Among the bacteria groups, most of them are known to be beneficial to human being whereas only a minority is being recognized as harmful. The pathogenicity of bacteria is due, in part, to their rapid adaptation in the presence of selective pressures exerted by the human host. In addition, through their genomes, bacteria are subject to mutations, various rearrangements or horizontal gene transfer among and/or within bacterial species. Bacteria's essential metabolic functions are generally encoding by the core genes. Apart of the core genes, there are several number of mobile genetic elements (MGE) acquired by horizontal gene transfer that might be beneficial under certain environmental conditions. These MGE namely bacteriophages, transposons, plasmids, and pathogenicity islands represent about 15% Staphylococcus aureus genomes. The acquisition of most of the MGE is made by horizontal genomic islands (GEI), recognized as discrete DNA segments between closely related strains, transfer. The GEI contributes to the wide spread of microorganisms with an important effect on their genome plasticity and evolution. The GEI are also involve in the antibiotics resistance and virulence genes dissemination. In this review, we summarize the mobile genetic elements of S. aureus.

• MeSH
• bakteriální chromozomy genetika   MeSH
• bakteriofágy genetika   MeSH
• genomové ostrovy genetika   MeSH
• lidé MeSH
• přenos genů horizontální genetika   MeSH
• rozptýlené repetitivní sekvence genetika   MeSH
• Staphylococcus aureus genetika   MeSH
• transpozibilní elementy DNA genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• transpozibilní elementy DNA MeSH

Staphylococcus petrasii is recently described coagulase negative staphylococcal species and an opportunistic human pathogen, still often misidentified in clinical specimens. Four subspecies are distinguished in S. petrasii by polyphasic taxonomical analyses, however a comparative study has still not been done on the majority of isolates and their genome properties have not yet been thoroughly analysed. Here, we describe the phenotypic and genotypic characteristics of 65 isolates and the results of de novo sequencing, whole genome assembly and annotation of draft genomes of five strains. The strains were identified by MALDI-TOF mass spectrometry to the species level and the majority of the strains were identified to the subspecies level by fingerprinting methods, (GTG)5 repetitive PCR and ribotyping. Macrorestriction profiling by pulsed-field gel electrophoresis was confirmed to be a suitable strain typing method. Comparative genomics revealed the presence of new mobile genetic elements carrying antimicrobial resistance factors such as staphylococcal cassette chromosome (SCC) mec, transposones, phage-inducible genomic islands, and plasmids. Their mosaic structure and similarity across coagulase-negative staphylococci and Staphylococcus aureus suggest the possible exchange of these elements. Numerous putative virulence factors such as adhesins, autolysins, exoenzymes, capsule formation genes, immunomodulators, the phage-associated sasX gene, and SCC-associated spermidine N-acetyltransferase gene, pseudouridine and sorbitol utilization operons might explain clinical manifestations of S. petrasii isolates. The increasing recovery of S. petrasii isolates from human clinical material, the multi-drug resistance including methicillin resistance of S. petrasii subsp. jettensis strains, and virulence factors homologous to other pathogenic staphylococci demonstrate the importance of the species in human disease.

• Klíčová slova
• Coagulase-negative staphylococci, MALDI-TOF MS, Methicillin resistance, Mobile genetic elements, Molecular subtyping, Virulence factors,
• MeSH
• faktory virulence genetika   MeSH
• fenotyp MeSH
• genom bakteriální * MeSH
• genomika MeSH
• genotyp MeSH
• lidé MeSH
• mikrobiální testy citlivosti MeSH
• pulzní gelová elektroforéza MeSH
• ribotypizace MeSH
• rozptýlené repetitivní sekvence * MeSH
• Staphylococcus klasifikace   genetika   patogenita   MeSH
• techniky typizace bakterií MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• srovnávací studie MeSH
• Názvy látek
• faktory virulence MeSH

Transposable elements (TEs, or mobile genetic elements, MGEs) are ubiquitous genetic elements that make up a substantial proportion of the genome of many species. The recent growing interest in understanding the evolution and function of TEs has revealed that TEs play a dual role in genome evolution, development, disease, and drug resistance. Cells regulate TE expression against uncontrolled activity that can lead to developmental defects and disease, using multiple strategies, such as DNA chemical modification, small RNA (sRNA) silencing, chromatin modification, as well as sequence-specific repressors. Advancements in bioinformatics and machine learning approaches are increasingly contributing to the analysis of the regulation mechanisms. A plethora of tools and machine learning approaches have been developed for prediction, annotation, and expression profiling of sRNAs, for methylation analysis of TEs, as well as for genome-wide methylation analysis through bisulfite sequencing data. In this review, we provide a guided overview of the bioinformatic and machine learning state of the art of fields closely associated with TE regulation and function.

• Klíčová slova
• DNA methylation, PIWI-interacting RNAs, bioinformatics methods, circular RNAs, machine learning, mobile genetic elements, small RNAs, transposable elements regulation,
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

• Klíčová slova
• Acinetobacter, Enterobacterales, Pseudomonas, antimicrobial resistance (AMR), high-risk clones, horizontal gene transfer, mobilome,
• MeSH
• bakteriální léková rezistence * genetika   MeSH
• gramnegativní bakterie genetika   MeSH
• mnohočetná bakteriální léková rezistence * genetika   MeSH
• rozptýlené repetitivní sekvence MeSH
• Publikační typ
• úvodníky MeSH

The recent revision of the Acidithiobacillia class using genomic taxonomy methods has shown that, in addition to the existence of previously unrecognized genera and species, some species of the class harbor levels of divergence that are congruent with ongoing differentiation processes. In this study, we have performed a subspecies-level analysis of sequenced strains of Acidithiobacillus ferrooxidans to prove the existence of distinct sublineages and identify the discriminant genomic/genetic characteristics linked to these sublineages, and to shed light on the processes driving such differentiation. Differences in the genomic relatedness metrics, levels of synteny, gene content, and both integrated and episomal mobile genetic elements (MGE) repertoires support the existence of two subspecies-level taxa within A. ferrooxidans. While sublineage 2A harbors a small plasmid related to pTF5, this episomal MGE is absent in sublineage 2B strains. Likewise, clear differences in the occurrence, coverage and conservation of integrated MGEs are apparent between sublineages. Differential MGE-associated gene cargo pertained to the functional categories of energy metabolism, ion transport, cell surface modification, and defense mechanisms. Inferred functional differences have the potential to impact long-term adaptive processes and may underpin the basis of the subspecies-level differentiation uncovered within A. ferrooxidans. Genome resequencing of iron- and sulfur-adapted cultures of a selected 2A sublineage strain (CCM 4253) showed that both episomal and large integrated MGEs are conserved over twenty generations in either growth condition. In turn, active insertion sequences profoundly impact short-term adaptive processes. The ISAfe1 element was found to be highly active in sublineage 2A strain CCM 4253. Phenotypic mutations caused by the transposition of ISAfe1 into the pstC2 encoding phosphate-transport system permease protein were detected in sulfur-adapted cultures and shown to impair growth on ferrous iron upon the switch of electron donor. The phenotypic manifestation of the △pstC2 mutation, such as a loss of the ability to oxidize ferrous iron, is likely related to the inability of the mutant to secure the phosphorous availability for electron transport-linked phosphorylation coupled to iron oxidation. Depletion of the transpositional △pstC2 mutation occurred concomitantly with a shortening of the iron-oxidation lag phase at later transfers on a ferrous iron-containing medium. Therefore, the pstII operon appears to play an essential role in A. ferrooxidans when cells oxidize ferrous iron. Results highlight the influence of insertion sequences and both integrated and episomal mobile genetic elements in the short- and long-term adaptive processes of A. ferrooxidans strains under changing growth conditions.

• MeSH
• Acidithiobacillus * genetika   metabolismus   MeSH
• oxidace-redukce MeSH
• síra metabolismus   MeSH
• transpozibilní elementy DNA * genetika   MeSH
• železo metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• síra MeSH
• transpozibilní elementy DNA * MeSH
• železo MeSH

BACKGROUND: The insertion sequence elements (IS elements) represent the smallest and the most abundant mobile elements in prokaryotic genomes. It has been shown that they play a significant role in genome organization and evolution. To better understand their function in the host genome, it is desirable to have an effective detection and annotation tool. This need becomes even more crucial when considering rapid-growing genomic and metagenomic data. The existing tools for IS elements detection and annotation are usually based on comparing sequence similarity with a database of known IS families. Thus, they have limited ability to discover distant and putative novel IS elements. RESULTS: In this paper, we present digIS, a software tool based on profile hidden Markov models assembled from catalytic domains of transposases. It shows a very good performance in detecting known IS elements when tested on datasets with manually curated annotation. The main contribution of digIS is in its ability to detect distant and putative novel IS elements while maintaining a moderate level of false positives. In this category it outperforms existing tools, especially when tested on large datasets of archaeal and bacterial genomes. CONCLUSION: We provide digIS, a software tool using a novel approach based on manually curated profile hidden Markov models, which is able to detect distant and putative novel IS elements. Although digIS can find known IS elements as well, we expect it to be used primarily by scientists interested in finding novel IS elements. The tool is available at https://github.com/janka2012/digIS.

• Klíčová slova
• Genome annotation, IS elements, Mobile element, Profile HMM, Prokaryotic genomes,
• MeSH
• genom bakteriální genetika   MeSH
• genomika MeSH
• lidé MeSH
• prokaryotické buňky * MeSH
• software MeSH
• transpozibilní elementy DNA * genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• transpozibilní elementy DNA * MeSH

Staphylococcus aureus is a serious human and veterinary pathogen in which new strains with increasing virulence and antimicrobial resistance occur due to acquiring new genes by horizontal transfer. It is generally accepted that temperate bacteriophages play a major role in gene transfer. In this study, we proved the presence of various bacterial genes of the S. aureus COL strain directly within the phage particles via qPCR and quantified their packaging frequency. Non-parametric statistical analysis showed that transducing bacteriophages φ11, φ80 and φ80α of serogroup B, in contrast to serogroup A bacteriophage φ81, efficiently package selected chromosomal genes localized in 4 various loci of the chromosome and 8 genes carried on variable elements, such as staphylococcal cassette chromosome SCCmec, staphylococcal pathogenicity island SaPI1, genomic islands vSaα and vSaβ, and plasmids with various frequency. Bacterial gene copy number per ng of DNA isolated from phage particles ranged between 1.05 × 10(2) for the tetK plasmid gene and 3.86 × 10(5) for the SaPI1 integrase gene. The new and crucial finding that serogroup B bacteriophages can package concurrently ccrA1 (1.16 × 10(4)) and mecA (1.26 × 10(4)) located at SCCmec type I into their capsids indicates that generalized transduction plays an important role in the evolution and emergence of new methicillin-resistant clones.

• MeSH
• bakteriální chromozomy genetika   MeSH
• bakteriální geny * MeSH
• bakteriální proteiny genetika   MeSH
• bakteriofágy genetika   metabolismus   MeSH
• DNA bakterií genetika   MeSH
• frekvence genu MeSH
• genetické lokusy MeSH
• klonování DNA MeSH
• penicilinasa genetika   MeSH
• plazmidy genetika   MeSH
• polymerázová řetězová reakce MeSH
• přenos genů horizontální MeSH
• proteiny vázající penicilin MeSH
• rezistence na methicilin genetika   MeSH
• rozptýlené repetitivní sekvence * MeSH
• sekvenční analýza DNA MeSH
• sestavení viru MeSH
• Staphylococcus aureus genetika   fyziologie   virologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální proteiny MeSH
• DNA bakterií MeSH
• mecA protein, Staphylococcus aureus MeSH Prohlížeč
• penicilinasa MeSH
• proteiny vázající penicilin MeSH

The study of the role of mobile elements and mobilization of resistance genes is crucial for understanding the epidemiology of antibiotic resistance. This review summarizes recent data on the insertion sequences, transposons, integrons and plasmids that are involved in the mobilization of bacterial antibiotic resistance genes.

• MeSH
• bakteriální léková rezistence genetika   MeSH
• integrony genetika   MeSH
• inverze sekvence MeSH
• inzerční mutageneze MeSH
• R-plasmidy genetika   MeSH
• transpozibilní elementy DNA genetika   MeSH
• Publikační typ
• anglický abstrakt MeSH
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• transpozibilní elementy DNA MeSH

A significant part of eukaryotic genomes is formed by transposable elements (TEs) containing not only genes but also regulatory sequences. Some of the regulatory sequences located within TEs can form secondary structures like hairpins or three-stranded (triplex DNA) and four-stranded (quadruplex DNA) conformations. This review focuses on recent evidence showing that G-quadruplex-forming sequences in particular are often present in specific parts of TEs in plants and humans. We discuss the potential role of these structures in the TE life cycle as well as the impact of G-quadruplexes on replication, transcription, translation, chromatin status, and recombination. The aim of this review is to emphasize that TEs may serve as vehicles for the genomic spread of G-quadruplexes. These non-canonical DNA structures and their conformational switches may constitute another regulatory system that, together with small and long non-coding RNA molecules and proteins, contribute to the complex cellular network resulting in the large diversity of eukaryotes.

• Klíčová slova
• DNA and RNA quadruplexes, G-quadruplexes, LTR retrotransposons, recombination, replication, transcription, transposable elements,
• MeSH
• DNA vazebné proteiny metabolismus   MeSH
• G-kvadruplexy * MeSH
• genomika MeSH
• lidé MeSH
• otevřené čtecí rámce MeSH
• regulace genové exprese MeSH
• regulační oblasti nukleových kyselin MeSH
• repetitivní sekvence nukleových kyselin MeSH
• replikace DNA MeSH
• retroelementy genetika   MeSH
• RNA chemie   genetika   MeSH
• rostliny genetika   MeSH
• transpozibilní elementy DNA genetika   MeSH
• vazba proteinů MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• DNA vazebné proteiny MeSH
• retroelementy MeSH
• RNA MeSH
• transpozibilní elementy DNA MeSH

The release of hazardous elements from the wastes of high-temperature processes represents a risk to the environment. We focused on the alteration of fly ash (FA) from glassworks collected from an electrostatic filter. FA contains elevated concentrations of Zn and Ba, among other elements. Overtime, small amounts of FA have been emitted from the factory and settled into the surrounding environment (soil). In order to assess the possible risks to the environment, samples of FA were placed in small nylon bags and deposited in 11 different soil horizons (containing diverse vegetation cover such as spruce and beech and also unforested areas). Samples of the FA in bags were exposed in the soils for 1 year. Then, the bags were collected, and the exposed soils in the direct vicinity of the FA bags were sampled. The total concentrations of Zn and Ba in the FA, as well as in the soil samples (original and exposed), were determined by ICP MS. The "mobile fraction" was determined as the exchangeable (acid extractable) fraction of the modified BCR sequential extraction procedure (SEP). The SEP results indicate that Zn and Ba may pose a potential environmental risk. Their concentrations in the first, most mobile, and bioavailable fraction increased in all the exposed soils. The most significant increases were observed in the upper soil horizons (litter and A horizon). The risk to the environment was evaluated on the basis of the Risk Assessment Code.

• MeSH
• baryum chemie   MeSH
• chemická frakcionace MeSH
• látky znečišťující půdu analýza   MeSH
• látky znečišťující vzduch analýza   MeSH
• monitorování životního prostředí * MeSH
• půda chemie   MeSH
• zinek chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• baryum MeSH
• látky znečišťující půdu MeSH
• látky znečišťující vzduch MeSH
• půda MeSH
• zinek MeSH