Chromosomal “Stress-Response ” Domains Govern the Spatiotemporal Expression of the Bacterial Virulence Program

X.J. and P.S. contributed equally to this article. ABSTRACT Recent studies strongly suggest that the gene expression sustaining both normal and pathogenic bacterial growth is governed by the structural dynamics of the chromosome. However, the mechanistic device coordinating the chromosomal con-figuration with selective expression of the adaptive traits remains largely unknown.We used a holistic approach exploring the inherent relationships between the physicochemical properties of the DNA and the expression of adaptive traits, including viru-lence factors, in the pathogenDickeya dadantii (formerly Erwinia chrysanthemi). In the transcriptomes obtained under adverse conditions encountered during bacterial infection, we explored the patterns of chromosomal DNA sequence organization, su-percoil dynamics, and gene expression densities, together with the long-range regulatory impacts of the abundant DNA architec-tural proteins implicated in pathogenicity control. By integrating these data, we identified transient chromosomal domains of coherent gene expression featuring distinct couplings between DNA thermodynamic stability, supercoil dynamics, and virulence traits. IMPORTANCE We infer that the organization of transient chromosomal domains serving specific functions acts as a fundamental device for versatile adjustment of the pathogen to environmental stress. We believe that the identification of chromosomal “stress-response ” domains harboring distinct virulence traits andmediating the cellular adaptive behavior provides a break