The structure of the biocrystalline nucleoid and its role in the regulation of dissociative phenotypic heterogeneity of microbial populations

The survival of the microbial population in constantly changing environmental conditions, including those unfavorable for growth, is ensured by: (1) the formation of a subpopulation of persister cells (P), maturing into ametabolic quiescent forms (RF); (2) protection of chromosomal DNA of stationary cells using the physicochemical mechanism of its co-crystallization with the nucleoid-associated protein Dps and the formation of a biocrystalline nucleoid (BN); (3) the ability of RF to germinate in a fresh environment with a mixed population of phenotypically different dissociators, one of which will be the most adaptive to it. This study addressed two questions: (1) how BN is structurally organized in prokaryotic RFs, and (2) how nucleoid biocrystallization is related to the phenotypic heterogeneity of populations growing from RFs. The work proposes a new model of BN decrystallization/recrystallization during heating/cooling of RF at sublethal temperatures in a non-growth environment, which reproduces the dynamics of BN formation in the model of nucleoid organization as a folded globule. Electron microscopic analysis of structural changes in BN in heated/cooled RFs, together with the determination of the dissociative spectra of the populations growing from them, allowed us to obtain the following new information. Biocrystallization of the nucleoid occurs in the following sequence: (1) the beginning co-crystallization of DNA-Dps is accompanied by the division of the nucleoid volume with the formation of a compacted nucleoid from superfolded DNA in the central region of the cell and loops of superfolded linear DNA extending from it; (2) co-crystallization of looped DNA-Dps with its different geometric arrangement – toroidal, lamellar, etc.; (3) crystallization of Dps-Dps, repeating the template folding of looped DNA-Dps and the formation of a multilayer structure of the Dps-Dps crystalline array. It was found that the actual heating of the PF (45‒700C, 15 min), leading to decrystallization of looped DNA-Dps while maintaining the structure of the compacted nucleoid, does not affect the dissociative (colonial-morphological) spectrum of the population growing from the PF. The change in its dissociative spectrum is influenced by the process of DNA-Dps recrystallization, during which, apparently, Dps binds not only to the former, but also to other DNA sites, also affinity for Dps and, possibly, partially occupied by other nucleoid-associated proteins, which influences changes in DNA topology and its transcription.