The DNA Binding Protein H-NS Binds to and Alters the Stability of RNA in vitro and in vivo

Brescia, Cristin C

doi:10.1016/s0022-2836(04)00382-1

Cited by 31 publications

(39 citation statements)

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“…Bacterial NAPs (e.g., the 9-kD HU, 11-kD Fis [for factor for inversion stimulation] and 15 kD H-NS proteins) have in common a low molecular mass, a high Lys content, and nonspecific binding to DNA (Luijsterburg et al, 2006;Dillon and Dorman, 2010) and to other nucleic acids (Balandina et al, 2002;Brescia et al, 2004;Kamashev et al, 2008). SWIB-4 has a histonelike domain that is likely to be involved in binding to DNA as well as RNA and single-stranded DNA as also shown for histones (Spelsberg et al, 1970).…”

Section: Discussionmentioning

confidence: 99%

The Core of Chloroplast Nucleoids Contains Architectural SWIB Domain Proteins

et al. 2012

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A highly enriched fraction of the transcriptionally active chromosome from chloroplasts of spinach (Spinacia oleracea) was analyzed by two-dimensional gel electrophoresis and mass spectrometry to identify proteins involved in structuring of the nucleoid core. Among such plastid nucleoid-associated candidate proteins a 12-kD SWIB (SWI/SNF complex B) domaincontaining protein was identified. It belongs to a subgroup of low molecular mass SWIB domain proteins, which in Arabidopsis thaliana has six members (SWIB-1 to SWIB-6) with predictions for localization in the two DNA-containing organelles. Green/red fluorescent protein fusions of four of them were shown to be targeted to chloroplasts, where they colocalize with each other as well as with the plastid envelope DNA binding protein in structures corresponding to plastid nucleoids. For SWIB-6 and SWIB-4, a second localization in mitochondria and nucleus, respectively, could be observed. SWIB-4 has a histone H1 motif next to the SWIB domain and was shown to bind to DNA. Moreover, the recombinant SWIB-4 protein was shown to induce compaction and condensation of nucleoids and to functionally complement a mutant of Escherichia coli lacking the histone-like nucleoid structuring protein H-NS.

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Section: Discussionmentioning

confidence: 99%

The Core of Chloroplast Nucleoids Contains Architectural SWIB Domain Proteins

et al. 2012

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“…H-NS is a small, abundant protein with DNA-and RNAbinding activity (Brescia et al, 2004). It consists of an amino-terminal oligomerization domain that is attached to a carboxyl-terminal nucleic acid-binding domain by a flexible linker peptide (Badaut et al, 2002;Dorman et al, 1999).…”

Section: H-ns and Transcription Repressionmentioning

confidence: 99%

Anti-silencing: overcoming H-NS-mediated repression of transcription in Gram-negative enteric bacteria

2008

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“…DsrA half-life was determined as described 37,55 . Cultures of wild-type and hfq − strains were grown at 30 °C to A 600 = 0.4-0.6.…”

Section: Purification Of Rna For Half-life Studiesmentioning

confidence: 99%

Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs

Mikulecky

Kaw

Brescia

et al. 2004

Nat Struct Mol Biol

225

395

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The bacterial Sm-like protein Hfq facilitates RNA-RNA interactions involved in posttranscriptional regulation of the stress response. Specifically, Hfq helps pair noncoding RNAs (ncRNAs) with complementary regions of target mRNAs. To probe the mechanism of this pairing, we generated a series of Hfq mutants and measured their affinity for RNAs like those with which Hfq must associate in vivo. We tested the mutants' DsrA-dependent activation of rpoS, and their ability to stabilize DsrA ncRNA against degradation in vivo. Our results suggest that Hfq has two independent RNA-binding surfaces. In addition to a well-known site around the core of the Hfq hexamer, we observe interactions with the distal face of Hfq, a new locus with which mRNAs and poly(A) sequences associate. Our model explains how Hfq can simultaneously bind a ncRNA and its mRNA target to facilitate the strand displacement reaction required for Hfq-dependent translational regulation.Hfq protein from Escherichia coli was first described in connection with Qβ-phage replication 1,2 . Hfq has recently emerged as a central player in post-transcriptional gene regulation as mediated by bacterial ncRNAs [3][4][5][6] . Escherichia coli Hfq mutants show disrupted signaling in stress response pathways 7,8 , arising from the need for Hfq to mediate base-pairing between regulatory ncRNAs and their mRNA targets. Examples of these partnerships include DsrA-rpoS 7,9,10 , OxyS-fhlA 11,12 , OxyS-rpoS 13 , RprA-rpoS 14 , RyhBsodB [15][16][17] .Complexes between ncRNAs and their mRNA targets function in several ways. Most commonly, complexed structures lead to translational activation or repression by remodeling mRNA regulatory regions containing the ribosome-binding site (RBS) and/or start codon. Alternatively, the interaction can enhance decay of the target mRNA16 or simply block translation11. Clearly, Hfq facilitates base-pairing between ncRNAs and their targets, but how it does so is poorly understood. How the chaperone function relates to other Hfq activities such as the control of poly(A) tail elongation19 , 20 and regulation of mRNA stability21 , 22 is also unknown. COMPETING INTERESTS STATEMENTThe authors declare that they have no competing financial interests. NIH Public Access Author ManuscriptNat Struct Mol Biol. Author manuscript; available in PMC 2011 April 5. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author ManuscriptHfq shares sequence similarity to the eukaryotic Lsm proteins [23][24][25][26][27] We addressed these questions through a mutational analysis of Hfq, probing in vitro binding to several model RNAs that represent species with which Hfq must interact. Hfq mutants were assayed in vivo using a reporter assay and RNA lifetime experiments. Together, the results support a model wherein at least two independent RNA-binding sites exist on the Hfq hexamer, and juxtaposition of bound RNAs facilitates base-pairing. RESULTS Hfq mutagenesisTo identify amino acids essential for RNA binding, we constructed a series of E. coli Hfq misse...

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The DNA Binding Protein H-NS Binds to and Alters the Stability of RNA in vitro and in vivo

Cited by 31 publications

References 0 publications

The Core of Chloroplast Nucleoids Contains Architectural SWIB Domain Proteins

The Core of Chloroplast Nucleoids Contains Architectural SWIB Domain Proteins

Anti-silencing: overcoming H-NS-mediated repression of transcription in Gram-negative enteric bacteria

Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs

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