Bacterial 3D genome architecture: organization, regulation, and synthetic biology applications

Bacterial chromosomes are compacted into hierarchical three-dimensional (3D) architectures that underpin essential processes such as replication, transcription, and segregation. However, detailed principles governing genome architecture and its regulation remain incompletely understood. Here we review current knowledge on structural organization of bacterial 3D genomes and their regulatory factors, integrating insights from chromosome conformation capture and imaging studies. We highlight how genome architecture dynamically responds to environmental cues. We also discuss potential applications of bacterial 3D genomics, particularly in synthetic biology. These findings provide a framework for understanding bacterial genomic homeostasis and adaptation, offering opportunities for engineering microbial systems and novel therapies.