA1 in astringency perception; however, other thermo- and mechanosensitive TRP channels expressed in oral epithelial cells and in trigeminal neurons innervating the mouth and tongue may also contribute to this complex sensation. This study explored the effects of structurally distinct representatives of astringent compounds on TRPV2 and TRPC5 channels. Using patch-clamp electrophysiology, microfluorimetry, molecular modeling, and mutagenesis, we show that the auto-oxidation products of the most abundant green tea polyphenol (-)-epigallocatechin-3-gallate (oxi-EGCG) significantly increase the activation of rat TRPV2 while blocking the human orthologue. The plant-derived isoflavone genistein, but not its glycoside form genistin, potentiated human TRPV2 and sensitized TRPC5-mediated currents activated by depolarizing voltage and the alpha subunit of G-proteins. Tannic acid, another astringent substance, potentiated rat TRPV2 and inhibited human TRPV2 and TRPC5. Furthermore, we show that both channels can interact with mucin 1, a transmembrane glycoprotein present in the native oral environment. Our data also provide the first evidence of heat-induced activation of human TRPV2. Considering previous evidence for TRPV2 and TRPC5 expression in the oral cavity and their roles in oral pain and cancer, our findings indicate that these polymodal channels may participate not only in detecting specific astringent compounds, but also in mediating their broader health-related and anesthetic actions.

Objective Transgenic mice with fluorescent protein (FP) reporters take full advantage of new in vivo imaging technologies. Therefore, we generated a TRPC5- and a TRPA1-reporter mouse based on FP C-terminal fusion, providing us with better alternatives for studying the physiology, interaction and coeffectors of these two TRP channels at the cellular and tissue level. Methods We generated transgenic constructs of the murine TRPC5- and TRPA1-gene with a 3*GGGGS linker and C-terminal fusion to mCherry and mTagBFP, respectively. We microinjected zygotes to generate reporter mice. Reporter mice were examined for visible fluorescence in trigeminal ganglia with two-photon microscopy, immunohistochemistry and calcium imaging. Results Both TRPC5-mCherry and TRPA1-mTagBFP knock-in mouse models were successful at the DNA and RNA level. However, at the protein level, TRPC5 resulted in no mCherry fluorescence. In contrast, sensory neurons derived from the TRPA1-reporter mice exhibited visible mTag-BFP fluorescence, although TRPA1 had apparently lost its ion channel function. Conclusions Creating transgenic mice with a TRP channel tagged at the C-terminus with a FP requires detailed investigation of the structural and functional consequences in a given cellular context and fine-tuning the design of specific constructs for a given TRP channel subtype. Different degrees of functional impairment of TRPA1 and TRPC5 constructs suggest a specific importance of the distal C-terminus for the regulation of these two channels in trigeminal neurons.

Ultra-thin, densely packed polymer brushes (PBs) with ultra-low fouling properties play a crucial role in recent developments of surface modification strategies for biomedical and biosensing technologies. However, micro-defects within PB structures can significantly impair their ultra-low fouling performance, thereby reducing their effectiveness and the application potential. Reliable detection of these micro-defects is essential for further evaluation and optimization of brush-based surfaces. In this study, we present a straightforward spectroscopic method for detection of micro-defects in PBs using Raman mapping. We employed random copolymer brushes of carboxybetaine methacrylamide (CBMAA) and N-(2-hydroxypropyl) methacrylamide (HPMAA) as examples of state-of-the-art ultra-low fouling PB systems prepared on a surface-enhanced Raman scattering (SERS)-active Ag nano-island layer fabricated on Au-coated glass substrates. Methylene blue, drop-deposited on the PB surface, is demonstrated as a suitable reporter molecule, providing spectroscopic information via both Raman and fluorescence signals. Analysis of the spectroscopic maps enabled not only the detection of micro-defects but also the differentiation between "shallow" and "deep" defects, providing detailed insights into the structural integrity of ultra-low fouling PBs.

We describe the photochemical generation of an alkoxycarbonylnitrene species in a supramolecular capsule and its reactivity. 2-Adamantyl-carbonazidate was co-crystallized in a supramolecular capsule consisting of two α-cyclodextrins (α-CDs) interacting through a hydrogen bond network. Irradiation of the co-crystal with UV light (254 nm) in the solid state or in suspension resulted in the extrusion of a nitrogen molecule and the corresponding nitrene formation inside the capsule. This reactive species provides selective C-H amination of the capsule wall, specifically at carbon 5 of the α-CD unit. The supramolecular assembly fixes the geometry of both reactants, the nitrene and the C-H bond, in line, mimicking the transition state for the triplet nitrene H-atom-abstraction reaction. Enantioselective intramolecular formation of a minor product, a carbamate, occurring concomitantly in the CD capsule, helps clarify the mechanisms of C-H amination reactions.

The vaccinia virus (VACV) is a prototypical poxvirus that was originally used to eradicate smallpox. Half a century ago, investigation into VACV mRNA substantially contributed to the fundamental discovery of the 5' mRNA cap, a hallmark of all eukaryotic and many viral mRNAs. VACV research also facilitated the identification and understanding of the general mechanism of 5' mRNA cap synthesis. We analyzed VACV transcripts at the level of individual mRNA molecules using a modified 5' RACE method. Our results demonstrate that VACV mRNAs containing long nontemplated 5' poly(A) leaders lack the 5' cap structure in vivo. The probability of the m7G cap occurrence decreases with the increasing number of nontemplated adenosines in the 5' poly(A) leader. Although half of VACV mRNAs with a single nontemplated adenosine still contain the m7G cap, only about 4% of viral mRNAs with leaders consisting of six or more nontemplated adenosines retain the cap. Uncapped mRNA can be transcribed from all genes containing adenosine-rich initiator sequences (INR) within their promoters. Early genes with INR still produce mostly capped transcripts (40%-59%, depending on the gene). However, intermediate mRNAs are less capped (11%-56%) and late mRNAs are mostly uncapped (0%-10% of capped mRNAs, depending on the gene).

13C NMR spectroscopic analyses of Cs symmetric guest molecules in the cyclodextrin host cavity, combined with molecular modelling and solid-state X-ray analysis, provides a detailed description of the spatial arrangement of cyclodextrin host–guest complexes in solution. The chiral cavity of the cyclodextrin molecule creates an anisotropic environment for the guest molecule resulting in a splitting of its prochiral carbon signals in 13C NMR spectra. This signal split can be correlated to the distance of the guest atoms from the wall of the host cavity and to the spatial separation of binding sites preferred by pairs of prochiral carbon atoms. These measurements complement traditional solid-state analyses, which rely on the crystallization of host–guest complexes and their crystallographic analysis.

Lysophosphatidylcholine (LPC) is a bioactive lipid present at high concentrations in inflamed and injured tissues where it contributes to the initiation and maintenance of pain. One of its important molecular effectors is the transient receptor potential canonical 5 (TRPC5), but the explicit mechanism of the activation is unknown. Using electrophysiology, mutagenesis and molecular dynamics simulations, we show that LPC-induced activation of TRPC5 is modulated by xanthine ligands and depolarizing voltage, and involves conserved residues within the lateral fenestration of the pore domain. Replacement of W577 with alanine (W577A) rendered the channel insensitive to strong depolarizing voltage, but LPC still activated this mutant at highly depolarizing potentials. Substitution of G606 located directly opposite position 577 with tryptophan rescued the sensitivity of W577A to depolarization. Molecular simulations showed that depolarization widens the lower gate of the channel and this conformational change is prevented by the W577A mutation or removal of resident lipids. We propose a gating scheme in which depolarizing voltage and lipid-pore helix interactions act together to promote TRPC5 channel opening.

Gyrophoric acid (GA), a lichen secondary metabolite, has attracted more attention during the last years because of its potential biological effects. Until now, its effect in vivo has not yet been demonstrated. The aim of our study was to evaluate the basic physicochemical and pharmacokinetic properties of GA, which are directly associated with its biological activities. The stability of the GA in various pH was assessed by conducting repeated UV-VIS spectral measurements. Microsomal stability in rat liver microsomes was performed using Ultra-Performance LC/MS. Binding to human serum albumin (HSA) was assessed using synchronous fluorescence spectra, and molecular docking analysis was used to reveal the binding site of GA to HSA. In the in vivo experiment, 24 Sprague-Dawley rats (Velaz, Únetice, Czech Republic) were used. The animals were divided as follows. The first group (n = 6) included healthy males as control intact rats (♂INT), and the second group (n = 6) included healthy females as controls (♀INT). Groups three and four (♂GA/n = 6 and ♀GA/n = 6) consisted of animals with daily administered GA (10 mg/kg body weight) in an ethanol-water solution per os for a one-month period. We found that GA remained stable under various pH and temperature conditions. It bonded to human serum albumin with the binding constant 1.788 × 106 dm3mol−1 to reach the target tissue via this mechanism. In vivo, GA did not influence body mass gain, food, or fluid intake during the experiment. No liver toxicity was observed. However, GA increased the rearing frequency in behavioral tests (p < 0.01) and center crossings in the elevated plus-maze (p < 0.01 and p < 0.001, respectively). In addition, the time spent in the open arm was prolonged (p < 0.01 and p < 0.001, respectively). Notably, GA was able to pass through the blood–brain barrier, indicating its ability to permeate into the brain and to stimulate neurogenesis in the hilus and subgranular zone of the hippocampus. These observations highlight the potential role of GA in influencing brain function and neurogenesis.

The transient receptor potential ion channel TRPA1 is a Ca2+-permeable nonselective cation channel widely expressed in sensory neurons, but also in many nonneuronal tissues typically possessing barrier functions, such as the skin, joint synoviocytes, cornea, and the respiratory and intestinal tracts. Here, the primary role of TRPA1 is to detect potential danger stimuli that may threaten the tissue homeostasis and the health of the organism. The ability to directly recognize signals of different modalities, including chemical irritants, extreme temperatures, or osmotic changes resides in the characteristic properties of the ion channel protein complex. Recent advances in cryo-electron microscopy have provided an important framework for understanding the molecular basis of TRPA1 function and have suggested novel directions in the search for its pharmacological regulation. This chapter summarizes the current knowledge of human TRPA1 from a structural and functional perspective and discusses the complex allosteric mechanisms of activation and modulation that play important roles under physiological or pathophysiological conditions. In this context, major challenges for future research on TRPA1 are outlined.

Recently published in vivo observations have highlighted the presence of cruciform structures within the genome, suggesting their potential significance in the rapid recognition of the target sequence for transcription factor binding. In this in vitro study, we investigate the organization and stability of the sense (coding) strand within the Serum Response Element of the c-Fos gene promoter (c-Fos SRE), specifically focusing on segments spanning 12 to 36 nucleotides, centered around the CArG-box. Through a thorough examination of UV absorption patterns with varying temperatures, we identified the emergence of a remarkably stable structure, which we conclusively characterized as a hairpin using complementary 1H NMR experiments. Our research decisively ruled out the formation of homoduplexes, as confirmed by supplementary fluorescence experiments. Utilizing molecular dynamics simulations with atomic distance constraints derived from NMR data, we explored the structural intricacies of the compact hairpin. Notably, the loop consisting of the six-membered A/T sequence demonstrated substantial stabilization through extensive stacking, non-canonical inter-base hydrogen bonding, and hydrophobic clustering of thymine methyl groups. These findings suggest the potential of the c-Fos SRE to adopt a cruciform structure (consisting of two opposing hairpins), potentially providing a topological recognition site for the SRF transcription factor under cellular conditions. Our results should inspire further biochemical and in vivo studies to explore the functional implications of these non-canonical DNA structures.

The sigma H (σΗ) and sigma E (σE) subunits of Corynebacterium glutamicum RNA polymerase belong to Group 4 of sigma factors, also called extracytoplasmic function (ECF) sigma factors. Genes of the C. glutamicum σΗ regulon that are involved in heat and oxidative stress response have already been defined, whereas the genes of the σE regulon, which is involved in cell surface stress response, have not been explored until now. Using the C. glutamicum RES167 strain and its derivative C. glutamicum ΔcseE with a deletion in the anti-σΕ gene, differential gene expression was analyzed by RNA sequencing. We found 296 upregulated and 398 downregulated genes in C. glutamicum ΔcseE compared to C. glutamicum RES167. To confirm the functional link between σΕ and the corresponding promoters, we tested selected promoters using the in vivo two-plasmid system with gfpuv as a reporter gene and by in vitro transcription. Analyses with RNAP+σΗ and RNAP+σΕ, which were previously shown to recognize similar promoters, proved that the σΗ and σE regulons significantly overlap. The σE-controlled genes were found to be involved for example in protein quality control (dnaK, dnaJ2, clpB, and clpC), the regulation of Clp proteases (clgR), and membrane integrity maintenance. The single-promoter analyses with σΗ and σΕ revealed that there are two groups of promoters: those which are exclusively σΗ-specific, and the other group of promoters, which are σΗ/σE-dependent. No exclusively σE-dependent promoter was detected. We defined the consensus sequences of exclusively σΗ-regulated promotors to be −35 GGAAt and − 10 GTT and σΗ/σE-regulated promoters to be −35 GGAAC and − 10 cGTT. Fifteen genes were found to belong to the σΗ/σΕ regulon. Homology modeling showed that there is a specific interaction between Met170 in σΗ and the nucleotides −31 and − 30 within the non-coding strand (AT or CT) of the σΗ-dependent promoters. In σE, Arg185 was found to interact with the nucleotides GA at the same positions in the σE-dependent promoters.

Katanin is an ATP-dependent microtubule severing enzyme involved in neuronal development and function. Neurodegeneration-related protein tau cooperatively forms dense envelopes on microtubules. These envelopes can protect the microtubule lattice from katanin-induced microtubule disassembly. Neurodegenerative processes and aging are accompanied by changes in the level of intracellular ATP, however, how is katanin-tau interplay regulated by ATP level is unclear. Here we show that in presence of katanin, ATP decrease causes enhanced disassembly of tau envelope-coated microtubules. Performing katanin-driven severing experiments at 3 and 10 mM ATP, we found that katanin ATP-ase activity on bare microtubules was identical. However, counterintuitively, in presence of tau envelopes, katanin severed microtubules significantly faster in the presence of 3 mM ATP compared to the increased ATP level. These results suggest that the protective function of tau envelopes is ATP-dependent, and links decreased ATP levels with microtubule disassembly.

Atranorin (ATR) is a secondary metabolite of lichens. While previous studies investigated the effects of this substance predominantly in an in vitro environment, in our study we investigated the basic physicochemical properties, the binding affinity to human serum albumin (HSA), basic pharmacokinetics, and, mainly, on the systematic effects of ATR in vivo. Sporadic studies describe its effects during, predominantly, cancer. This project is original in terms of testing the efficacy of ATR on a healthy organism, where we can possibly attribute negative effects directly to ATR and not to the disease. For the experiment, 24 Sprague Dawley rats (Velaz, Únetice, Czech Republic) were used. The animals were divided into four groups. The first group (n = 6) included healthy males as control intact rats (♂INT) and the second group (n = 6) included healthy females as control intact rats (♀INT). Groups three and four (♂ATR/n = 6 and ♀ATR/n = 6) consisted of animals with daily administered ATR (10mg/kg body weight) in an ethanol–water solution per os for a one-month period. Our results demonstrate that ATR binds to HSA near the binding site TRP214 and acts on a systemic level. ATR caused mild anemia during the treatment. However, based on the levels of hepatic enzymes in the blood (ALT, ALP, or bilirubin levels), thiobarbituric acid reactive substances (TBARS), or liver histology, no impact on liver was recorded. Significantly increased creatinine and lactate dehydrogenase levels together with increased defecation activity during behavioral testing may indicate the anabolic effect of ATR in skeletal muscles. Interestingly, ATR changed some forms of behavior. ATR at a dose of 10 mg/kg body weight is non-toxic and, therefore, could be used in further research.

Polycyclic compounds with N-methyl substitution, structurally related to Amaryllidaceae alkaloids, have been synthesised, together with their analogues bearing a quaternary nitrogen atom. To prevent the lone electron pair of the nitrogen from interfering with the reaction sequence, two approaches to the synthesis were investigated: N-oxidation and Boc protection of the nitrogen. The second method was more successful due to the limited stability of N-oxides in the halocyclisation step. An asymmetric version of the synthesis was also developed for this type of compounds. The prepared products were tested in vitro for their cholinesterase inhibitory activity and the results were rationalised by molecular docking studies with human acetylcholinesterase (hAChE) and butyrylcholinesterase (hBuChE). In general, our products were more active against BuChE than against AChE, and it was noted that larger ligands should be prepared for future studies, since in some cases acetylcholine can still fit into the active site along with the bound ligand.

Bacterial RNA polymerase (RNAP) is an essential multisubunit enzyme performing transcription.Regulation of this process is secured through the stage-dependent interactions of RNAP with different factors (mostly proteins).Here we report the structurefunction analysis of the functional complexes between RNAP and a unique helicase-like factor HelD [1] which is present in many Gram-positive bacteria (e.g.Bacillus subtilis and Mycobacterium smegmatis) [2, 3].HelD forms tightly bound complexes with RNAP.It simultaneously penetrates into RNAP primary and secondary channels which are responsible for nucleic acids binding and substrate delivery.HelD can also interact with the RNAP active site.Structurally, these interactions are incompatible with the binding of DNA to the RNAP core and thus with the elongation stage of transcription.This is in accordance to our functional data showing that HelD is capable of clearing RNAP of nucleic acids and that HelD can dismantle RNAP-DNA complexes.HelD itself is composed of several domains, showing structural changes in solution [2] as well as in complexes with RNAP (three different structural states obtained from the cryo-EM analysis) [3].Although we were able to link the observed dynamic behaviour with the DNA-clearing role of HelD, the recycling of HelD-bound RNAP and subsequent restart of transcription remains to be explained.HelD as well as its complexes with RNAP resisted our attempts to crystallize them for many years.In order to get to the structural details we took the advantage of recent developments in the field of single-particle cryo-EM and were able to obtain ~3Å resolution structures.The structure of HelD itself was completely unknown with no homologue in the PDB.We combined X-ray crystallography (structure of one domain) and cryo-EM, together with bioinformatics and homologous modelling and successfully built de novo a complete atomic model of the HelD protein.For the analysis of condition-dependent dynamic behaviour we used small-angle X-ray scattering [2].Results from our structural studies were supplemented with biochemical and biophysical assays (enzymology, analysis of interactions and stability) and by computational analyses [3].

Diffusion is the most fundamental mode of protein translocation within cells. Confined diffusion of proteins along the electrostatic potential constituted by the surface of microtubules, although modeled meticulously in molecular dynamics simulations, has not been experimentally observed in real-time. Here, we used interferometric scattering microscopy to directly visualize the movement of the microtubule-associated protein Ase1 along the microtubule surface at nanometer and microsecond resolution. We resolved millisecond confinements of Ase1 and fast leaps between these positions of dwelling preferentially occurring along the microtubule protofilaments, revealing Ase1’s mode of diffusive translocation along the microtubule’s periodic surface. The derived interaction potential closely matches the tubulin-dimer periodicity and the distribution of the electrostatic potential on the microtubule lattice. We anticipate that mapping the interaction landscapes for different proteins on microtubules, finding plausible energetic barriers of different positioning and heights, will provide valuable insights into regulating the dynamics of essential cytoskeletal processes, such as intracellular cargo trafficking, cell division, and morphogenesis, all of which rely on diffusive translocation of proteins along microtubules.