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bioRxiv · 10.1101/2025.09.29.679290

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

Gockel, P.·Mijakovic, I.·Palsson, B.·Zielinski, D. C.·Özdemir, E.·Yang, L.
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Abstract

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.

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Gockel, P., Mijakovic, I., Palsson, B., Zielinski, D. C., Özdemir, E., Yang, L.. 2025-09-30. Expanding the iModulon Knowledgebase for Bacillus subtilis: Updated Transcriptome Decomposition Reveals Novel Regulatory Mechanisms. https://doi.org/10.1101/2025.09.29.679290

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