In Silico Profiling of Small Open Reading Frames in hsdM-Deficient Group A Streptococcus and Their Predicted Role in Membrane Adaptation

Chung Yuen Khew; Nur Afiqah Mohd Azali; Nurnazatul Syiffa Muhammad Bahrain; Norfarhan  Mohd-Assaad

doi:10.55230/mabjournal.v55i3.3857

Authors

Chung Yuen Khew Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
Nur Afiqah Mohd Azali Department of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
Nurnazatul Syiffa Muhammad Bahrain Department of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
Norfarhan Mohd-Assaad
n_farhan@ukm.edu.my
Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia; Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia https://orcid.org/0000-0002-7543-5805

Keywords:

Bacterial transformation, Group A Streptococcus, RNA-Seq, Small open reading frame, Streptococcus pyogenes, WGCNA

Abstract

Small open reading frames (sORFs) are emerging as key players in bacterial gene regulation, yet their roles remain underexplored in many pathogens. This study investigates the regulatory landscape of sORFs in Group A Streptococcus (GAS) by integrating transcriptomic data and weighted gene co-expression network analysis (WGCNA). We focused on the functional consequences of inactivating the Type 1 Restriction-Modification (RM) system, specifically the hsdM subunit, which is a known barrier to genetic transformation in GAS. By reanalysing the transcriptomic profile of the hyper-transformable 854ΔhsdM strain, we identified 28 sORFs localised within significantly altered co-expression modules. Notably, sORF_00369 (associated with fatty acid biosynthesis) and sORF_00282 (linked to ABC transport) were significantly downregulated. These findings suggest that the inactivation of the RM system, while improving transformation efficiency, may trigger a targeted shift in sORF-mediated metabolism and membrane integrity. Our results propose that sORFs are candidate regulators within the epigenetically mediated regulatory networks of GAS, providing new insights into how genetic recalcitrance and metabolic fitness might be linked. This in silico study lays a theoretical foundation for potentially targeting sORFs in antimicrobial strategy development and optimising GAS as a chassis for synthetic biology.

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