Lack of the H-NS Protein Results in Extended and Aberrantly Positioned DNA during Chromosome Replication and Segregation in Escherichia coli

Abstract

The architectural protein H-NS binds nonspecifically to hundreds of sites throughout the chromosome and can multimerize to stiffen segments of DNA as well as to form DNA-protein-DNA bridges. H-NS has been suggested to contribute to the orderly folding of the Escherichia coli chromosome in the highly compacted nucleoid. In this study, we investigated the positioning and dynamics of the origins, the replisomes, and the SeqA structures trailing the replication forks in cells lacking the H-NS protein.In H-NS mutant cells, foci of SeqA, replisomes, and origins were irregularly positioned in the cell. Further analysis showed that the average distance between the SeqA structures and the replisome was increased by ϳ100 nm compared to that in wild-type cells, whereas the colocalization of SeqA-bound sister DNA behind replication forks was not affected. This result may suggest that H-NS contributes to the folding of DNA along adjacent segments. H-NS mutant cells were found to be incapable of adopting the distinct and condensed nucleoid structures characteristic of E. coli cells growing rapidly in rich medium. It appears as if H-NS mutant cells adopt a "slow-growth" type of chromosome organization under nutrient-rich conditions, which leads to a decreased cellular DNA content. IMPORTANCE It is not fully understood how and to what extent nucleoid-associated proteins contribute to chromosome folding and organization during replication and segregation in Escherichia coli. In this work, we find in vivo indications that cells lacking the nucleoid-associated protein H-NS have a lower degree of DNA condensation than wild-type cells. Our work suggests that H-NS is in-volved in condensing the DNA along adjacent segments on the chromosome and is not likely to tether newly replicated strands of sister DNA. We also find indications that H-NS is required for rapid growth with high DNA content and for the formation of a highly condensed nucleoid structure under such conditions. A cross all domains of life, it is crucial that genomes are structurally organized in a way that compacts DNA to fit inside the confined space of a cell and at the same time allows for interaction with key proteins performing replication, transcription, recombination, and repair (1-7). Unlike eukaryotic cells, bacterial cells do not possess an envelope-enclosed organelle for storage and handling of genomic DNA. The DNA is instead organized into compact bodies called nucleoids (3)(4)(5)8). These nucleoids are highly complex, and the underlying organizational mechanisms appear to be remarkably similar to that of eukaryotic cells (3, 9). The nucleoid occupies the central part of the bacterial cell (8), and its shape is dependent on a variety of factors, such as environmental conditions or genetic mutations (7, 10-13). For example, significant nucleoid compaction occurs after exposure of Escherichia coli to UV light, due to a global reorganization in response to DNA damage and the activation of the SOS response (12, 13).Certain types of proteins, called nucle...

Charged residues in the H-NS linker drive DNA binding and gene silencing in single cells

“…Our observation that H-NS does not play a major role in nucleoid compaction also explains why hns deletions are tolerated in E. coli, since nucleoid relaxation would be expected to be deleterious. In previous reports, the number of origins in an hns null was less than the wild type (39)(40)(41), with fewer DNA replication forks and less DNA content. This could explain why ΔL has a more compact nucleoid (12% smaller than wild type).…”

Nucleoid Associated Proteins: The Small Organizers That Help to Cope With Stress

“…Depending on a given NAP's DNA-binding specificity and number of target DNA sequences, it can simultaneously affect the transcription of many genes/gene clusters or act as a specific switch that alters the expression levels of certain genes (Gordon et al, 2010;Prieto et al, 2012;Gehrke et al, 2019;Shahul Hameed et al, 2019). H-NS, which exhibits DNA-bridging activity (Figure 1), was shown to be a global transcription repressor in human pathogens, including Salmonella enterica serovar Typhimurium, Vibrio cholerae, and toxigenic strains of E. coli (Ayala et al, 2015;Helgesen et al, 2016;Shahul Hameed et al, 2019). Additionally, it was shown that a H-NS paralog, StpA protein cooperate with H-NS to alter virulence genes expression in uropathogenic E. coli strains (Müller et al, 2006).…”

The MukB–topoisomerase IV interaction is required for proper chromosome compaction

“…Binding of nucleoid-associated proteins clearly plays a role, as does DNA topology modulated through the action of topoisomerases (2,3) and transcription and translation (31). Recent studies have indicated that the nucleoid-associated protein H-NS may be responsible for condensing DNA along adjacent segments of the chromosome (32), whereas changes in the multimerization state of HU brought about by the differential expression of the two alleles can allow dynamic changes in nucleoid architecture (33).…”