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Comparative genomics and functional analysis of a highly adhesive dairy Lactobacillus paracasei subsp. paracasei IBB3423 strain
Get PDFarious Lactobacillus paracasei strains are found in diverse environments, including dairy and plant materials and the intestinal tract of humans and animals, and are also used in the food industry or as probiotics. In this study, we have isolated a new strain L. paracasei subsp. paracasei IBB3423 from samples of raw cow milk collected in a citizen science project. IBB3423 showed some desired probiotic features such as high adhesion capacity and ability to metabolize inulin. Its complete genome sequence comprising the chromosome of 3,183,386 bp and two plasmids of 5986 bp and 51,211 bp was determined. In silico analysis revealed numerous genes encoding proteins involved in carbohydrate metabolism and of extracellular localization likely supporting interaction with host tissues. In vitro tests confirmed the high adhesion capacity of IBB3423 and showed that it even exceeds that of the highly adhesive L. rhamnosus GG. Curing of the larger plasmid indicated that the adhesive properties depend on the plasmid and thus could be determined by its pilus-encoding spaCBA genes
Does the partial molar volume of a solute reflect the free energy of hydrophobic solvation?
Get PDFHalogenated heterocyclic ligands are widely used as the potent and frequently selective inhibitors of protein kinases. However, the exact contribution of the hydrophobic solvation of a free ligand is rarely accounted for the
balance of interactions contributing to the free energy of ligand binding. Herein, we propose a new experimental
method based on volumetric data to estimate the hydrophobicity of a ligand. We have tested this approach for a series of ten variously halogenated benzotriazoles, the binding affinity of which to the target protein kinase CK2
was assessed with the use of thermal shift assay. According to the hierarchical clustering procedure, the excess
volume, defined as the difference between the experimentally determined partial molar volume and the calculated in silico molecular volume, was found to be distant from any commonly used hydrophobicity descriptors of the ligand. The excess volume, however, properly predicts solute binding affinity. On the way, we have proved that the binding of halogenated benzotriazoles to the protein kinase CK2 is driven mostly by hydrophobic interaction
Insight into the Structural Dynamics of the Lysenin During Prepore-to-Pore Transition Using Hydrogen–Deuterium Exchange Mass Spectrometry
Get PDFLysenin is a pore-forming toxin of the aerolysin family, which is derived from coelomic fluid of the earthworm Eisenia fetida. Upon binding to sphingomyelin (SM)-containing membranes, lysenin undergoes a series of structural changes promoting the conversion of water-soluble monomers into oligomers, leading to its insertion into the membrane and the formation of a lytic β-barrel pore. The soluble monomer and transmembrane pore structures were recently described, but the underlying structural details of oligomerization remain unclear. To investigate the molecular mechanisms controlling the conformational rearrangements accompanying pore formation, we compared the hydrogen–deuterium exchange pattern between lyseninWT and its mutant lyseninV88C/Y131C. This mutation arrests lysenin oligomers in the prepore state at the membrane surface and does not affect the structural dynamics of the water-soluble form of lysenin. In contrast, membrane-bound lyseninV88C/Y131C exhibited increased structural stabilization, especially within the twisted β-sheet of the N-terminal domain. We demonstrated that the structural stabilization of the lysenin prepore started at the site of lysenin’s initial interaction with the lipid membrane and was transmitted to the twisted β-sheet of the N-terminal domain, and that lyseninV88C/Y131C was arrested in this conformation. In lyseninWT, stabilization of these regions drove the conformational changes necessary for pore formation
Climatic conditions at Arctowski Station (King George Island, West Antarctica) in 2013–2017 against the background of observed regional changes.
Get PDFMeteorological conditions at Arctowski Station during 2013–2017 were presented against the background of regional climate changes, especially air temperature decline. Air temperature, relative air humidity, air pressure, solar radiation, wind speed and direction, snow cover and precipitation were collected with an automatic weather station and manual measurements and were further analysed. The obtained results were compared with data from previous years and with data from other stations located on King George Island. Our observations confirm that the vicinity of Arctowski Station also experienced a decrease in air temperature during summer, which supports the hypothesis of regional cooling
RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution
Get PDFHolliday junctions (HJs) are four-way DNA structures that occur in DNA repair by homologous recombination. Specialized nucleases, termed resolvases, remove (i.e., resolve) HJs. The bacterial protein RuvC is a canonical resolvase that introduces two symmetric cuts into the HJ. For complete resolution of the HJ, the two cuts need to be tightly coordinated. They are also specific for cognate DNA sequences. Using a combination of structural biology, biochemistry, and a computational approach, here we show that correct positioning of the substrate for cleavage requires conformational changes within the bound DNA. These changes involve rare high-energy states with protein-ssisted base flipping that are readily accessible for the cognate DNA sequence but not for non-cognate sequences. These conformational changes and the relief of protein-induced structural tension of the DNA facilitate coordination between the two cuts. The unique DNA cleavage mechanism of RuvC demonstrates the importance of high-energy conformational states in nucleic acid readout
Potential of Lactobacillus plantarum IBB3036 and Lactobacillus salivarius IBB3154 to persistence in chicken after in ovo delivery
No full textThe aim of this study was to characterize and compare selected Lactobacillus strains originating from different environments (cow milk and hen feces) with respect to their applicative potential to colonize gastrointestinal track of chickens before hatching from an egg. In vitro phenotypic characterization of lactobacilli strains included the investigation of the important prerequisites for persistence in gastrointestinal tract, such as a capability to survive in the presence of bile salts and at low pH, enzymatic and sugar metabolic profiles, adhesion abilities, and resistance to osmolytes, temperature, and antibiotics. Regarding the resistance of lactobacilli to most of the various stress factors tested, the milk isolate Lactobacillus plantarum IBB3036 showed better abilities than the chicken feces isolate Lactobacillus salivarius IBB3154. However, regarding the acidification tolerance and adherence ability, L. salivarius IBB3154 revealed better characteristics. Use of these two selected lactobacilli isolates together with proper prebiotics resulted in the preparation of two S1 and S2 bioformulations, which were injected in ovo into hen Cobb500 FF fertilized eggs. Furthermore, in vivo tests assessing the persistence of L. plantarum IBB3036 and L. salivarius IBB3154 in the chicken gastrointestinal tract was monitored by PCR‐based classical and quantitative techniques and revealed the presence of both strains in fecal samples collected 3 days after hatching. Subsequently, the number of L. salivarius IBB3154 increased significantly in the chicken intestine, whereas the presence of L. plantarum IBB3036 was gradually decreased
High‐throughput sequencing approach in analysis of microbial communities colonizing natural gas pipelines
Get PDFThis study provides a deep modern insight into the phylogenetic diversity among bacterial consortia found in working and nonworking high‐methane natural gas pipelines located in Poland. The working pipeline was characterized by lower biodiversity (140–154 bacterial genera from 22 to 23 classes, depending on the source of the debris) in comparison to the off‐gas pipeline (169 bacterial genera from 23 classes). The sediment recovered from the working pipeline contained mostly DNA identified as belonging to the phylum Firmicutes (66.4%–45.9% operational taxonomic units [OTUs]), predominantly Bacillus (41.4%–31.1% OTUs) followed by Lysinibacillus (2.6%–1.5% OTUs) and Clostridium (2.4%–1.8% OTUs). In the nonworking pipeline, Proteobacteria (46.8% OTUs) and Cyanobacteria (27.8% OTUs) were dominant. Over 30% of the Proteobacteria sequences showed homologies to Gammaproteobacteria, with Pseudomonas (7.1%), Enhydrobacter (2.1%), Stenotrophomonas (0.5%), and Haempohilus (0.4%) among the others. Differences were noted in terms of the chemical compositions of deposits originating from the working and nonworking gas pipelines. The deposits from the nonworking gas pipeline contained iron, as well as carbon (42.58%), sulphur (15.27%), and oxygen (15.32%). This composition can be linked to both the quantity and type of the resident microorganisms. The presence of a considerable amount of silicon (17.42%), and of aluminum, potassium, calcium, and magnesium at detectable levels, may likewise affect the metabolic activity of the resident consortia in the working gas pipeline. All the analyzed sediments included both bacteria known for causing and intensifying corrosion (e.g., Pseudomonas, Desulfovibrio, Shewanella, Serratia) and bacteria that can protect the surface of pipelines against deterioration (e.g., Bacillus). Biocorrosion is not related to a single mechanism or one species of microorganism, but results from the multidirectional activity of multiple microbial communities. The analysis presented here of the state of the microbiome in a gas pipeline during the real gas transport is a particularly valuable element of this work
The Smooth Evolution of the Universal Genetic Code. Main Episodes
Get PDFThe possible scenario of the origin and evolution of genetic code is proposed, being primarily implicated
by the working hypothesis which states that the chronological order of amino acids evolutionary implementation
monotonically correlates with their increasing mass. It fulfills the minimalistic claim of the smallest changes of the
evolving system at increasing complexity, hereinafter called "the smooth evolution". The working hypothesis was
postulated concerning the results of statistical analysis indicating a strong correlation between amino acid mass and
the chosen parameters of contemporary genetic code, which are expected to change in a certain individual direction
during the evolution of the initial genetic system. It was additionally supplemented by the most common
hypotheses adopted from the literature, as stereochemical, 'frozen accident' and coevolutional. The developed
scenario allows a detailed description of the twenty-two consecutive episodes of the history of code definition and
the estimation of its dynamics. It reveals the main eras of evolution conditioned by the environmental and structural
constraints. It also lets the estimation of the evolutionary frequencies of codon sense expansion, and redefinition.
Dominating trends and amino acids were indicated. The underlying assumptions, limits, exceptions, and the future
of the code evolution have been discusse
Synergy between the alteration in the N-terminal region of butyrylcholinesterase K variant and apolipoprotein E4 in late-onset Alzheimer’s disease
Get PDFWhile the life expectancy of the population has increased, Alzheimer’s disease (AD) has emerged as
one of the greatest health problems of old age. AD is characterized by neuronal loss and cognitive
decline. In the AD brain, there is a decrease in levels of acetylcholinesterase (AChE) and an increase in
the levels of the related enzyme butyrylcholinesterase (BChE), that accumulate in plaques and tangles.
Apolipoprotein E (ApoE) is a major cholesterol carrier and plays an important role in maintaining
lipid homeostasis. APOE-ε4 constitutes the most important known genetic risk factor for late-onset
AD. It has been proposed that the BCHE-K allele (Ala539Thr) acts in synergy with the APOE-ε4
allele to promote risk for AD. However, there is insufcient evidence to support a correlation. Most
studies focused only on the coding regions of the genes. In this study, we analyzed sequence regions
beyond the BCHE coding sequence. We found synergy between APOE-ε4 and SNPs localized in 5′UTR
(rs1126680) and in intron 2 (rs55781031) of the BCHE-K allele (rs1803274) in 18% of patients with
late-onset AD (n=55). The results show that the coexistence of the APOE-ε4 allele and 3 SNPs in the
BCHE gene is associated with a highly elevated risk of late-onset AD. SNP (rs1126680) in 5′UTR of the
BCHE gene is located 32 nucleotides upstream of the 28 amino acid signal peptide. Mass spectrometry
analysis of the BChE protein produced by SNP (rs1126680) showed that the mutation caused an in
frame N-terminal extension of 41 amino acids of the BChE signal peptide. The resultant variant with a
69 amino acid signal peptide, designated N-BChE, may play a role in development of AD
UV-B Induces Chloroplast Movements in a Phototropin-Dependent Manner
Get PDFWe examined the impact of UV-B irradiation on chloroplast movements in Arabidopsis leaves. Directional chloroplast movements induced by blue light have been described in multiple plant species. In weak light, chloroplasts accumulate at periclinal cell walls to increase light capture. In strong light, chloroplasts exhibit the avoidance response, as they move towards anticlinal walls to protect the photosynthetic apparatus from light-induced damage. In Arabidopsis, chloroplast movements are triggered by phototropins, phot1 and phot2, which are known as blue/UV-A photoreceptors. We found that irradiation with UV-B of 3.3 µmol·m−2·s−1 induced chloroplast accumulation in wild-type plants. UV-B-triggered accumulation was dependent on the presence of phototropins, especially phot1, but not on UVR8 (the canonical UV-B photoreceptor). Irradiation with strong UV-B of 20 µmol·m−2·s−1 did not induce substantial chloroplast relocations in wild-type leaves. However, in the jac1 mutant, which is defective in chloroplast accumulation, strong UV-B elicited chloroplast avoidance. This indicated that UV-B can also activate signaling to the avoidance response. To assess the possibility of indirect effects of UV-B on chloroplast movements, we examined the impact of UV-B on the actin cytoskeleton, which serves as the motile system for chloroplast movements. While irradiation with UV-B of 3.3 µmol·m−2·s−1 did not affect the actin cytoskeleton, strong UV-B disrupted its structure as shown using an Arabidopsis line expressing Lifeact-green fluorescent protein (GFP). In wild-type plants, pretreatment with strong UV-B attenuated chloroplast responses triggered by subsequent blue light irradiation, further indicating that this UV-B intensity also indirectly affects chloroplast movements. Taken together, our results suggest that the effect of UV-B on chloroplast movement is twofold: it directly induces phototropin-mediated movements; however, at higher intensities, it attenuates the movements in a nonspecific manner