Molecular Cytology of ‘Little Animals’: Personal Recollections of Escherichia coli (and Bacillus subtilis)

Nanninga, Nanne

doi:10.3390/life13081782

Cited by 2 publications

(2 citation statements)

References 164 publications

(293 reference statements)

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“…They also calculated theoretical RI values, using the data of Churchward and Bremer [ 29 ] for the macromolecular composition of E. coli and the measurements of cellular and nucleoid volumes of their cells. For these volume measurements, they used an early confocal scanning light microscope (CSLM) developed by Brakenhoff et al [ 30 ] (for a review of its rediscovery, see Nanninga [ 31 ]). This microscope had improved optical resolution and visualized the unstained nucleoid by mere absorption contrast (see Figure 1 in [ 28 ]).…”

Section: The Nucleoid As a Low-density Structurementioning

confidence: 99%

Compaction and Segregation of DNA in Escherichia coli

Woldringh

2024

Life

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Theoretical and experimental approaches have been applied to study the polymer physics underlying the compaction of DNA in the bacterial nucleoid. Knowledge of the compaction mechanism is necessary to obtain a mechanistic understanding of the segregation process of replicating chromosome arms (replichores) during the cell cycle. The first part of this review discusses light microscope observations demonstrating that the nucleoid has a lower refractive index and thus, a lower density than the cytoplasm. A polymer physics explanation for this phenomenon was given by a theory discussed at length in this review. By assuming a phase separation between the nucleoid and the cytoplasm and by imposing equal osmotic pressure and chemical potential between the two phases, a minimal energy situation is obtained, in which soluble proteins are depleted from the nucleoid, thus explaining its lower density. This theory is compared to recent views on DNA compaction that are based on the exclusion of polyribosomes from the nucleoid or on the transcriptional activity of the cell. These new views prompt the question of whether they can still explain the lower refractive index or density of the nucleoid. In the second part of this review, we discuss the question of how DNA segregation occurs in Escherichia coli in the absence of the so-called active ParABS system, which is present in the majority of bacteria. How is the entanglement of nascent chromosome arms generated at the origin in the parental DNA network of the E. coli nucleoid prevented? Microscopic observations of the position of fluorescently-labeled genetic loci have indicated that the four nascent chromosome arms synthesized in the initial replication bubble segregate to opposite halves of the sister nucleoids. This implies that extensive intermingling of daughter strands does not occur. Based on the hypothesis that leading and lagging replichores synthesized in the replication bubble fold into microdomains that do not intermingle, a passive four-excluding-arms model for segregation is proposed. This model suggests that the key for segregation already exists in the structure of the replication bubble at the very start of DNA replication; it explains the different patterns of chromosome arms as well as the segregation distances between replicated loci, as experimentally observed.

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Section: The Nucleoid As a Low-density Structurementioning

confidence: 99%

Compaction and Segregation of DNA in Escherichia coli

Woldringh

2024

Life

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“…Nanninga [9] gives his recollections of the origins of electron microscopy at Amsterdam University, and the importance of freeze-fracturing. He relates how the study of the cell cycle used electron microscopy to analyze bacteria grown in a steady state, and to show that the zonal growth of the envelope could not be responsible for the segregation of envelopeattached DNA.…”

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confidence: 99%