Biology subjects

Grinholc, M.

Publications and source records attributed to Grinholc, M..

3 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

Time-resolved transcriptomic mapping reveals conserved stress programs and metabolic rewiring in Escherichia coli under antimicrobial photodynamic and blue light exposure.

Antimicrobial photodynamic inactivation (aPDI) and antimicrobial blue light (aBL) are emerging, resistance-agnostic strategies for controlling bacterial pathogens, yet their systems-level impact on prokaryotic physiology remains incompletely understood. Here, we used time-resolved global transcriptomics to define how Escherichia coli reprograms gene expression in response to diverse photodynamic stresses. E. coli K-12 BW25113 was exposed to five phototreatments differing in photosensitizer chemistry and light wavelength, including rose bengal, TMPyP, new methylene blue, aBL alone, and aBL combined with 5-aminolevulinic acid, and transcriptional responses were profiled after short (30 min) and prolonged (7-8 h) exposure. Short-term phototreatments triggered rapid and extensive transcriptional remodeling, affecting up to [~]58% of the genes and dominated by conserved stress programs including oxidative defense, sulfur metabolism, and a broad downshift in biosynthesis and energy generation. In contrast, prolonged exposure elicited more restrained but highly treatment-specific adaptive responses, characterized by suppression of core energy metabolism, including oxidative phosphorylation and the tricarboxylic acid cycle, coupled with activation of alternative catabolic pathways. Together, these findings reveal a common acute stress architecture across photodynamic modalities followed by divergent long-term adaptive trajectories, providing a systems-level framework for understanding bacterial responses to light-based antimicrobials and informing the rational optimization of photodynamic therapies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=66 SRC="FIGDIR/small/703343v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@a990a1org.highwire.dtl.DTLVardef@5670bcorg.highwire.dtl.DTLVardef@1035840org.highwire.dtl.DTLVardef@96ff67_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

Cationic heme-mimetic gallium porphyrin kills bacteria and disrupts biofilms

The emergence of antimicrobial resistance in ESKAPE pathogens remains a clinical challenge and limits the utility of conventional antibiotics. Antimicrobial photodynamic inactivation (aPDI) using metal porphyrins is of interest, but the activity of heme-mimetic gallium porphyrins against structured biofilms has not been well defined. In this study, we evaluated a newly synthesized cationic heme-mimetic gallium porphyrin (GaCHP-2-3) activated with visible light against biofilms formed by ESKAPE representatives under static and flow conditions and on titanium surface. Light-activated GaCHP-2-3 reduced biofilm viable counts by up to 4 log10 CFU/mL. Prolonged serial passaging of planktonic bacteria in the presence of GaCHP-2-3 for 20 passages did not yield increases in MIC, indicating no detectable resistance development under these conditions. This work presents GaCHP-2-3 aPDI as a candidate approach for biofilm control and treatment of infections where antibiotic resistance limits the option.

microbiology↗