Accessory Factors and Nucleoid Binding Proteins

In bacteria such as E. coli, there are several rather nonspecific DNA-binding proteins that are sometimes referred to as accessory factors or histone-like proteins. They function partly in affecting chromosome structure and partly in gene regulation. Some tend histone-like protein Bacterial protein that binds nonspecifically to DNA and participates in maintaining the structure of the nucleoid;they do not actually have much in common with true histones

Action at a Distance and DNA Looping 257

Bacterial DNA is covered with non-specific binding proteins.

Action at a Distance and DNA Looping 257

FIGURE 9.24 H-NS Binds Preferentially to Curved DNA

A. Structure of the linear DNA fragment used as predicted by the CURVATURE program. The fragment is shown in the plane of its intrinsic curvature. B. Atomic force microscope (AFM) image of naked linear DNA molecules with the curved region at one-third of their length. The image shows an area 900 x 900 nm. C. AFM image of DNA after incubation with H-NS (1 monomer per 20 bp). H-NS-DNA complexes are specifically formed at the position of the curved region only. The image shows a 300 x 300 nm surface area. The color scale ranges from 0.0 to 3.0 nm (from dark to bright). From: Structural basis for preferential binding of H-NS to curved DNA Dame RT, Wyman C, Goosen N, Biochimie 83 (2001) 231-234.

FIGURE 9.24 H-NS Binds Preferentially to Curved DNA

A. Structure of the linear DNA fragment used as predicted by the CURVATURE program. The fragment is shown in the plane of its intrinsic curvature. B. Atomic force microscope (AFM) image of naked linear DNA molecules with the curved region at one-third of their length. The image shows an area 900 x 900 nm. C. AFM image of DNA after incubation with H-NS (1 monomer per 20 bp). H-NS-DNA complexes are specifically formed at the position of the curved region only. The image shows a 300 x 300 nm surface area. The color scale ranges from 0.0 to 3.0 nm (from dark to bright). From: Structural basis for preferential binding of H-NS to curved DNA Dame RT, Wyman C, Goosen N, Biochimie 83 (2001) 231-234.

to have negative effects on gene expression (e.g., H-NS, StpA), whereas, others usually act in a positive manner (e.g., HU, IHF). However, these regulatory effects tend to be indirect and rather nonspecific.

The primary role of the H-NS (histone-like nucleoid structuring) protein of E. coli and related bacteria is to maintain the structure of the bacterial nucleoid. The term nucleoid refers to the compact structure formed by the bacterial chromosome together with its accessory proteins. H-NS protein binds in a relatively nonspecific manner, although it prefers regions of bent DNA as illustrated in Fig. 9.24. H-NS consists of two domains, one for DNA-binding and one for protein-protein interaction. These domains are joined by a linker region. H-NS binds to DNA and then the H-NS proteins bind to each other, forming aggregates of four or more H-NS units, thus helping the condensation of the DNA into the nucleoid.

In addition, H-NS binds with higher affinity to the regulatory regions of a wide range of genes scattered throughout the bacterial chromosome. Most of these genes respond to some sort of environmental conditions, but apart from this they are unrelated. The presence of H-NS represses these genes. In contrast to genuine global regulators, H-NS does not control a specific response nor does it respond to any particular signal; therefore, this effect is referred to as silencing. Induction of these genes requires specific transcriptional activators to overcome the silencing.

The StpA protein is very similar to H-NS but is present in smaller amounts and appears predominantly under certain stressful conditions (e.g., high temperature or high osmotic pressure). The protein-binding domains of StpA and H-NS bind to each other so that mixed aggregates are formed. StpA silences fewer genes than H-NS. In particular, it allows expression of genes induced by stress. For example, the proU gene, expressed at high osmotic pressure, is silenced by H-NS but not by StpA.

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