Genome-wide identification of H-NS-controlled, temperature-regulated genes in Escherichia coli K-12

Global regulator H-NS and lipoprotein NlpI influence production of extracellular DNA in Escherichia coli

Extracellular DNA (eDNA) is a structural component of the polymeric matrix of biofilms from different species. Different mechanisms for DNA release have been proposed including lysis of cells, lysis of DNA-containing vesicles, and DNA secretion. Here, a genome-wide screen of 3985 non-lethal mutations was performed to identify genes whose deletion alters eDNA release in Escherichia coli. Deleting nlpI, yfeC, and rna increased eDNA from planktonic cultures while deleting hns and rfaD decreased eDNA production. The lipoprotein NlpI negatively affects eDNA release since the overexpression of nlpI decreases eDNA 16 fold while deleting nlpI increases eDNA threefold. The global regulator H-NS is required for eDNA production since DNA was not detected for the hns mutant and production of H-NS restored eDNA production to wild-type levels. Therefore our results suggest that secretion may play a role in eDNA release in E. coli since the effect of the hns deletion on cell lysis (slight decrease) and membrane vesicles (threefold increase) does not account for the reduction in eDNA.

Controlling biofilm formation, prophage excision and cell death by rewiring global regulator H-NS of Escherichia coli

The global regulator H-NS of Escherichia coli controls genes related to stress response, biofilm formation and virulence by recognizing curved DNA and by silencing acquired genes. Here, we rewired H-NS to control biofilm formation using protein engineering; H-NS variant K57N was obtained that reduces biofilm formation 10-fold compared with wild-type H-NS (wild-type H-NS increases biofilm formation whereas H-NS K57N reduces it). Whole-transcriptome analysis revealed that H-NS K57N represses biofilm formation through its interaction with the nucleoid-associated proteins Cnu and StpA and in the absence of these proteins, H-NS K57N was unable to reduce biofilm formation. Significantly, H-NS K57N enhanced the excision of defective prophage Rac while wild-type H-NS represses excision, and H-NS controlled only Rac excision among the nine resident E. coli K-12 prophages. Rac prophage excision not only led to the change in biofilm formation but also resulted in cell lysis through the expression of toxin HokD. Hence, the H-NS regulatory system may be evolved through a single-amino-acid change in its N-terminal oligomerization domain to control biofilm formation, prophage excision and apoptosis.

The absence of inorganic salt is required for the crystallization of the complete oligomerization domain of Salmonella typhimurium histone-like nucleoid-structuring protein

The histone-like nucleoid-structuring protein (H-NS) plays an important role in both DNA packaging and global gene regulation in enterobacteria. Self-association of the N-terminal domain results in polydisperse oligomers that are critical to the function of the protein. This heterogeneity in oligomer size has so far prevented structure determination of the complete oligomerization domain by NMR or X-ray crystallography. In the absence of inorganic salt, the H-NS oligomerization domain is predominantly restricted to an equilibrium between a homodimer and homotetramer, allowing a protein solution to be prepared that is sufficiently homogeneous for successful crystallization. Crystallization was achieved by tailoring the conditions screened to those identified as minimizing the potential disruption of protein-solution homogeneity. This finding provides a significant step towards resolving the structure of this important prokaryotic protein.

Microbial thermosensors

Temperature is among the most important of the parameters that free-living microbes monitor. Microbial physiology needs to be readjusted in response to sudden temperature changes. When the ambient temperature rises or drops to potentially harmful levels, cells mount protective stress responses--so-called heat or cold shock responses, respectively. Pathogenic microorganisms often respond to a temperature of around 37 degrees C by inducing virulence gene expression. There are two main ways in which temperature can be measured. Often, the consequences of a sudden temperature shift are detected. Such indirect signals are known to be the accumulation of denatured proteins (heat shock) or stalled ribosomes (cold shock). However, this article focuses solely on direct thermosensors. Since the conformation of virtually every biomolecule is susceptible to temperature changes, primary sensors include DNA, RNA, proteins and lipids.

Investigation of the self-association and hetero-association interactions of H-NS and StpA from Enterobacteria

The nucleoid-associated protein H-NS and its paralogue StpA are global regulators of gene expression and form an integral part of the protein scaffold responsible for DNA condensation in Escherichia coli and Salmonella typhimurium. Although protein oligomerization is a requirement for this function, it is not entirely understood how this is accomplished. We address this by reporting on the self-association of H-NS and its hetero-association with StpA. We identify residues 1-77 of H-NS as being necessary and sufficient for high-order association. A multi-technique-based approach was used to measure the effects of salt concentration on the size distribution of H-NS and the thermal stability of H-NS and StpA dimers. The thermal stability of the StpA homodimer is significantly greater than that of H-NS(1-74). Investigation of the hetero-association of H-NS and StpA proteins suggested that the association of H-NS with StpA is more stable than the self-association of either H-NS or StpA with themselves. This provides a clear understanding of the method of oligomerization of these important proteins in effecting DNA condensation and reveals that the different associative properties of H-NS and StpA allow them to perform distinct, yet complementary roles in the bacterial nucleoid.

Genome-wide identification of H-NS-controlled, temperature-regulated genes in Escherichia coli K-12

DNA microarrays demonstrate that H-NS controls 69% of the temperature regulated genes in Escherichia coli K-12. H-NS is shown to be a common regulator of multiple iron and other nutrient acquisition systems preferentially expressed at 37 degrees C and of general stress response, biofilm formation, and cold shock genes highly expressed at 23 degrees C.