Biology subjects

Mijakovic, I.

Publications and source records attributed to Mijakovic, I..

5 recordsLinked to original sources

bioRxiv2025

Expanding the iModulon Knowledgebase for Bacillus subtilis: Updated Transcriptome Decomposition Reveals Novel Regulatory Mechanisms

1.The Gram-positive bacterium Bacillus subtilis is widely used as a model organism for studying cell differentiation, microbial physiology and gene regulation. Its genetic accessibility and strong protein secretion machinery make it an excellent host for industrial protein production. Transcriptomics has become an essential tool in understanding these traits and the organisms response to environmental stimuli. Recent advantages in transcriptomics have enabled genome-wide analysis of gene expression patterns under various environmental conditions and genetic perturbations, interpreting such data, however, remains challenging. Independent Component Analysis (ICA) has emerged as a powerful method to decompose bacterial transcriptomes into sets of co-regulated genes - so-called iModulons. In this study, we present an updated iModulon decomposition of Bacillus subtilis transcriptomes, generated from a compendium of 782 high-quality RNAseq samples. This dataset includes a wide range of environmental and genetic conditions. ICA decomposition revealed 142 iModulons, that captured 80% of the expression variance. We compare our version of the modularized B. subtilis transcriptome with previous decompositions and show that the updated composition enhances our understanding of B. subtilis gene regulation and enables novel insights into the organisms regulon structure and gene memberships of the WalR regulon.

systems biology↗

bioRxiv2025

Evolutionary expression patterns in developing biofilms of uropathogenic Escherichia coli reveal embryo-like features

Developing biofilms of the gram-positive, soil-dwelling bacterium Bacillus subtilis exhibit expression patterns and evolutionary imprints similar to those observed in eukaryotic embryos. However, the universality of these evolutionary and developmental regularities has not yet been explored in other biofilm-forming bacteria, including pathogens. To broaden the perspective on ontogeny-phylogeny correlations in bacteria, we recovered phylotranscriptomic and phyloproteomic trajectories throughout the entire biofilm development of uropathogenic Escherichia coli UTI89. Here, we show that biofilm growth in E. coli UTI89 positively correlates with the evolutionary age of expressed genes, with developing biofilms progressively expressing younger and more divergent genes. These findings suggest that biofilm formation in gram-negative bacteria is not macroevolutionarily naive and that evolutionary imprints are a pervasive feature of bacterial biofilm development. While these regularities apply to the developmental expression patterns of bulk biofilms, the question remains whether evolutionary stratification occurs within the spatial regions of individual biofilms. To address this, we analyzed expression profiles across concentric regions of E. coli UTI89 biofilms at three developmental stages. This analysis revealed that gene expression, functional patterns, and evolutionary imprints are influenced by both developmental timing and distance from the biofilm center. Together, these findings demonstrate that the growth of uropathogenic E. coli biofilms is governed by both temporal and spatial macroevolutionary logic, drawing intriguing parallels to organismal development in multicellular eukaryotic lineages.

evolutionary biology↗

bioRxiv2025

Targeted Sortase A Inhibition by Novel Peptidomimetic Antivirulents against Staphylococcal Infections

Antibiotic resistance is a critical public health issue, causing resistant bacterial strains to be increasingly difficult to control. Antivirulence therapies, which target bacterial virulence factors rather than kill bacteria, present a promising approach. Sortase enzymes, particularly SrtA, are crucial for Gram-positive bacterial virulence by anchoring surface proteins essential for bacterial adhesion and biofilm formation to the bacterial outer cell wall. This study evaluates the selectivity of the peptidomimetic inhibitor BzLPRDSar towards various Gram-positive bacteria. The BzLPRDSar significantly inhibited biofilm formation in multidrug-resistant S. aureus and S. epidermidis. Conversely, it showed variable and generally lower selectivity to Gram-positive species such as E. faecalis, B. cereus and S. agalactiae. The selectivity towards Staphylococcus species is attributed to conserved structural elements in the SrtA enzyme, particularly the {beta}7/{beta}8 loop region with a key tryptophan, likely facilitating strong binding interactions with the inhibitor. ImportanceThis study addresses the pressing issue of antibiotic resistance by exploring antivirulence therapy as an innovative alternative to conventional antibiotics, focusing on inhibiting bacterial virulence rather than bacterial growth. By evaluating the selectivity of the peptidomimetic inhibitor BzLPRDSar against various Gram-positive bacteria, the study highlights its potent selectivity in inhibiting biofilm formation in multidrug-resistant S. aureus and S. epidermidis. The findings underscore the potential of targeting conserved structural elements in bacterial Sortase enzymes, particularly in Staphylococcal species, to develop more selective and effective antivirulence therapies.

microbiology↗

bioRxiv2020

Integrated metabolic modeling, culturing and transcriptomics explains enhanced virulence of V. cholerae during co-infection with ETEC

Gene essentiality is altered during polymicrobial infections. Nevertheless, most studies rely on single-species infections to assess pathogen gene essentiality. Here, we use genome-scale metabolic models to explore the effect of co-infection of the diarrheagenic pathogen Vibrio cholerae (V. cholerae) with another enteric pathogen, enterotoxigenic E. coli (ETEC). Model predictions showed that V. cholerae metabolic capabilities were increased due to ample cross-feeding opportunities enabled by ETEC. This is in line with increased severity of cholera symptoms known to occur in patients with dual-infections by the two pathogens. In vitro co-culture systems confirmed that V. cholerae growth is enhanced in co-cultures relative to single-cultures. Further, expression levels of several V. cholerae metabolic genes were significantly perturbed as shown by dual RNAseq analysis of its co-cultures with different ETEC strains. A decrease in ETEC growth was also observed, probably mediated by non-metabolic factors. Single gene essentiality analysis predicted conditionally-independent genes that are essential for the pathogen’s growth in both single- and co-infection scenarios. Our results reveal growth differences that are of relevance to drug targeting and efficiency in polymicrobial infections.Importance Most studies proposing new strategies to manage and treat infections have been largely focused on identifying druggable targets that can inhibit a pathogen’s growth when it is the single cause of infection. In vivo, however, infections can be caused by multiple species. This is important to take into account when attempting to develop or use current antibacterials since their efficacy can change significantly between single and co-infections. In this study, we used genome-scale metabolic models (GEMs) to interrogate the growth capabilities of Vibrio cholerae (V. cholerae) in single and co-infections with enterotoxigenic E. coli (ETEC), which co-occur in large fraction of diarrheagenic patients. Co-infection model predictions showed that V. cholerae growth capabilities are enhanced in presence of ETEC relative to V. cholerae single-infection, through cross-fed metabolites made available to V. cholerae by ETEC. In vitro, co-cultures of the two enteric pathogens further confirmed model predictions showing an increased growth of V. cholerae in co-culture relative to V. cholerae single-cultures while ETEC growth was suppressed. Dual RNAseq analysis of the co-cultures also confirmed that the transcriptome of V. cholerae is distinct during co-infection compared to single infection scenarios where processes related to metabolism were significantly perturbed. Further, in silico gene-knock out simulations uncovered discrepancies in gene essentiality for V. cholerae growth between single and co-infections. Integrative model-guided analysis thus identified druggable targets that would be critical for V. cholerae growth in both single and co-infections, thus designing inhibitors against those targets would provide a broader spectrum coverage against cholera infections.View Full Text

systems biology↗

bioRxiv2020

Embryo-like features in developing Bacillus subtilis biofilms

Correspondence between evolution and development has been discussed for more than two centuries1. Recent work reveals that phylogeny-ontogeny correlations are indeed present in developmental transcriptomes of eukaryotic clades with complex multicellularity2-10. Nevertheless, it has been largely ignored that the pervasive presence of phylogeny-ontogeny correlations is a hallmark of development in eukaryotes6, 10-12. This perspective opens a possibility to look for similar parallelisms in biological settings where developmental logic and multicellular complexity are more obscure13-16. For instance, it has been increasingly recognized that multicellular behaviour underlies biofilm formation in bacteria13, 14, 17-19. However, it remains unclear whether bacterial biofilm growth shares some basic principles with development in complex eukaryotes14-16, 18, 20. Here we show that the ontogeny of growing Bacillus subtilis biofilms recapitulates phylogeny at the expression level. Using time-resolved transcriptome and proteome profiles, we found that biofilm ontogeny correlates with the evolutionary measures, in a way that evolutionary younger and more diverged genes were increasingly expressed towards later timepoints of biofilm growth. Molecular and morphological signatures also revealed that biofilm growth is highly regulated and organized into discrete ontogenetic stages, analogous to those of eukaryotic embryos11, 21. Together, this suggests that biofilm formation in Bacillus is a bona fide developmental process comparable to organismal development in animals, plants and fungi. Given that most cells on Earth reside in the form of biofilms22 and that biofilms represent the oldest known fossils23, we anticipate that the widely-adopted vision of the first life as a single-cell and free-living organism needs rethinking.

evolutionary biology↗