A5012624091- RNA and protein synthesis mechanisms
- Mycobacterium research and diagnosis
- RNA modifications and cancer
- Bacterial Genetics and Biotechnology
- RNA Research and Splicing
- Tuberculosis Research and Epidemiology
- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- Nuclear Structure and Function
- Bacteriophages and microbial interactions
- Infectious Diseases and Mycology
- Cancer Research and Treatments
- DNA Repair Mechanisms
- Neurogenetic and Muscular Disorders Research
- Antibiotic Resistance in Bacteria
- Animal Genetics and Reproduction
- Education, Psychology, and Social Research
- Protein Structure and Dynamics
- Cancer-related molecular mechanisms research
- Signaling Pathways in Disease
- Microbial Natural Products and Biosynthesis
- Enzyme Structure and Function
- Protein Degradation and Inhibitors
- Ubiquitin and proteasome pathways
Charles University
2024-2025
Czech Academy of Sciences
2009-2024
Czech Academy of Sciences, Institute of Microbiology
2013-2024
Czech Academy of Sciences, Institute of Molecular Genetics
2009-2014
Institute of Molecular Genetics
2008
There is increasing evidence to suggest that splicing decisions are largely made when the nascent RNA still associated with chromatin. Here we demonstrate activity of histone deacetylases (HDACs) influences splice site selection. Using splicing-sensitive microarrays, identified ∼700 genes whose was altered after HDAC inhibition. We provided inhibition induced H4 acetylation and increased Polymerase II (Pol II) processivity along an alternatively spliced element. In addition, reduced...
The Cajal body (CB) is a nuclear structure closely associated with import and biogenesis of small ribonucleoprotein particles (snRNPs). Here, we tested whether CBs also contain mature snRNPs CB integrity depends on the ongoing snRNP splicing cycle. Sm proteins tagged photoactivatable color-maturing variants fluorescent were used to monitor behavior in living cells over time; accumulated CBs, traveled from one another, they not preferentially replaced by newly imported snRNPs. To test cycle,...
Brd2 is a member of the bromodomain extra terminal (BET) protein family, which consists four chromatin-interacting proteins that regulate gene expression. Each BET contains two N-terminal bromodomains, recognize acetylated histones, and C-terminal protein–protein interaction domain. Using genome-wide screen, we identify 1450 genes whose transcription regulated by Brd2. In addition, almost 290 change their alternative splicing pattern upon depletion. specifically localized at promoters target...
While the reported incidence of non-tuberculous mycobacterial (NTM) infections is increasing, true prevalence remains uncertain due to limitations in diagnostics and surveillance. The emergence rare novel species underscores need for characterization improve surveillance, detection, management. We performed whole-genome sequencing (WGS) and/or targeted deep-sequencing using Deeplex Myc-TB assay on all NTM isolates collected Slovakia Czech Republic between years 2019 2023 that were...
Background Nuclear myosin I (NM1) was the first molecular motor identified in cell nucleus. Together with nuclear actin, they participate crucial events such as transcription, chromatin movements, and remodeling. NM1 is an isoform of 1c (Myo1c) that earlier known to act cytoplasm. differs from "cytoplasmic" only by additional 16 amino acids at N-terminus molecule. This acid stretch therefore suggested direct into Methodology/Principal Findings We investigated mechanism import detail. Using...
Small RNAs (sRNAs) are molecules essential for a number of regulatory processes in the bacterial cell. Here we characterize Ms1, sRNA that is highly expressed Mycobacterium smegmatis during stationary phase growth. By glycerol gradient ultracentrifugation, RNA binding assay, and co-immunoprecipitation, show Ms1 interacts with polymerase (RNAP) core free primary sigma factor (σA) or any other σ factor. This contrasts situation most species where it 6S RNAP this interaction requires presence...
Ms1 is a sRNA recently found in mycobacteria and several other actinobacterial species. interacts with the RNA polymerase (RNAP) core devoid of sigma factors, which differs from 6S that binds to RNAP holoenzymes containing primary factor. Here we show most abundant non-rRNA transcript stationary phase Mycobacterium smegmatis. The accumulation stems its high-level synthesis combined decreased degradation. We identify promoter, PMs1 , cis-acting elements important for activity. Furthermore,...
Abstract Bacteria have evolved structured RNAs that can associate with RNA polymerase (RNAP). Two of them been known so far—6S and Ms1 but it is unclear if any other types binding to RNAP exist in bacteria. To identify all interacting the primary σ factors, we established performed native RIP-seq Bacillus subtilis, Corynebacterium glutamicum, Streptomyces coelicolor, Mycobacterium smegmatis pathogenic tuberculosis. Besides 6S B. subtilis M. smegmatis, detected MTS2823, a homologue Ms1, on In...
The AD29 mutation in HPRP31 belongs to a series of mutations that were initially linked with the autosomal dominant disorder retinitis pigmentosa (RP) type 11. gene encodes hPrp31 protein specifically associates spliceosomal small nuclear ribonucleoprotein particles (snRNPs). Despite intensive research, it is still unclear how (Ala216Pro) causes RP. In this study, we report expression mutant affects cell proliferation and alters structure Cajal bodies are connected snRNP metabolism....
Bacterial RNA polymerase (RNAP) is essential for gene expression and as such a valid drug target. Hence, it imperative to know its structure dynamics. Here, we present two as-yet-unreported forms of Mycobacterium smegmatis RNAP: core holoenzyme containing σA but no other factors. Each form was detected by cryo-electron microscopy in major conformations. Comparisons these structures with known RNAPs reveal high degree conformational flexibility the mycobacterial enzyme confirm that region 1.1...
Histone acetylation modulates alternative splicing of several hundred genes. Here, we tested the role histone acetyltransferase p300 in and showed that knockdown promotes inclusion fibronectin (FN1) EDB exon. associates with CRE sites promoter via CREB transcription factor. We created mini-gene reporters driven by an artificial containing sites. Both deletion mutation site affected same manner as knockdown. Next controls H4 along FN1 gene. Consistently, depletion deletion/mutation both...
ABSTRACT In mycobacteria, σ A is the primary sigma factor. This essential protein binds to RNA polymerase (RNAP) and mediates transcription initiation of housekeeping genes. Our knowledge about this factor in mycobacteria limited. Here, we performed an unbiased search for interacting partners Mycobacterium smegmatis . The revealed a number proteins; prominent among them was MoaB2. -MoaB2 interaction validated characterized by several approaches, revealing that it likely does not require RNAP...
HelD protein, also named HelR (encoded by MSMEG_2174 in Mycobacterium smegmatis), interacts with mycobacterial RNA polymerase (RNAP) and affects rifampicin resistance abscessus. Here, we provide data on helD presence the genomes of other clinically relevant nontuberculous mycobacteria. We show that is primarily found rapidly growing mycobacteria, such as M. smegmatis, where detected at a subset promoters can associate CarD RbpA. Transcriptome analysis deletion strain using RNA-seq revealed...
ABSTRACT Chemical modifications of RNA affect essential properties transcripts, such as their translation, localization and stability. 5’-end capping with the ubiquitous redox cofactor nicotinamide adenine dinucleotide (NAD + ) has been discovered in organisms ranging from bacteria to mammals. However, hypothesis that NAD might be universal all domains life not proven yet, information on this modification is missing for Archaea. Likewise, studied clinically important Mycobacterium genus....
The σI sigma factor from Bacillus subtilis is a σ associated with RNA polymerase (RNAP) that was previously implicated in adaptation of the cell to elevated temperature. Here, we provide comprehensive characterization this transcriptional regulator. By transcriptome sequencing (RNA-seq) wild-type (wt) and σI-null strains at 37°C 52°C, identified ∼130 genes affected by absence Further analysis revealed majority these were indirectly regulon, i.e., directly regulated σI, consists 16 genes,...
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 for maintenance genome integrity. Recently, it was reported proteins high G+C Actinobacteria, called HelR, are able to dissociate rifampicin-stalled provide rifampicin resistance. This achieved ability HelR RNAP. The HelR-mediated mechanism resistance discussed here, roles HelD/HelR in...
Bacteria employ small non-coding RNAs (sRNAs) to regulate gene expression. Ms1 is an sRNA that binds the RNA polymerase (RNAP) core and affects intracellular level of this essential enzyme. structurally related 6S a different form RNAP, holoenzyme bearing primary sigma factor. are widespread in bacterial kingdom except for industrially medicinally important Actinobacteria. While was identified Mycobacterium, it not clear whether present also other Actinobacteria species. Here, using...
ABSTRACT 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 M. accurate antibiotic susceptibility data are essential for effective treatment infections caused by this pathogen. This retrospective nationwide study included all clinical isolates ( n = 59) from 29 diagnosed in Czech Republic Slovakia between...
Bacterial transcription regulation is critical for adaptation and survival. CarD an essential factor in mycobacteria involved of gene expression. We searched interaction partners the model organism Mycobacterium smegmatis identified two proteins: ApeB (MSMEG_5828) uncharacterized protein, which we named CrsL (MSMEG_5890). While interacted with only when was overexpressed, associated at its physiological levels. a 5.7 kDa protein shown by NMR to be intrinsically disordered. homologs are...
SUMMARY RNA synthesis is central to life, and polymerase depends on accessory factors for recovery from stalled states adaption environmental changes. Here we investigated the mechanism by which a helicase-like factor HelD recycles polymerase. We report cryo-EM structure of an unprecedented complex between Mycobacterium smegmatis HelD. The crescent-shaped simultaneously penetrates deep into two channels that are responsible DNA binding substrate delivery active site, thereby locking in...
Bacterial RNA polymerase (RNAP) is an essential multisubunit enzyme performing transcription.Regulation of this process secured through the stage-dependent interactions RNAP with different factors (mostly proteins).Here we report structurefunction analysis functional complexes between and a unique helicase-like factor HelD [1] which present in many Gram-positive bacteria (e.g.Bacillus subtilis Mycobacterium smegmatis) [2, 3].HelD forms tightly bound RNAP.It simultaneously penetrates into...