Bacteria have evolved structured RNAs that can associate with RNA polymerase (RNAP). Two of them have been known so far-6S RNA and Ms1 RNA but it is unclear if any other types of RNAs binding to RNAP exist in bacteria. To identify all RNAs interacting with RNAP and the primary σ factors, we have established and performed native RIP-seq in Bacillus subtilis, Corynebacterium glutamicum, Streptomyces coelicolor, Mycobacterium smegmatis and the pathogenic Mycobacterium tuberculosis. Besides known 6S RNAs in B. subtilis and Ms1 in M. smegmatis, we detected MTS2823, a homologue of Ms1, on RNAP in M. tuberculosis. In C. glutamicum, we discovered novel types of structured RNAs that associate with RNAP. Furthermore, we identified other species-specific RNAs including full-length mRNAs, revealing a previously unknown landscape of RNAs interacting with the bacterial transcription machinery.

• MeSH
• Bacillus subtilis genetika   metabolismus   MeSH
• bakteriální proteiny * metabolismus   genetika   MeSH
• bakteriální RNA * metabolismus   genetika   MeSH
• Corynebacterium glutamicum genetika   metabolismus   MeSH
• DNA řízené RNA-polymerasy * metabolismus   genetika   MeSH
• genetická transkripce MeSH
• konformace nukleové kyseliny MeSH
• Mycobacterium smegmatis genetika   metabolismus   enzymologie   MeSH
• Mycobacterium tuberculosis genetika   metabolismus   MeSH
• nekódující RNA MeSH
• regulace genové exprese u bakterií MeSH
• sigma faktor * metabolismus   genetika   MeSH
• Streptomyces coelicolor genetika   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Rifampicin is a clinically important antibiotic that binds to, and blocks the DNA/RNA channel of bacterial RNA polymerase (RNAP). Stalled, nonfunctional RNAPs can be removed from DNA by HelD proteins; this is important for maintenance of genome integrity. Recently, it was reported that HelD proteins from high G+C Actinobacteria, called HelR, are able to dissociate rifampicin-stalled RNAPs from DNA and provide rifampicin resistance. This is achieved by the ability of HelR proteins to dissociate rifampicin from RNAP. The HelR-mediated mechanism of rifampicin resistance is discussed here, and the roles of HelD/HelR in the transcriptional cycle are outlined. Moreover, the possibility that the structurally similar HelD proteins from low G+C Firmicutes may be also involved in rifampicin resistance is explored. Finally, the discovery of the involvement of HelR in rifampicin resistance provides a blueprint for analogous studies to reveal novel mechanisms of bacterial antibiotic resistance.

• MeSH
• antibakteriální látky farmakologie   MeSH
• Bacteria * genetika   metabolismus   MeSH
• bakteriální léková rezistence MeSH
• DNA řízené RNA-polymerasy genetika   metabolismus   MeSH
• DNA MeSH
• rifampin * farmakologie   MeSH
• Publikační typ
• časopisecké články MeSH

Successful surgeries involving orthopedic implants depend on the avoidance of biofilm development on the implant surface during the early postoperative period. Here, we investigate the potential of novel antibacterial compounds-second-generation lipophosphonoxins (LPPOs II)-as additives to surgical bone cements. We demonstrate (i) excellent thermostability of LPPOs II, which is essential to withstand elevated temperatures during exothermic cement polymerization; (ii) unchanged tensile strength and elongation at the break properties of the composite cements containing LPPOs II compared to cements without additives; (iii) convenient elution kinetics on the order of days; and (iv) the strong antibiofilm activity of the LPPO II-loaded cements even against bacteria resistant to the medicinally utilized antibiotic, gentamicin. Thus, LPPOs II display promising potential as antimicrobial additives to surgical bone cements.

• Klíčová slova
• lipofosfonoxiny,
• MeSH
• antiinfekční látky * analýza   terapeutické užití   MeSH
• biofilmy MeSH
• grampozitivní bakterie MeSH
• hydrofobní a hydrofilní interakce MeSH
• iminosacharidy analýza   terapeutické užití   MeSH
• infekce spojené s protézou prevence a kontrola   MeSH
• kostní cementy * analýza   terapeutické užití   MeSH
• lidé MeSH
• mikrobiální testy citlivosti metody   MeSH
• nukleosidy analýza   terapeutické užití   MeSH
• organofosfonáty analýza   terapeutické užití   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• hodnotící studie MeSH
• práce podpořená grantem MeSH

A strategy for complete backbone and side-chain resonance assignment of disordered proteins with highly repetitive sequence is presented. The protocol is based on three resolution-enhanced NMR experiments: 5D HN(CA)CONH provides sequential connectivity, 5D HabCabCONH is utilized to identify amino acid types, and 5D HC(CC-TOCSY)CONH is used to assign the side-chain resonances. The improved resolution was achieved by a combination of high dimensionality and long evolution times, allowed by non-uniform sampling in the indirect dimensions. Random distribution of the data points and Sparse Multidimensional Fourier Transform processing were used. Successful application of the assignment procedure to a particularly difficult protein, δ subunit of RNA polymerase from Bacillus subtilis, is shown to prove the efficiency of the strategy. The studied protein contains a disordered C-terminal region of 81 amino acids with a highly repetitive sequence. While the conventional assignment methods completely failed due to a very small differences in chemical shifts, the presented strategy provided a complete backbone and side-chain assignment.

• MeSH
• algoritmy MeSH
• deuterium MeSH
• Fourierova analýza MeSH
• izotopy dusíku MeSH
• izotopy uhlíku MeSH
• molekulární sekvence - údaje MeSH
• nukleární magnetická rezonance biomolekulární metody   MeSH
• proteiny chemie   MeSH
• repetitivní sekvence nukleových kyselin MeSH
• sekundární struktura proteinů MeSH
• sekvence aminokyselin MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

S3EPY is a Python extension to the program Sparky written to facilitate the assessment of coupling constants from in-phase/antiphase and spin-state-selective excitation (S(3)E) experiments. It enables the routine use of small scalar couplings by automating the coupling evaluation procedure. S3EPY provides an integrated graphical user interface to programs which outputs graphs and the table of determined couplings.

• MeSH
• Bacillus subtilis enzymologie   MeSH
• DNA řízené RNA-polymerasy chemie   MeSH
• nukleární magnetická rezonance biomolekulární metody   MeSH
• software MeSH
• uživatelské rozhraní počítače MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Bacterial elongation factor Tu (EF-Tu) is a model monomeric G protein composed of three covalently linked domains. Previously, we evaluated the contributions of individual domains to the thermostability of EF-Tu from the thermophilic bacterium Bacillus stearothermophilus. We showed that domain 1 (G-domain) sets up the basal level of thermostability for the whole protein. Here we chose to locate the thermostability determinants distinguishing the thermophilic domain 1 from a mesophilic domain 1. By an approach of systematically swapping protein regions differing between G-domains from mesophilic Bacillus subtilis and thermophilic B. stearothermophilus, we demonstrate that a small portion of the protein, the N-terminal 12 amino acid residues, plays a key role in the thermostability of this domain. We suggest that the thermostabilizing effect of the N-terminal region could be mediated by stabilizing the functionally important effector region. Finally, we demonstrate that the effect of the N-terminal region is significant also for the thermostability of the full-length EF-Tu.

• MeSH
• Bacillus subtilis genetika   MeSH
• elongační faktor Tu genetika   chemie   MeSH
• Geobacillus stearothermophilus genetika   MeSH
• molekulární modely MeSH
• molekulární sekvence - údaje MeSH
• sekvence aminokyselin MeSH
• stabilita proteinů účinky léků   MeSH
• terciární struktura proteinů genetika   MeSH
• vysoká teplota MeSH
• Publikační typ
• práce podpořená grantem MeSH

We identify here a pattern in the transcription start sites (+1A or +1G) of sigma(A)-dependent promoters of genes that are up-/downregulated in response to amino acid starvation (stringent response) in Bacillus subtilis. Upregulated promoters initiate mostly with ATP and downregulated promoters with GTP. These promoters appear to be sensitive to changes in initiating nucleoside triphosphate concentrations. During the stringent response in B. subtilis, when ATP and GTP levels change reciprocally, the identity of the +1 position (A or G) of these promoters is a factor important in their regulation. Mutations that change the identity of position +1 (A for G and vice versa) change the response of the promoter to amino acid starvation.

• MeSH
• aminokyseliny metabolismus   MeSH
• Bacillus subtilis genetika   metabolismus   MeSH
• bakteriální proteiny genetika   MeSH
• financování organizované MeSH
• genetická transkripce MeSH
• nukleotidy metabolismus   MeSH
• počátek transkripce MeSH
• promotorové oblasti (genetika) MeSH
• regulace genové exprese u bakterií MeSH
• sekvence nukleotidů MeSH
• sekvenční seřazení MeSH

The ybxF gene is a member of the streptomycin operon in a wide range of gram-positive bacteria. In Bacillus subtilis, it codes for a small basic protein (82 amino acids, pI 9.51) of unknown function. We demonstrate that, in B. subtilis, YbxF localizes to the ribosome, primarily to the 50S subunit, with dependence on growth phase. Based on three-dimensional structures of YbxF generated by homology modeling, we identified helix 2 as important for the interaction with the ribosome. Subsequent mutational analysis of helix 2 revealed Lys24 as crucial for the interaction. Neither the B. subtilis ybxF gene nor its paralogue, the ymxC gene, is essential, as shown by probing DeltaybxF, DeltaymxC, or DeltaybxF DeltaymxC double deletion strains in several functional assays.

• MeSH
• Bacillus subtilis genetika   metabolismus   růst a vývoj   MeSH
• bakteriální geny MeSH
• bakteriální proteiny genetika   chemie   metabolismus   MeSH
• delece genu MeSH
• financování organizované MeSH
• fluorescenční mikroskopie MeSH
• molekulární modely MeSH
• mutace MeSH
• mutageneze cílená MeSH
• počítačová simulace MeSH
• rekombinantní fúzní proteiny genetika   chemie   metabolismus   MeSH
• ribozomy metabolismus   MeSH
• sekundární struktura proteinů MeSH
• vazba proteinů MeSH
• zelené fluorescenční proteiny genetika   metabolismus   MeSH

• Publikační typ
• abstrakt z konference MeSH

Local carriers of antibacterial (AB) compounds are used in the musculoskeletal (MS) infection therapy. High doses of antibiotics (ATB) have been added to bone cement (other materials). Now other AB compounds are looked for in the same indication due to disadvantages of ATB. Lipophosphonoxins (LPPOs) with a wide AB scope and a minimal risk of resistance development have been discovered in the Czech Republic recently. The goal of the proposed project is: 1) to test their ability to absorb on standard biomaterials used in orthopedics and traumatology (ORT-T); 2) to describe the modified material; including experiments on animals; 3) to test its toxicity/immunogenicity; 4) to modify the properties of current/to develop new LPPOs. Besides an excellent AB effect, the materials must meet all the requirements for biomaterials. Their clinical application will improve efficacy of the MS infections surgical therapy. In particular, they will decrease the rate of recurrent infection, morbidity/mortality in patients having ORT-T surgeries and decrease costs related to the therapy of MS infectio...

V terapii infekcí muskuloskeletálního (MS) aparátu používáme lokální nosiče antibakteriálních (AB) látek. Dosud jsme spoléhali na antibiotika (ATB), která se ve vysokých dávkách přidávala do kostního cementu (jiných materiálů). Vzhledem k nevýhodám ATB se hledají jiné AB látky ve stejné indikaci. V ČR byly nedávno objeveny lipofosfonoxiny (LPPO), které mají široký AB záběr a minimální riziko vzniku rezistence. Cílem navrhovaného projektu je: 1) ověřit jejich schopnost navázat se na standardní biomateriály používané v ortopedii a traumatologii (ORT-T); 2) popsat AB vlastnosti takto upraveného materiálu; včetně experimentu na zvířeti; 3) určit jeho toxicitu/ imunogenicitu; 4) upravit vlastnosti stávajících/vyvinout nové LPPO. Kromě excelentního AB efektu musí řešení splňovat všechny další nároky kladené na biomateriály. Jejich nasazením v klinické praxi se zlepší účinnost operační terapie infekcí MS aparátu. Konkrétně dojde k snížení četnosti recidiv infekce, snížení morbidity/mortality pacientů podstupujících ORT-T operace a snížení nákladů spojených s terapií infekcí MS aparátu.

• Klíčová slova
• lipofosfonoxiny,
• MeSH
• antibakteriální látky terapeutické užití   MeSH
• biokompatibilní materiály terapeutické užití   MeSH
• hodnocení léčiv MeSH
• infekce farmakoterapie   MeSH
• kontrola infekce metody   MeSH
• lidé MeSH
• muskuloskeletální nemoci farmakoterapie   prevence a kontrola   MeSH
• nosiče léků terapeutické užití   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• hodnotící studie MeSH

• Konspekt
• Patologie. Klinická medicína
• NLK Obory
• infekční lékařství
• ortopedie
• farmacie a farmakologie
• NLK Publikační typ
• závěrečné zprávy o řešení grantu AZV MZ ČR