Marek Schwarz
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View article: Expanding the CarD interaction network: CrsL is a novel transcription factor in<i>Mycobacterium smegmatis</i>
Expanding the CarD interaction network: CrsL is a novel transcription factor in<i>Mycobacterium smegmatis</i> Open
Bacterial transcription regulation is critical for adaptation and survival. CarD is an essential transcription factor in mycobacteria involved in regulation of gene expression. We searched for CarD interaction partners in the model organis…
View article: HelD is a Global Transcription Factor Enhancing Gene Expression in Rapidly Growing Mycobacteria
HelD is a Global Transcription Factor Enhancing Gene Expression in Rapidly Growing Mycobacteria Open
HelD protein, also named HelR (encoded by MSMEG_2174 in Mycobacterium smegmatis ), interacts with mycobacterial RNA polymerase (RNAP) and affects rifampicin resistance in Mycobacterium abscessus . Here, we provide data on rifampicin resist…
View article: High rate of macrolide resistance and closely genetically related <i>Mycobacterium abscessus</i> complex strains identified among both cystic fibrosis and non-cystic fibrosis patients within two countries
High rate of macrolide resistance and closely genetically related <i>Mycobacterium abscessus</i> complex strains identified among both cystic fibrosis and non-cystic fibrosis patients within two countries Open
Mycobacterium abscessus is an emerging opportunistic pathogen affecting patients with chronic lung diseases, primarily cystic fibrosis (CF), or those under immunosuppression. Hence, investigations into the epidemiology and transmission of …
View article: Mycobacterial HelD connects RNA polymerase recycling with transcription initiation
Mycobacterial HelD connects RNA polymerase recycling with transcription initiation Open
Mycobacterial HelD is a transcription factor that recycles stalled RNAP by dissociating it from nucleic acids and, if present, from the antibiotic rifampicin. The rescued RNAP, however, must disengage from HelD to participate in subsequent…
View article: RIP-seq reveals RNAs that interact with RNA polymerase and primary sigma factors in bacteria
RIP-seq reveals RNAs that interact with RNA polymerase and primary sigma factors in bacteria Open
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…
View article: σE of Streptomyces coelicolor can function both as a direct activator or repressor of transcription
σE of Streptomyces coelicolor can function both as a direct activator or repressor of transcription Open
σ factors are considered as positive regulators of gene expression. Here we reveal the opposite, inhibitory role of these proteins. We used a combination of molecular biology methods and computational modeling to analyze the regulatory act…
View article: Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search
Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search Open
Bacteria employ small non-coding RNAs (sRNAs) to regulate gene expression. Ms1 is an sRNA that binds to the RNA polymerase (RNAP) core and affects the intracellular level of this essential enzyme. Ms1 is structurally related to 6S RNA that…
View article: NAD<sup>+</sup>capping of RNA in Archaea and Mycobacteria
NAD<sup>+</sup>capping of RNA in Archaea and Mycobacteria Open
Chemical modifications of RNA affect essential properties of transcripts, such as their translation, localization and stability. 5’-end RNA capping with the ubiquitous redox cofactor nicotinamide adenine dinucleotide (NAD + ) has been disc…
View article: Kinetic Modeling and Meta-Analysis of the Bacillus subtilis SigB Regulon during Spore Germination and Outgrowth
Kinetic Modeling and Meta-Analysis of the Bacillus subtilis SigB Regulon during Spore Germination and Outgrowth Open
The exponential increase in the number of conducted studies combined with the development of sequencing methods have led to an enormous accumulation of partially processed experimental data in the past two decades. Here, we present an appr…
View article: rboAnalyzer: A Software to Improve Characterization of Non-coding RNAs From Sequence Database Search Output
rboAnalyzer: A Software to Improve Characterization of Non-coding RNAs From Sequence Database Search Output Open
Searching for similar sequences in a database via BLAST or a similar tool is one of the most common bioinformatics tasks applied in general, and to non-coding RNAs in particular. However, the results of the search might be difficult to int…
View article: Návrh železobetonové nosné konstrukce tribuny fotbalového stadionu
Návrh železobetonové nosné konstrukce tribuny fotbalového stadionu Open
Tato diplomová práce se zabývá problematikou návrhu konstrukcí tribun fotbalových stadionů. Hlavním tématem je návrh železobetonového prefabrikovaného lavicového nosníku, který je pro konstrukce tribun typický, a vhodný konstrukční detail …
View article: DNA mapping and kinetic modeling of the HrdB regulon in<i>Streptomyces coelicolor</i>
DNA mapping and kinetic modeling of the HrdB regulon in<i>Streptomyces coelicolor</i> Open
HrdB in streptomycetes is a principal sigma factor whose deletion is lethal. This is also the reason why its regulon has not been investigated so far. To overcome experimental obstacles, for investigating the HrdB regulon, we constructed a…
View article: σ <sup>I</sup> from Bacillus subtilis: Impact on Gene Expression and Characterization of σ <sup>I</sup> -Dependent Transcription That Requires New Types of Promoters with Extended −35 and −10 Elements
σ <sup>I</sup> from Bacillus subtilis: Impact on Gene Expression and Characterization of σ <sup>I</sup> -Dependent Transcription That Requires New Types of Promoters with Extended −35 and −10 Elements Open
In bacteria, σ factors are essential for transcription initiation. Knowledge about their regulons (i.e., genes transcribed from promoters dependent on these σ factors) is the key for understanding how bacteria cope with the changing enviro…
View article: An Algorithm for Template-Based Prediction of Secondary Structures of Individual RNA Sequences
An Algorithm for Template-Based Prediction of Secondary Structures of Individual RNA Sequences Open
While understanding the structure of RNA molecules is vital for deciphering their functions, determining RNA structures experimentally is exceptionally hard. At the same time, extant approaches to computational RNA structure prediction hav…