Living systems navigate environments using noisy and incomplete sensory signals. In unicellular algae, phototaxis is often modeled as a mechanistic run--tumble process driven by stimulus--response rules. However, such descriptions overlook how organisms actively sample their environment to reduce sensory ambiguity. From a minimal cognition perspective, we reframe this navigation as a subjective, information-driven sensorimotor process. To this end, we propose a framework linking a Partially Observable Markov Decision Process (POMDP) with biochemical reaction dynamics. Environmental variables are hidden, while the cell updates a minimal internal state from each observation through a memoryless Bayesian step. These internal dynamics balance orienting toward light with exploratory reorientation and can be implemented through Chemical-Reaction-Network Ordinary Differential Equations (CRN--ODEs). Our model includes a biophysical observation process for photoreception and a chemically computable polynomial bound on information gain. Using Inverse Reinforcement Learning (IRL) on 30 experimentally recorded Chlamydomonas trajectories, we infer the behavioral objective consistent with observed phototactic motion and benchmark the resulting dynamics with standard Stochastic Simulation Algorithm (SSA) baselines. Our model reproduces the empirical alignment-to-light distribution, comparable to objective SSA baselines on this dataset. Within this framework, run--tumble alternation emerges as an information-acquisition strategy: tumbling reorients the cell to sample new sensory configurations and resolve sensor ambiguity, demonstrating how intracellular biochemical networks can support adaptive information-seeking behavior in cellular navigation.
DNA gyrase is an essential bacterial enzyme and a clinically validated target for the treatment of tuberculosis. However, the discovery of new inhibitors remains limited by the many challenges regarding the manipulation on pathogenic mycobacteria. This study validates Corynebacterium glutamicum (Cglu) as a safe, non-pathogenic surrogate for Mycobacterium tuberculosis (Mtb) to investigate DNA gyrase and facilitate the identification of new inhibitors. Using Cglu as a target allows for fast whole-cell screening under safe conditions while ensuring efficient drug uptake. Cglu shares key physiological features with Mtb, including genome size, complex cell wall structure, and a single type I and type II topoisomerase. Structural and functional comparisons emphasize the similarity of Cglu and Mtb gyrases, which share 70% sequence identity and show comparable catalytic properties and responsiveness to known inhibitors. Thus, the cryo-EM structure of the Cglu gyrase-DNA complex at 3.2 Å resolution reveals highly conserved drug-binding pockets for known anti-gyrase inhibitors and the genetic depletion of gyrA or gyrB in Cglu causes severe growth and morphological defects, mirroring the effects of chemical inhibition and allowing to link gyrase function to cellular phenotypes. Comparative imaging of different inhibitor classes (fluoroquinolones, aminocoumarins, NBTIs) uncovers distinct morphological signatures that reflect the mode of action of each compound. Finally, cross-species complementation confirms functional conservation but also highlights subtle structural differences affecting efficiency. Together, these findings establish Cglu as a robust and biosafe model for dissecting gyrase function, visualizing DNA topology dynamics, and accelerating the discovery of gyrase-targeting antimicrobials. More generally, our studies demonstrate the feasibility of using Cglu as a cell-based screening platform to discover new anti-tuberculous compounds targeting conserved mechanisms, not only for validated TB drug targets such as DNA gyrase but also for new, yet to be identified, targets. ### Competing Interest Statement The authors have declared no competing interest. ANR, ANR-18-IDEX-0001, ANR-11-EQPX-0008, ANR-10–INSB–04 Institut Pasteur, PTR\_726\_BactImMorph Fondation pour la Recherche Médicale, EQU202303016284
The architecture of Bacillus subtilis biofilms is influenced by the coordinated regulation of cellular specialization, matrix assembly, and metabolism. B. subtilis can form different types of biofilm in diverse physical and chemical environments. Understanding the molecular mechanisms that drive biofilm heterogeneity and adaptation to different environmental niches is crucial for developing more effective strategies to control their formation. In this study, we developed a tightly dual-regulated CRISPR interference (CRISPRi) system and employed multi-scale imaging to investigate the functions of individual genes in two distinct biofilm models: the floating pellicle and the intricate, three-dimensionally structured macrocolony, which develop at the liquid-air and solid-air interfaces, respectively. Our findings validated the CRISPRi approach as a powerful method for studying biofilm development over extended periods and revealed that numerous small non-coding RNAs are involved in regulating biofilm growth dynamics and architecture. The CRISPRi approach was also applied to a pool of 507 genes and transcription units, including protein-coding genes and non-coding RNAs, to screen for cell fitness in these two biofilm models. We discovered that, while both biofilm forms rely on fundamental processes such as cell wall synthesis and nucleotide metabolism, they exhibit different genetic dependencies with regard to matrix composition, motility, and signaling. Exopolysaccharide production, motility, and chemotaxis are crucial for pellicle formation. In contrast, macrocolony development is influenced by γ-polyglutamate synthesis and nutrient acquisition functions. Genes of unknown function were also identified to play a differentially important role in the two biofilm forms. Additionally, the CRISPRi screens revealed further non-coding RNAs regulating biofilm architecture and growth dynamics, adding to the existing layers of post-transcriptional control. Collectively, these results demonstrate that biofilm formation at different physical interfaces is governed by a combination of shared and unique genetic pathways tailored to the specific biofilm environment, thereby opening research avenues into the molecular mechanisms specific to the solid-air and liquid-air interfaces. ### Competing Interest Statement The authors have declared no competing interest.
Rxiv mechanobio