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) formation of a subpopulation of persister cells (Ps), maturing into ametabolic dormant forms (DFs); (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); and (3) the ability of DFs to germinate in a fresh environment, yielding a mixed population of phenotypically different variants, one of which will be the most adaptive to it. This study addressed two questions: (1) how BN is structurally organized in prokaryotic DFs, and (2) how nucleoid biocrystallization is related to the phenotypic heterogeneity of populations growing from DFs. The present work proposes a new model of BN decrystallization/recrystallization during heating/cooling of DFs 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 DFs, together with 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) incipient co-crystallization of DNA−Dps is accompanied by the division of the nucleoid volume with 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 is accompanied by its diverse geometric arrangement—toroidal, lamellar, etc.; and (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 DF (45‒70°C, 15 min), leading to decrystallization of looped DNA−Dps while maintaining the structure of the compacted nucleoid, did not affect the phase variation (colonial-morphological) spectrum of the population growing from the DFs. 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 having affinity for Dps and, possibly, partially occupied by other nucleoid-associated proteins. This influences changes in DNA topology and its transcription.