Solution structure of the DNA binding domain of a nucleoid‐associated protein, H‐NS, from <i>Escherichia coli</i>

Shindo, Heisaburo; Iwaki, Takanobu; Ieda, Ryoichi; Kurumizaka, Hitoshi; Ueguchi, Chiharu; Mizuno, Takeshi; Morikawa, Souichi; Nakamura, Haruki; Kuboniwa, Hitoshi

doi:10.1016/0014-5793(95)00079-o

Cited by 124 publications

(137 citation statements)

References 27 publications

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“…The two helices are perpendicular to and packed against each other through hydrophobic interactions among residues Ile83, Arg84, Ala87, Val94, Ile100, and Val104 and aromatic stacking between Trp86 and Tyr108. The structure of Lsr2C is unique and distinct from that of H-NS, which consists of two short β-strands and an α-helix linked by a loop (40,41). A protein structure database search using DALI did not identify any structure with a z-score over 3.0.…”

Section: Lsr2mentioning

confidence: 95%

Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes inMycobacterium tuberculosis

Gordon

Li²,

Wang

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

202

250

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Bacterial nucleoid-associated proteins play important roles in chromosome organization and global gene regulation. We find that Lsr2 of Mycobacterium tuberculosis is a unique nucleoid-associated protein that binds AT-rich regions of the genome, including genomic islands acquired by horizontal gene transfer and regions encoding major virulence factors, such as the ESX secretion systems, the lipid virulence factors PDIM and PGL, and the PE/PPE families of antigenic proteins. Comparison of genome-wide binding data with expression data indicates that Lsr2 binding results in transcriptional repression. Domain-swapping experiments demonstrate that Lsr2 has an N-terminal dimerization domain and a C-terminal DNA-binding domain. Nuclear magnetic resonance analysis of the DNA-binding domain of Lsr2 and its interaction with DNA reveals a unique structure and a unique mechanism that enables Lsr2 to discriminately target AT-rich sequences through interactions with the minor groove of DNA. Taken together, we provide evidence that mycobacteria have employed a structurally distinct molecule with an apparently different DNA recognition mechanism to achieve a function similar to the Enterobacteriaceae H-NS, likely coordinating global gene regulation and virulence in this group of medically important bacteria.

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Section: Lsr2mentioning

confidence: 95%

Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes inMycobacterium tuberculosis

Gordon

Li²,

Wang

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

202

250

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“…2). The DNA-binding region was identified by showing that a C-terminal 47-amino-acid fragment of proteolytically digested H-NS protein binds to curved DNA, although with much lower affinity than intact H-NS (Shindo et al, 1995). This DNA-binding domain appears to be unique as its three-dimensional structure does not show any similarity to other DNA-binding proteins (Fig.…”

Section: Structure and Isoforms Of H-nsmentioning

confidence: 99%

“…eco: E. coli; shi: Shigella flexneri; sty : Salmonella typhimurium; sma: Serratia marcescens; pvu : Proteus vulgaris; hin: Haemophilus influenzae; Asterisks indicate identical amino acids in all sequences, and full points indicate conserved amino acids. The E. coli H-NS dimerization domain (Williams et al, 1996) and the DNA-binding domain and its secondary structure (Shindo et al, 1995) are indicated above the sequence. Jagged lines, ␤1 and ␤2 indicate ␤-sheets; solid lines indicate L1, L2 and L3; loops indicate ␣-helix.…”

Section: Figmentioning

confidence: 99%

H‐NS: a modulator of environmentally regulated gene expression

Atlung

Ingmer

1997

Molecular Microbiology

455

409

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SummaryH-NS is a small chromatin-associated protein found in enterobacteria. H-NS has affinity for all types of nucleic acids but binds preferentially to intrinsically curved DNA. The major role of H-NS is to modulate the expression of a large number of genes, mostly by negatively affecting transcription. Many of the H-NS-modulated genes are regulated by environmental signals, and expression of most of these genes is positively regulated by specific transcription factors. Therefore one of the purposes of H-NS could be to repress expression of some genes under conditions characteristic of a non-intestinal environment, but allow expression of specific genes in response to certain stimuli in the intestinal environment. The hns gene is autoregulated. In vivo the H-NS to DNA ratio is fairly constant except during cold shock, when it increases threeto fourfold. In this review we propose that only the preferential binding to intrinsically curved DNA plays a role under normal growth conditions, and we discuss the different mechanisms by which H-NS might affect gene expression and how H-NS could be involved in the response to different stress situations. Finally, we summarize the evolutionary and functional relationship between H-NS and the homologous StpA.

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“…Moreover, using FROST, a fold-recognition method (http://www-mig. jouy.inra.fr), this domain was predicted to share the same three-dimensional structure as the E. coli H-NS C-domain resolved previously by NMR (Shindo et al, 1995). Finally, the expression of the strain Y1000 protein structural gene in an E. coli mutant fully reversed additional hns-related phenotypes, for example, the loss of motility on semi-solid medium and the ability to use b-glucoside as a sole carbon source, as observed previously with other H-NS-like proteins (Goyard & Bertin, 1997;Bertin et al, 1999Bertin et al, , 2001Tendeng et al, 2000).…”

mentioning

confidence: 96%