Twelve Species of the Nucleoid-associated Protein from Escherichia coli

Azam, Talukder Ali; Ishihama, Akira

doi:10.1074/jbc.274.46.33105

Cited by 428 publications

(360 citation statements)

References 71 publications

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“…The fits to the data corresponding to 1,250 nM IHF yielded the fractional compaction L 1 ͞L 0 , the length of the segment associated with an IHF molecule ᐉ, and an effective dissociation constant K dis , which we display in Table 1. The values of K dis for both fixed and slide cases are higher by Ϸ3 orders of magnitude than the nanomolar scale characteristic specific binding and are in reasonable agreement with the accepted value (Ϸ1.5 M) for nonspecific binding (24)(25)(26). We note, however, that the values of K dis deduced from our measurements comprise a weighted average over all binding sites on the -DNA molecule, with all their spectrum of affinities, and therefore cannot be faithfully compared with measurements carried out on small oligomers with binding sites of well-characterized affinity.…”

Section: Number Of Bound Ihf Molecules In a -Dna-ihf Complexsupporting

confidence: 70%

Compaction of single DNA molecules induced by binding of integration host factor (IHF)

Ali

Amit

Braslavsky

et al. 2001

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

116

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We studied the interaction between the integration host factor (IHF), a major nucleoid-associated protein in bacteria, and single DNA molecules. Force-extension measurements of DNA and an analysis of the Brownian motion of small beads tethered to a surface by single short DNA molecules, in equilibrium with an IHF solution, indicate that: (i) the DNA-IHF complex retains a random, although more compact, coiled configuration for zero or small values of the tension, (ii) IHF induces DNA compaction by binding to multiple DNA sites with low specificity, and (iii) with increasing tension on the DNA, the elastic properties of bare DNA are recovered. This behavior is consistent with the predictions of a statistical mechanical model describing how proteins bending DNA are driven off by an applied tension on the DNA molecule. Estimates of the amount of bound IHF in DNA-IHF complexes obtained from the model agree very well with independent measurements of this quantity obtained from the analysis of DNA-IHF crosslinking. Our findings support the long-held view that IHF and other histone-like proteins play an important role in shaping the longscale structure of the bacterial nucleoid.T he genetic material in bacterial cells is organized in a structure called the nucleoid (1-3). In Escherichia coli, this nucleoprotein complex consists of a single circular DNA molecule 4.7 million bp long, RNA, and a large variety of bound proteins. Among these, about 10 so-called histone-like proteins, including HU, integration host factor (IHF), and H-NS (1-3), shape the short-scale structure of the nucleoid by bending DNA locally on binding. These proteins therefore play an important role in compacting the DNA molecule, in addition to other factors such as supercoiling (4), macromolecular crowding (5), and osmotic effects (6).The level of nucleoid-associated proteins changes as a function of bacterial growth. For example, the level of IHF was shown to increase on entry to the stationary phase of growth, becoming one of the major histone-like proteins in the cell (7-10). By binding to specific DNA sites, IHF participates in forming higher-order DNA structures required for replication, sitespecific recombination, phage packaging, and regulation of transcription initiation (8). IHF can also bind to DNA nonspecifically and can be substituted by HU. In fact, IHF and HU possess similar overall structures and share several regions of conserved homologies (11,12).Very little is known about the structural modifications on DNA induced by histone-like proteins in nucleoid formation. In particular, the degree of compaction induced by each of these proteins has not been quantified, and information about the large-scale structure of nucleoprotein complexes is scarce. This deficiency stems in part from the fact that classical techniques used in molecular biology are designed for studying relatively strong DNA-binding sites and cannot appropriately assess the contribution of nonspecific low-affinity interactions. Furthermore, analyses based on electron micr...

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Section: Number Of Bound Ihf Molecules In a -Dna-ihf Complexsupporting

confidence: 70%

Compaction of single DNA molecules induced by binding of integration host factor (IHF)

Ali

Amit

Braslavsky

et al. 2001

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

116

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“…DsrA binds to the protein Hfq (21,26), which is associated with ribosomes in E. coli cells (28). Hfq interacts with a variety of RNA and DNA sequences (29,30). Western blotting analysis using Hfq antisera (the kind gift of Gisela Storz) demonstrated no detectable levels of Hfq in either 30 S ribosomal subunit or 70 S ribosome preparations (data not shown), strongly suggesting that binding of the DsrA to the 30 S subunit resulted from an interaction of the ncRNA with 16 S rRNA or small subunit ribosomal proteins.…”

Section: Resultsmentioning

confidence: 99%

“…We expected that Hfq might be associated with our 30 S subunits and be involved in DsrA ncRNA binding. Hfq specifically binds a 3Ј domain in DsrA (26) and has been shown to interact strongly with DNA sequences (29,30). Western blot analysis using Hfq antisera demonstrates it is not present at detectable levels in our 30 S subunit preparations and therefore is not responsible for the interaction of the molecules with the 30 S subunit in our in vitro assays.…”

Section: Discussionmentioning

confidence: 98%

Interactions of the Non-coding RNA DsrA and RpoS mRNA with the 30 S Ribosomal Subunit

Worhunsky

Godek

Litsch

et al. 2003

Journal of Biological Chemistry

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“…It exists in one of its homodimeric forms (HUa 2 or HUb 2 ) or its heterodimeric form (HUab) in virtually all bacterial species (Grove, 2011). In Escherichia coli, HU proteins are differentially expressed during different phases of growth (Ali Azam et al, 1999) and recently it has been determined that this is also true for the bacterium Legionella pneumophila (Morash et al, 2009). With regard to function, HU has been shown to compact and prevent denaturation of DNA under detrimental conditions (Drlica & Rouviere-Yaniv, 1987;Oberto et al, 2009;Swinger & Rice, 2004) and to be involved in changing DNA topology (Swinger & Rice, 2004), specifically introducing negative supercoiling into relaxed DNA in the presence of topoisomerase I, in vitro (Bensaid et al, 1996).…”

Section: Introductionmentioning

confidence: 99%

The nucleoid-associated protein HUβ affects global gene expression in Porphyromonas gingivalis

et al. 2013

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HU is a non-sequence-specific DNA-binding protein and one of the most abundant nucleoidassociated proteins in the bacterial cell. Like Escherichia coli, the genome of Porphyromonas gingivalis is predicted to encode both the HUa (PG1258) and the HUb (PG0121) subunit. We have previously reported that PG0121 encodes a non-specific DNA-binding protein and that PG0121 is co-transcribed with the K-antigen capsule synthesis operon. We also reported that deletion of PG0121 resulted in downregulation of capsule operon expression and produced a P. gingivalis strain that is phenotypically deficient in surface polysaccharide production. Here, we show through complementation experiments in an E. coli MG1655 hupAB double mutant strain that PG0121 encodes a functional HU homologue. Microarray and quantitative RT-PCR analysis were used to further investigate global transcriptional regulation by HUb using comparative expression profiling of the PG0121 (HUb) mutant strain to the parent strain, W83. Our analysis determined that expression of genes encoding proteins involved in a variety of biological functions, including iron acquisition, cell division and translation, as well as a number of predicted nucleoid associated proteins were altered in the PG0121 mutant. Phenotypic and quantitative real-time-PCR (qRT-PCR) analyses determined that under iron-limiting growth conditions, cell division and viability were defective in the PG0121 mutant. Collectively, our studies show that PG0121 does indeed encode a functional HU homologue, and HUb has global regulatory functions in P. gingivalis; it affects not only production of capsular polysaccharides but also expression of genes involved in basic functions, such as cell wall synthesis, cell division and iron uptake. INTRODUCTIONPorphyromonas gingivalis is a Gram-negative obligate anaerobe belonging to the family Bacteroidaceae that persists as a natural member of the human oral microbiota. A shift in the microbial community leading to outgrowth of this anaerobe is directly linked to periodontitis, a chronic inflammatory disease that leads to destruction of the tissues supporting the gums and ultimately, exfoliation of the teeth (Choil et al., 1990;Dzink et al., 1988;Grossi et al., 1994;Lamont & Jenkinson, 2000;Moore et al., 1991). This commensal can colonize, invade and multiply within gingival epithelial cells, as well as penetrate into deeper epithelial cell layers, potentially releasing the whole organism and/or virulence factors into the bloodstream (reviewed by Yilmaz, 2008). In addition to its ability to cause disease in the oral cavity, there are data indicating a role in systemic disease, including its ability to invade vascular endothelial cells (Dorn et al., 2000(Dorn et al., , 2002Jandik et al., 2008) and to cause aggregation of platelets (Pham et al., 2002). For many pathogenic bacteria, surface polysaccharides play a key role in immune modulation et al., 1996). HU typically acts as an accessory protein in virtually all types of nucleoprotein-mediated processes (reviewed by...

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Twelve Species of the Nucleoid-associated Protein from Escherichia coli

Cited by 428 publications

References 71 publications

Compaction of single DNA molecules induced by binding of integration host factor (IHF)

Compaction of single DNA molecules induced by binding of integration host factor (IHF)

Interactions of the Non-coding RNA DsrA and RpoS mRNA with the 30 S Ribosomal Subunit

The nucleoid-associated protein HUβ affects global gene expression in Porphyromonas gingivalis

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