Physical map location of a set of Escherichia coli genes (hde) whose expression is affected by the nucleoid protein H-NS

Yoshida, Takayuki; Ueguchi, Chiharu; Mizuno, Takeshi

doi:10.1128/jb.175.23.7747-7748.1993

Cited by 22 publications

(15 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Whereas transcript levels from many genes increased or decreased severalfold (Table 1), a number of genes related to acid resistance were strongly induced by DsrA overproduction ( Table 1, top). The hdeAB operon, which encodes the H-NS-repressed acid resistance proteins HdeA and HdeB (12,46,47), produced 10-to 26-fold higher hdeA transcript levels and 12-to 43-fold higher hdeB transcript levels when DsrA was overproduced (Table 1, lines 1 and 2). Other H-NS-and RpoS-regulated acid resistance operon elements were also induced.…”

Section: Resultsmentioning

confidence: 99%

The Small Noncoding DsrA RNA Is an Acid Resistance Regulator inEscherichia coli

et al. 2004

View full text Add to dashboard Cite

DsrA RNA is a small (87-nucleotide) regulatory RNA of Escherichia coli that acts by RNA-RNA interactions to control translation and turnover of specific mRNAs. Two targets of DsrA regulation are RpoS, the stationary-phase and stress response sigma factor ( s ), and H-NS, a histone-like nucleoid protein and global transcription repressor. Genes regulated globally by RpoS and H-NS include stress response proteins and virulence factors for pathogenic E. coli. Here, by using transcription profiling via DNA arrays, we have identified genes induced by DsrA. Steady-state levels of mRNAs from many genes increased with DsrA overproduction, including multiple acid resistance genes of E. coli. Quantitative primer extension analysis verified the induction of individual acid resistance genes in the hdeAB, gadAX, and gadBC operons. E. coli K-12 strains, as well as pathogenic E. coli O157:H7, exhibited compromised acid resistance in dsrA mutants. Conversely, overproduction of DsrA from a plasmid rendered the acid-sensitive dsrA mutant extremely acid resistant. Thus, DsrA RNA plays a regulatory role in acid resistance. Whether DsrA targets acid resistance genes directly by base pairing or indirectly via perturbation of RpoS and/or H-NS is not known, but in either event, our results suggest that DsrA RNA may enhance the virulence of pathogenic E. coli.Regulation by RNA, termed riboregulation, plays a substantial role in modulating gene expression in bacteria (reviewed in references 14, 17, 26, 33, 42, 43, and 44). In addition to their classically studied role in plasmid maintenance (reviewed in reference 42), Escherichia coli small RNAs act to change the conformation of target mRNAs (DsrA and RprA), block mRNA translation by occlusion of Shine-Dalgarno sequences (MicF, OxyS, Spf, and RyhB), degrade target mRNAs (DsrA, Oop, and RyhB), and titrate specific protein factors (OxyS and CsrB RNAs, 6S RNA), sometimes in combination.Several E. coli small RNAs coordinate stress responses or virulence factors (reviewed in reference 14). A principal advantage of small RNAs as regulators is that they are not translated and therefore cost less energy to produce than do proteins. Also, many bacterial small RNAs are relatively stable and can persist to target transcripts with high specificity by antisense interactions (reviewed in references 17 and 43). Some small RNAs are degraded together with their target mRNAs (22).One such RNA, DsrA RNA, is a small (87 nucleotides), multifunctional genetic regulator of E. coli. DsrA RNA modulates the levels of two global transcription regulators, RpoS ( s , the product of the rpoS gene) and H-NS (a nucleoid protein and transcription silencer in bacteria, produced from the hns gene). DsrA acts by sequence-specific RNA-RNA interactions to enhance translation of rpoS RNA and to stabilize rpoS message (18)(19)(20)35). In addition to its role at rpoS, DsrA also binds hns mRNA by specific base-pairing interactions and blocks H-NS translation as it sharply increases hns mRNA turnover (18). The first stem-loop reg...

show abstract

Section: Resultsmentioning

confidence: 99%

The Small Noncoding DsrA RNA Is an Acid Resistance Regulator inEscherichia coli

et al. 2004

View full text Add to dashboard Cite

show abstract

“…The hdeAB operon is located immediately downstream of hdeD and is transcribed in the opposite direction (58). Expression of all three genes increases in stationary phase, and induction of the hdeAB operon is S dependent (4,56,59).…”

Section: Discussionmentioning

confidence: 99%

Global Analysis of Escherichia coli Gene Expression during the Acetate-Induced Acid Tolerance Response

et al. 2001

View full text Add to dashboard Cite

The ability of Escherichia coli to survive at low pH is strongly affected by environmental factors, such as composition of the growth medium and growth phase. Exposure to short-chain fatty acids, such as acetate, proprionate, and butyrate, at neutral or nearly neutral pH has also been shown to increase acid survival of E. coli and Salmonella enterica serovar Typhimurium. To investigate the basis for acetate-induced acid tolerance in E. coli O157:H7, genes whose expression was altered by exposure to acetate were identified using gene arrays. The expression of 60 genes was reduced by at least twofold; of these, 48 encode components of the transcriptiontranslation machinery. Expression of 26 genes increased twofold or greater following treatment with acetate. This included six genes whose products are known to be important for survival at low pH. Five of these genes, as well as six other acetate-induced genes, are members of the E. coli RpoS regulon. RpoS, the stress sigma factor, is known to be required for acid tolerance induced by growth at nonlethal low pH or by entry into stationary phase. Disruption of the rpoS gene by a transposon insertion mutation also prevented acetateinduced acid tolerance. However, induction of RpoS expression did not appear to be sufficient to activate the acid tolerance response. Treatment with either NaCl or sodium acetate (pH 7.0) increased expression of an rpoS::lacZ fusion protein, but only treatment with acetate increased acid survival.

show abstract

“…The E. coli yjbJ gene, with sequence similarity to the uncharacterized ORF ywmH in B. subtilis, encodes a small 69-aminoacid protein that is highly abundant during early stationary phase in rich media. HdeA is a 121-amino-acid protein with a 23-amino-acid signal peptide whose expression is affected by mutations that eliminate the protein HU-1 (45,46). The HdeA protein is abundant during growth in minimal media and during stationary phase in rich media (25).…”

mentioning

confidence: 99%

Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: application to open reading frame characterization

1997

View full text Add to dashboard Cite

We have developed a new system of chromosomal mutagenesis in order to study the functions of uncharacterized open reading frames (ORFs) in wild-type Escherichia coli. Because of the operon structure of this organism, traditional methods such as insertional mutagenesis run the risk of introducing polar effects on downstream genes or creating secondary mutations elsewhere in the genome. Our system uses crossover PCR to create in-frame, tagged deletions in chromosomal DNA. These deletions are placed in the E. coli chromosome by using plasmid pKO3, a gene replacement vector that contains a temperature-sensitive origin of replication and markers for positive and negative selection for chromosomal integration and excision. Using kanamycin resistance (Kn r ) insertional alleles of the essential genes pepM and rpsB cloned into the replacement vector, we calibrated the system for the expected results when essential genes are deleted. Two poorly understood genes, hdeA and yjbJ, encoding highly abundant proteins were selected as targets for this approach. When the system was used to replace chromosomal hdeA with insertional alleles, we observed vastly different results that were dependent on the exact nature of the insertions. When a Kn r gene was inserted into hdeA at two different locations and orientations, both essential and nonessential phenotypes were seen. Using PCR-generated deletions, we were able to make in-frame deletion strains of both hdeA and yjbJ. The two genes proved to be nonessential in both rich and glucose-minimal media. In competition experiments using isogenic strains, the strain with the insertional allele of yjbJ showed growth rates different from those of the strain with the deletion allele of yjbJ. These results illustrate that in-frame, unmarked deletions are among the most reliable types of mutations available for wild-type E. coli. Because these strains are isogenic with the exception of their deleted ORFs, they may be used in competition with one another to reveal phenotypes not apparent when cultured singly.

show abstract

Physical map location of a set of Escherichia coli genes (hde) whose expression is affected by the nucleoid protein H-NS

Cited by 22 publications

References 10 publications

The Small Noncoding DsrA RNA Is an Acid Resistance Regulator inEscherichia coli

The Small Noncoding DsrA RNA Is an Acid Resistance Regulator inEscherichia coli

Global Analysis of Escherichia coli Gene Expression during the Acetate-Induced Acid Tolerance Response

Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: application to open reading frame characterization

Contact Info

Product

Resources

About