Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins

• Published in: mSystems Vol. 8; no. 3; p. e0024723
• Main Authors: Hirose, Yujiro, Poudel, Saugat, Sastry, Anand V, Rychel, Kevin, Lamoureux, Cameron R, Szubin, Richard, Zielinski, Daniel C, Lim, Hyun Gyu, Menon, Nitasha D, Bergsten, Helena, Uchiyama, Satoshi, Hanada, Tomoki, Kawabata, Shigetada, Palsson, Bernhard O, Nizet, Victor
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 29.06.2023
• Subjects: Algorithms; Bacteria; Bacterial Proteins - genetics; Carbon sources; Computational Biology; Decomposition; Dextrin; E coli; Genes; Humans; Hypotheses; independent component analysis; Maltose; modulon; Pathogens; regulatory network; Research Article; Streptococcus infections; Streptococcus pyogenes; Streptococcus pyogenes - genetics; Toxins, Biological - metabolism; transcription; Transcriptome; Transcriptomes; Transcriptomics; Virulence; Virulence - genetics; United States > US; dextrin; maltose; modulon; independent component analysis; regulatory network; transcription; Streptococcus pyogenes
• ISSN: 2379-5077; 2379-5077
• DOI: 10.1128/msystems.00247-23

can cause a wide variety of acute infections throughout the body of its human host. An underlying transcriptional regulatory network (TRN) is responsible for altering the physiological state of the bacterium to adapt to each unique host environment. Consequently, an in-depth understanding of the comprehensive dynamics of the TRN could inform new therapeutic strategies. Here, we compiled 116 existing high-quality RNA sequencing data sets of invasive serotype M1 and estimated the TRN structure in a top-down fashion by performing independent component analysis (ICA). The algorithm computed 42 independently modulated sets of genes (iModulons). Four iModulons contained the virulence-related operon, which allowed us to identify carbon sources that control its expression. In particular, dextrin utilization upregulated the operon by activation of two-component regulatory system CovRS-related iModulons, altering bacterial hemolytic activity compared to glucose or maltose utilization. Finally, we show that the iModulon-based TRN structure can be used to simplify the interpretation of noisy bacterial transcriptome data at the infection site. IMPORTANCE is a pre-eminent human bacterial pathogen that causes a wide variety of acute infections throughout the body of its host. Understanding the comprehensive dynamics of its TRN could inform new therapeutic strategies. Since at least 43 . transcriptional regulators are known, it is often difficult to interpret transcriptomic data from regulon annotations. This study shows the novel ICA-based framework to elucidate the underlying regulatory structure of allows us to interpret the transcriptome profile using data-driven regulons (iModulons). Additionally, the observations of the iModulon architecture lead us to identify the multiple regulatory inputs governing the expression of a virulence-related operon. The iModulons identified in this study serve as a powerful guidepost to further our understanding of TRN structure and dynamics.