[P004] Poster

1:00 PM - 1:50 PM JST(4:00 AM - 4:50 AM UTC)

[P02-246] Decoding the Transcriptional Landscape of a Methylocystis sp. MJC1 through iModulon Analysis

○Sukjae Han¹, Hyeonwoo Mun², Geunyung Park¹, Keonwoo Kim², Seongjun Park², Kwanwoo Kim², Sangwoo Seo^1,2 (1. Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul 08826, Republic of Korea (Korea), 2. School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul 08826, Republic of Korea (Korea))

Keywords:

iModulon,global transcriptional regulation,Methylocystis,methanotroph

Methanotrophic bacteria are central to the global methane cycle, yet the transcriptional regulatory architecture underlying their metabolic versatility remains largely unexplored. Here, we applied Independent Component Analysis (ICA)-based iModulon decomposition to construct the first transcriptional regulatory map of a methanotrophic bacterium, Methylocystis sp. MJC1. UMI-based bulk RNA-seq was performed on 108 samples across 54 growth conditions spanning carbon source variations (methane, methanol, acetate, formate), nitrogen and sulfur limitations, pH and osmotic stresses, temperature shifts, and formaldehyde toxicity. OptICA determined the optimal dimensionality for ICA decomposition of the expression matrix (4,135 genes). The resulting iModulons revealed several key aspects of MJC1 transcriptional regulation. A dedicated particulate methane monooxygenase (pMMO) iModulon containing one pmoCAB operon and an additional pmoC paralog was identified, while other pMMO gene copies distributed across separate iModulons exhibited distinct activation patterns, suggesting multi-layered transcriptional control of methane oxidation in this organism. Under nitrogen limitation, phasin-containing iModulons were strongly and specifically activated, reflecting coordinated polyhydroxybutyrate (PHB) accumulation as a carbon storage response. A sulfur homeostasis regulon was also delineated, comprising sulfate ABC transporters, cysteine synthase, and rhodanese-like proteins, activated exclusively under sulfate-depleted conditions. Notably, correlation analysis between iModulon activities revealed a tightly co-regulated growth cluster linking ribosomal protein genes, methanol dehydrogenase, and pMMO subunits, indicating that translational capacity and C1 oxidation are transcriptionally coupled during active growth. The high proportion of uncharacterized iModulons (57%) reflects the absence of a curated transcriptional regulatory network for this non-model organism and underscores the discovery potential of unsupervised decomposition in understudied species. This work establishes a systems-level framework for understanding transcriptional regulation in methanotrophs and provides candidate regulatory modules for future experimental validation.