Biology subjects

Szczesniak, M. W.

Publications and source records attributed to Szczesniak, M. W..

6 recordsLinked to original sources

bioRxiv2026

Common Ground in Chaos: Diversified Photodynamic Treatments Converge on a Unified Stress Architecture in Escherichia coli

The rise of antimicrobial resistance has intensified interest in antimicrobial photodynamic inactivation (aPDI) and antimicrobial blue light (aBL) as alternatives or adjuvants to conventional antibiotics. However, whether chemically distinct photodynamic treatments elicit a shared bacterial response remains unclear. Here, we integrated transcriptomic profiles of Escherichia coli BW25113 exposed to five short-term, sub-lethal photodynamic treatments: antimicrobial blue light (aBL), aBL combined with 5-aminolevulinic acid (aBL+ALA), rose bengal (RB), new methylene blue (NMB), and the cationic porphyrin TMPyP. Intersection analysis identified 891 conserved core genes differentially expressed across all treatments, of which approximately 98% changed in a consistent direction despite differences in photosensitizer chemistry and activating wavelength. Random-effects meta-analysis and robust rank aggregation prioritized 88 high-confidence genes, revealing induction of envelope stress and cytoplasmic protein quality control pathways alongside repression of acid resistance, hydrogen metabolism, molybdate transport, and biofilm formation. Regulon enrichment indicated that heat-shock sigma factor {sigma}32/RpoH and the envelope-stress regulators CpxR, BaeR, {sigma}24/RpoE, and PspF were enriched among induced genes, whereas GadW/GadX/GadE, Fur, and {sigma}38/RpoS were enriched among repressed genes. Functional validation using selected single-gene Keio knockouts confirmed that deletion of conserved-core genes sensitized E. coli to photodynamic treatment and delayed post-treatment recovery in a modality-dependent manner. Moreover, RT-qPCR analysis of selected transcriptional responses confirmed the direction and overall pattern of RNA-seq-derived expression changes. Together, these findings define a unified conserved early survival program in E. coli after chemically distinct photodynamic treatments and identify stress-response modules that may serve as targets for potentiating aPDI. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/744726v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@dbbadaorg.highwire.dtl.DTLVardef@1c85538org.highwire.dtl.DTLVardef@152d699org.highwire.dtl.DTLVardef@18705a6_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Deciphering the antifungal mechanism of Polish ethanolic extracts of propolis against Candida albicans: Evidence for a multi-target mode of action

Propolis, a resinous product of plant origin collected by honeybees, has long been used in traditional medicine for its antimicrobial properties. However, its antifungal mechanism of action against Candida albicans remains incompletely understood. This study aimed to elucidate the antifungal mechanism of ethanolic extracts of Polish propolis (EEP) and a defined mixture of its key flavonoid constituents against C. albicans. Antifungal activity was assessed using Time-kill assay and broth microdilution method under different medium supplementation conditions. Cellular responses were analysed by fluorescence microscopy (FM) and flow cytometry (FCM) in regard to: membrane integrity, reactive oxygen species (ROS) accumulation, mitochondrial membrane potential changes, cytosolic Ca{superscript 2} levels, and morphological transition. Transcriptomic changes were evaluated by RNA sequencing (RNA-seq) and validated by quantitative reverse transcription PCR (RT-qPCR). EEP exhibited concentration-dependent, extract-specific antifungal activity, with selected samples showing rapid fungicidal effects. Mechanistic studies demonstrated membrane permeabilization, reactive oxygen species (ROS) accumulation, mitochondrial dysfunction, disruption of Ca{superscript 2} homeostasis, and inhibition of hyphal formation. Ergosterol supplementation reduced antifungal efficacy, indicating membrane sterols as primary targets. Transcriptomic analysis revealed downregulation of genes associated with DNA replication, transcription, and biosynthesis, alongside upregulation of stress-response pathways, including oxidative stress, protein folding, and mitochondrial processes. Polish propolis exerts antifungal activity through a multi-target mechanism involving membrane disruption and induction of cellular stress. Transcriptomic data indicate coordinated suppression of essential cellular functions and activation of stress-response pathways, supporting a system-level disruption of fungal homeostasis.

microbiology↗

bioRxiv2026

Antisense lncRNA transcription promotes A-to-I RNA editing via intermolecular dsRNA in breast cancer

A-to-I RNA editing, catalysed by ADAR enzymes, is the most prevalent post-transcriptional RNA modification in mammals, yet the regulatory inputs shaping cell-type-specific editomes remain incompletely understood. Here we characterise over 2.2 million unique A-to-I editing sites across MCF7 (ER+) and MDA-MB-231 (triple-negative) breast cancer cell lines and 117 patient tumours. MCF7 exhibited substantially more editing per sample, driven by higher ADAR1 expression and a shifted ADAR1/ADAR2 ratio that favoured broad intronic Alu editing in the luminal line versus site-selective synonymous coding editing in the aggressive line. Despite this divergence, approximately 2,500 sites were constitutively edited in both cell lines, defining a conserved core editome. We demonstrate that natural antisense lncRNA transcription constitutes an independent, additive pathway for editing through intermolecular dsRNA formation: editing density at sense-antisense overlaps reversed from depletion to enrichment as a function of balanced co-expression, antisense overlap increased editing probability without affecting density among edited genes, and a factorial analysis across all expressed genes established that inverted Alu pairs are the dominant editing substrate while antisense lncRNA transcription provides an independent contribution whose magnitude scales with overlap length and Alu content. Experimental validation at the NDUFS1/NDUFS1-AS1 locus confirmed co-expression of sense and antisense transcripts, verified editing at computationally predicted positions by Sanger sequencing with genomic DNA controls, and demonstrated differential editing and expression between cell lines. Differentially edited genes included the oncogene VOPP1 and fatty acid metabolism genes at antisense loci, linking epitranscriptomic regulation to the lipid metabolic phenotype of aggressive breast cancer. Our findings establish a two-tier model: a dominant ADAR1-driven programme targeting intramolecular Alu dsRNA, upon which an independent lncRNA antisense pathway is superimposed via intermolecular dsRNA, jointly producing subtype-specific editing landscapes that preserve a constitutive core but diverge in magnitude, functional distribution, and site selection.

cancer biology↗

bioRxiv2023

Interplay between m6A modification and overall transcripts quantity: Impacts on mRNA composition in plant stress granules

Stress granules (SGs) are cytoplasmic structures that emerge in response to unfavorable environmental conditions. They contain a rich pool of RNA, including non-translated mRNA. The mechanisms governing transcripts accumulation in SGs is only partially understood. Despite the recognized role of m6A in plant transcriptome regulation, its impact on SGs composition and assembly remains elusive. We examined the formation of SGs, the presence of m6A, and the transcription-level-dependent localization of selected mRNAs within these granules during hypoxia in the roots of Lupinus angustifolius and Arabidopsis thaliana. In lupine, SGs exhibit a distinctive bi-zonal structure, comprising of a ring and a central area with differences in ultrastructure and composition. Following the transcriptome analysis, mRNAs were selected for examination of their localization in SGs and m6A levels. Transcripts from genes responsive to hypoxia (ADH1 and HUP7) exhibited significant lower levels of m6A compared to housekeeping genes but only ADH1 was not present in SGs. HUP7 mRNA with low quantity of m6A, is present both in the SGs and cytoplasm probably due to extremely high expression level. It was also shown that the amount of m6A in SGs was higher than in the cytoplasm only in the first hours of hypoxia and then decreased. In mutants of A. thaliana with reduced level of m6A, formation and quantity of SGs were studied. In this line, ECT2 was not observed and poly(A) RNA levels were slightly reduced in SGs. Additionally the number of SGs was lower than that of the wild type. In summary, our findings demonstrate the limited impact of m6A modification on SGs assembly. However the interplay between m6A modification and the overall transcript quantity in the cytoplasm plays a regulatory role in mRNA partitioning into SGs.

cell biology↗

bioRxiv2023

Novel function of U7 snRNA in the repression of HERV1/LTR12s and lincRNAs in human cells

U7 snRNA is part of U7 snRNP, a complex required for the 3end processing of replication-dependent histone pre-mRNAs in the S phase of the cell cycle. During this maturation event, the 5 region of U7 snRNA hybridizes with the highly complementary sequence present in the 3UTR of histone pre-mRNAs, called histone downstream element, HDE. This base-pair interaction triggers subsequent reactions that eventually result in cleavage and release of mature histone transcripts. Intriguingly, U7 snRNP is constitutively expressed throughout the cell cycle and in nondividing cells, suggesting another function of U7 snRNA/snRNP in cells. Here, we show that several human endogenous retroviruses (HERVs) are significantly upregulated in HEK293T cells with U7 snRNA knockdown. They predominantly belong to the LTR12 class. Interestingly, some of them are located within long intergenic noncoding RNAs (lincRNAs), which in turn are upregulated in U7 snRNA knockdown cells as well. Significantly, both these HERV1/LTR12s and lincRNAs contain two or more sequence motifs that perfectly match the 5 end of U7 snRNA, which we called HDE-like motifs. We confirmed that mutations within the HDE-like motifs abrogate U7 snRNA regulatory function and stimulate the expression of selected lincRNAs. Furthermore, we demonstrate that U7 snRNA inhibits HERV1/LTR12 and lincRNA expression at the transcription level. We propose a mechanism in which U7 snRNA hampers binding/activity of NF-Y transcription factor to CCAAT motifs that are frequently found in LTRs as well as in a close proximity to HDE-like motifs. The expression of many HERV1/LTR12s and lincRNAs regulated by U7 snRNA seems to be tissue specific, therefore, we suggest that U7 snRNA plays a protective role in keeping deleterious genetic elements in silence in selected types of cells.

molecular biology↗

bioRxiv2022

FUS modulates the level of ribosomal RNA modifications by regulating a subset of snoRNA expression

FUS is a multifunctional protein involved in many aspects of RNA metabolism, including transcription, splicing, translation, miRNA processing, and replication-dependent histone gene expression. In this paper, we show that FUS depletion results in differential expression of numerous small nucleolar RNAs (snoRNAs) that guide 2-O methylation (2-O-Me) and pseudouridylation of specific positions in ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). Using RiboMeth-seq and HydraPsiSeq for the profiling of 2-O-Me and pseudouridylation status of rRNA species, we demonstrated considerable hypermodification at several sites in HEK293T and SH-SY5Y cells with FUS knockout (FUS KO) compared to wild-type cells. We observed a similar direction of changes in rRNA modification in differentiated SH-SY5Y cells with the FUS mutation (R495X) related to the severe disease phenotype of amyotrophic lateral sclerosis (ALS). Furthermore, the pattern of modification of some rRNA positions was correlated with the abundance of corresponding guide snoRNAs in FUS KO and FUS R495X cells. Our findings reveal a new role for FUS in modulating the modification pattern of rRNA molecules, that in turn might generate ribosome heterogeneity and constitute a fine-tuning mechanism for translation efficiency/fidelity. Therefore, we suggest that increased levels of 2-O-Me and pseudouridylation at particular positions in rRNAs from cells with the ALS-linked FUS mutation may represent a possible new translation-related mechanism that underlies disease development and/or progression.

molecular biology↗