Growth phase variation of integration host factor level in Escherichia coli

Ditto, Mary; Roberts, DeWayne; Weisberg, Robert A.

doi:10.1128/jb.176.12.3738-3748.1994

Cited by 127 publications

(105 citation statements)

References 76 publications

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“…Reporter enzyme assays and nested deletion experiments have suggested the presence of an IHF site in the arcA promoter regulatory region and shown that arcA gene expression is elevated more than 3-fold in an IHF Ϫ E. coli strain growing in glucose minimal medium under aerobic conditions. 5 We have identified an IHF-binding site in the arcA promoter regulatory region, and our data show a 3.9-fold increase in arcA mRNA expression in strain IH105 growing under similar conditions. Gunsalus and co-workers (49 -52) also use reporter enzyme assays to examine the expression of several tricarboxylic acid cycle (fumA, gltA, icdA, mdh, mur, and sucA) and respiratory genes (atp, cydA, and cyoA) in IHF ϩ and IHF Ϫ strains.…”

Section: Examples Of Direct Effects Of Ihf On Gene Expression Profilementioning

confidence: 66%

“…They are abundant proteins that bind to many sequence-specific but degenerate DNA sites and affect processes that require DNA duplex destabilization such as DNA replication, recombination, and transcription (5)(6)(7)(8)(9)(10). These proteins also affect the expression of many genes (operons), but unlike the global regulators of the previous class, they do not respond to small molecule metabolic co-regulators and there is no obvious metabolic coherence among the genes whose expression they affect.…”

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confidence: 99%

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Global Gene Expression Profiling in Escherichia coliK12

Arfin

Long

Ito

et al. 2000

Journal of Biological Chemistry

253

202

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We have used nylon membranes spotted in duplicate with full-length polymerase chain reaction-generated products of each of the 4,290 predicted Escherichia coli K12 open reading frames (ORFs) to measure the gene expression profiles in otherwise isogenic integration host factor IHF ؉ and IHF ؊ strains. Our results demonstrate that random hexamer rather than 3 ORF-specific priming of cDNA probe synthesis is required for accurate measurement of gene expression levels in bacteria. This is explained by the fact that the currently available set of 4,290 unique 3 ORF-specific primers do not hybridize to each ORF with equal efficiency and by the fact that widely differing degradation rates (steady-state levels) are observed for the 25-base pair region of each message complementary to each ORF-specific primer. To evaluate the DNA microarray data reported here, we used a linear analysis of variance (ANOVA) model appropriate for our experimental design. These statistical methods allowed us to identify and appropriately correct for experimental variables that affect the reproducibility and accuracy of DNA microarray measurements and allowed us to determine the statistical significance of gene expression differences between our IHF ؉ and IHF ؊ strains. Our results demonstrate that small differences in gene expression levels can be accurately measured and that the significance of differential gene expression measurements cannot be assessed simply by the magnitude of the fold difference. Our statistical criteria, supported by excellent agreement between previously determined effects of IHF on gene expression and the results reported here, have allowed us to identify new genes regulated by IHF with a high degree of confidence.

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Section: Examples Of Direct Effects Of Ihf On Gene Expression Profilementioning

confidence: 66%

mentioning

confidence: 99%

Global Gene Expression Profiling in Escherichia coliK12

Arfin

Long

Ito

et al. 2000

Journal of Biological Chemistry

253

202

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“…Antibodies were generated with the following peptide to the C terminus of HU PG0121: ISIPARKVVRFKPGSTLELK by Robert Sargeant (Ramona, CA), as previously described for generating antibodies to histone-like proteins (Ditto et al, 1994).…”

Section: Methodsmentioning

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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“…In E. coli, the four most abundant nucleoid-associated proteins are factor for inversion stimulation (Fis), histone-like nucleoid structuring protein (H-NS), heat-unstable nucleoid protein (HU) and integration host factor (IHF) [19][20][21][22][23][24][25]. However, at present, a clear picture of how the E. coli nucleoid is organized is far from being complete.…”

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confidence: 99%

Growth phase dependent changes in the structure and protein composition of nucleoid in Escherichia coli

Talukder

Ishihama

2015

Sci. China Life Sci.

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The genomic DNA of bacteria is highly compacted in a single or a few bodies known as nucleoids. Here, we have isolated Escherichia coli nucleoid by sucrose density gradient centrifugation. The sedimentation rates, structures as well as protein/DNA composition of isolated nucleoids were then compared under various growth phases. The nucleoid structures were found to undergo changes during the cell growth; i. e., the nucleoid structure in the stationary phase was more tightly compacted than that in the exponential phase. In addition to factor for inversion stimulation (Fis), histone-like nucleoid structuring protein (H-NS), heat-unstable nucleoid protein (HU) and integration host factor (IHF) here we have identified, three new candidates of E. coli nucleoid, namely DNA-binding protein from starved cells (Dps), host factor for phage Q Hfq) and suppressor of td  phenotype A (StpA). Our results reveal that the major components of exponential phase nucleoid are Fis, HU, H-NS, StpA and Hfq, while Dps occupies more than half of the stationary phase nucleoid. It has been known for a while that Dps is the main nucleoid-associated protein at stationary phase. From these results and the prevailing information, we propose a model for growth phase dependent changes in the structure and protein composition of nucleoid in E. coli. growth phase, sucrose gradient, bacterial nucleoid, DNA binding protein, DNA compaction Citation:Talukder AA, Ishihama A. Growth phase dependent changes in the structure and protein composition of nucleoid in Escherichia coli. Sci China Life Sci, 2015, 58: 902 -911,

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Growth phase variation of integration host factor level in Escherichia coli

Cited by 127 publications

References 76 publications

Global Gene Expression Profiling in Escherichia coliK12

Global Gene Expression Profiling in Escherichia coliK12

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

Growth phase dependent changes in the structure and protein composition of nucleoid in Escherichia coli

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