Transcriptional Analysis of the grlRA Virulence Operon from Citrobacter rodentium

ABSTRACT The locus for enterocyte effacement (LEE) is the virulence hallmark of the attaching-and-effacing (A/E) intestinal pathogens, namely, enteropathogenic Escherichia coli, enterohemorrhagic E. coli, and Citrobacter rodentium. The LEE carries more than 40 genes that are arranged in several operons, e.g., LEE1 to LEE5. Expression of the various transcriptional units is subject to xenogeneic silencing by the histone-like protein H-NS. The LEE1-encoded regulator, Ler, plays a key role in relieving this repression at several major LEE promoters, including LEE2 to LEE5. To achieve appropriate intracellular concentrations of Ler in different environments, A/E pathogens have evolved a sophisticated regulatory network to control ler expression. For example, the LEE-encoded GrlA and GrlR proteins work as activator and antiactivator, respectively, of ler transcription. Thus, control of the transcriptional activities of the LEE1 (ler) promoter and the grlRA operon determines the rate of transcription of all of the LEE-encoded virulence factors. To date, only a single promoter has been identified for the grlRA operon. In this study, we showed that the non-LEE-encoded AraC-like regulatory protein RegA of C. rodentium directly stimulates transcription of the grlRA promoter by binding to an upstream region in the presence of bicarbonate ions. In addition, in vivo and in vitro transcription assays revealed a σ70 promoter that is specifically responsible for transcription of grlA. Expression from this promoter was strongly repressed by H-NS and its paralog StpA but was activated by Ler. DNase I footprinting demonstrated that Ler binds to a region upstream of the grlA promoter, whereas H-NS interacts specifically with a region extending from the grlA core promoter into its coding sequence. Together, these findings provide new insights into the environmental regulation and differential expressions of the grlR and grlA genes of C. rodentium.

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The ArgP Protein Stimulates the Klebsiella pneumoniae gdhA Promoter in a Lysine-Sensitive Manner

Journal of Bacteriology ◽

10.1128/jb.00295-08 ◽

2008 ◽

Vol 190 (12) ◽

pp. 4351-4359 ◽

Cited By ~ 11

Author(s):

Thomas J. Goss

Keyword(s):

Klebsiella Pneumoniae ◽

Upstream Region ◽

Mobility Shift ◽

Base Pairs ◽

Dnase I Footprinting ◽

Sensitive Factor ◽

Electrophoretic Mobility Shift Assays ◽

Knockout Mutation

ABSTRACT The lysine-sensitive factor that binds to the upstream region of the Klebsiella pneumoniae gdhA promoter and stimulates gdhA transcription during growth in minimal medium has been proposed to be the K. pneumoniae ArgP protein (M. R. Nandineni, R. S. Laishram, and J. Gowrishankar, J. Bacteriol. 186:6391-6399, 2004). A knockout mutation of the K. pneumoniae argP gene was generated and used to assess the roles of exogenous lysine and argP in the regulation of the gdhA promoter. Disruption of argP reduced the strength and the lysine-dependent regulation of the gdhA promoter. Electrophoretic mobility shift assays using crude extracts prepared from wild-type and argP-defective strains indicted the presence of an argP-dependent factor whose ability to bind the gdhA promoter was lysine sensitive. DNase I footprinting studies using purified K. pneumoniae ArgP protein indicated that ArgP bound the region that lies approximately 50 to 100 base pairs upstream of the gdhA transcription start site in a manner that was sensitive to the presence of lysine. Substitutions within the region bound by ArgP affected the binding of ArgP to the gdhA promoter region in vitro and the argP-dependent stimulation of the gdhA promoter in vivo. These observations suggest that elevated intracellular levels of lysine reduce the affinity of ArgP for its binding site at the gdhA promoter, preventing ArgP from binding to and stimulating transcription from the promoter in vivo.

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Evolutionary Adaptation of an AraC-Like Regulatory Protein in Citrobacter rodentium and Escherichia Species

Infection and Immunity ◽

10.1128/iai.02697-14 ◽

2015 ◽

Vol 83 (4) ◽

pp. 1384-1395 ◽

Cited By ~ 9

Author(s):

Aimee Tan ◽

Nicola K. Petty ◽

Dianna Hocking ◽

Vicki Bennett-Wood ◽

Matthew Wakefield ◽

...

Keyword(s):

Pathogenic Bacteria ◽

Regulatory Protein ◽

Gene Repertoire ◽

Citrobacter Rodentium ◽

Environmental Strain ◽

Content Type ◽

E Coli ◽

Genes Encoding

The evolution of pathogenic bacteria is a multifaceted and complex process, which is strongly influenced by the horizontal acquisition of genetic elements and their subsequent expression in their new hosts. A well-studied example is the RegA regulon of the enteric pathogenCitrobacter rodentium. The RegA regulatory protein is a member of the AraC/XylS superfamily, which coordinates the expression of a gene repertoire that is necessary for full pathogenicity of this murine pathogen. Upon stimulation by an exogenous, gut-associated signal, namely, bicarbonate ions, RegA activates the expression of a series of genes, including virulence factors, such as autotransporters, fimbriae, a dispersin-like protein, and thegrlRAoperon on the locus of enterocyte effacement pathogenicity island. Interestingly, the genes encoding RegA homologues are distributed across the genusEscherichia, encompassing pathogenic and nonpathogenic subtypes. In this study, we carried out a series of bioinformatic, transcriptional, and functional analyses of the RegA regulons of these bacteria. Our results demonstrated thatregAhas been horizontally transferred toEscherichiaspp. andC. rodentium. Comparative studies of two RegA homologues, namely, those fromC. rodentiumandE. coliSMS-3-5, a multiresistant environmental strain ofE. coli, showed that the two regulators acted similarlyin vitrobut differed in terms of their abilities to activate the virulence ofC. rodentiumin vivo, which evidently was due to their differential activation ofgrlRA. Our data indicate that RegA fromC. rodentiumhas strain-specific adaptations that facilitate infection of its murine host. These findings shed new light on the development of virulence byC. rodentiumand on the evolution of virulence-regulatory genes of bacterial pathogens in general.

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Contributions of [4Fe-4S]-FNR and Integration Host Factor to fnr Transcriptional Regulation

Journal of Bacteriology ◽

10.1128/jb.00052-07 ◽

2007 ◽

Vol 189 (8) ◽

pp. 3036-3043 ◽

Cited By ~ 27

Author(s):

Erin L. Mettert ◽

Patricia J. Kiley

Keyword(s):

Binding Site ◽

In Vitro Transcription ◽

Integration Host Factor ◽

Host Factor ◽

Upstream Region ◽

Anaerobic Conditions ◽

Protein Levels ◽

Dnase I Footprinting

ABSTRACT Maintaining appropriate levels of the global regulator FNR is critical to its function as an O2 sensor. In this study, we examined the mechanisms that control transcription of fnr to increase our understanding of how FNR protein levels are regulated. Under anaerobic conditions, one mechanism that controls fnr expression is negative autoregulation by the active [4Fe-4S] form of FNR. Through DNase I footprinting and in vitro transcription experiments, we observed that direct binding of [4Fe-4S]-FNR to the predicted downstream FNR binding site is sufficient for repression of the fnr promoter in vitro. In addition, the downstream FNR binding site was required for repression of transcription from fnr′-lacZ fusions in vivo. No repression of fnr was observed in vivo or in vitro with the apoprotein form of FNR, indicating that repression requires the dimeric, Fe-S cluster-containing protein. Furthermore, our in vitro and in vivo data suggest that [4Fe-4S]-FNR does not bind to the predicted upstream FNR binding site within the fnr promoter. Rather, we provide evidence that integration host factor binds to this upstream region and increases in vivo expression of Pfnr under both aerobic and anaerobic conditions.

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ilvIH Operon Expression in Escherichia coli Requires Lrp Binding to Two Distinct Regions of DNA

Journal of Bacteriology ◽

10.1128/jb.184.19.5293-5300.2002 ◽

2002 ◽

Vol 184 (19) ◽

pp. 5293-5300 ◽

Cited By ~ 20

Author(s):

Samina Jafri ◽

Shaolin Chen ◽

Joseph M. Calvo

Keyword(s):

Escherichia Coli ◽

Promoter Activity ◽

Regulatory Protein ◽

Upstream Region ◽

Promoter Activation ◽

Downstream Region ◽

Activation Of Transcription ◽

Operon Expression

ABSTRACT The leucine-responsive regulatory protein Lrp regulates the expression of a number of operons in Escherichia coli, including the ilvIH operon. Earlier in vitro experiments showed purified Lrp binding to two regions of DNA proximal to the ilvIH promoter, an upstream region (−260 to −190) and a downstream region (−150 to −40). The effect of mutations in these regions on ilvIH promoter expression in vivo led to the proposal that activation of transcription required Lrp binding to downstream sites 3, 4, 5, and 6. Binding of Lrp to upstream sites 1 and 2 seemed to enhance promoter expression but was not absolutely required (Q. Wang and J. M. Calvo, J. Mol. Biol. 229:306-318, 1993). Here we present data that require a reevaluation of the above conclusion. Constructs having either a deletion of DNA or a 100-bp substitution of DNA upstream of position −160 showed no ilvIH promoter activity in vivo. These results unambiguously establish that DNA at or upstream of position −160 is required for ilvIH promoter expression. Together with previous results, we conclude that Lrp bound at downstream sites is necessary but not sufficient for promoter activation. In addition, insertion of 4, 6, 8, or 10 bp between the upstream and downstream regions also resulted in a very strong reduction of in vivo promoter expression, even though the binding of Lrp in vitro was not greatly affected by these mutations. Closer inspection showed that the affinity of Lrp for the upstream region of all of these constructs was about the same but that Lrp bound to the downstream region of the wild-type construct with a higher degree of cooperativity than in the case of the others. These mutations may have reduced promoter activity in vivo by eliminating a binding site for some transcription factor other than Lrp. Alternatively, the small-addition mutations may have affected the geometry of these complexes, preventing either an interaction between Lrps bound at upstream and downstream sites (which might be necessary for promoter expression) or preventing the positioning of Lrp bound at upstream sites for productive interaction with the promoter.

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Postexponential Regulation of sin Operon Expression in Bacillus subtilis

Journal of Bacteriology ◽

10.1128/jb.184.2.564-571.2002 ◽

2002 ◽

Vol 184 (2) ◽

pp. 564-571 ◽

Cited By ~ 56

Author(s):

Sasha H. Shafikhani ◽

Ines Mandic-Mulec ◽

Mark A. Strauch ◽

Issar Smith ◽

Terrance Leighton

Keyword(s):

Bacillus Subtilis ◽

Sigma Factor ◽

Promoter Region ◽

Regulatory Protein ◽

Gene Products ◽

Phosphorylated Form ◽

Dnase I Footprinting ◽

Operon Expression

ABSTRACT The expression of many gene products required during the early stages of Bacillus subtilis sporulation is regulated by sinIR operon proteins. Transcription of sinIR from the P1 promoter is induced at the end of exponential growth. In vivo transcription studies suggest that P1 induction is repressed by the transition-state regulatory protein Hpr and is induced by the phosphorylated form of Spo0A. In vitro DNase I footprinting studies confirmed that Hpr, AbrB, and Spo0A are trans-acting transcriptional factors that bind to the P1 promoter region of sinIR. We have also determined that the P1 promoter is transcribed in vitro by the major vegetative sigma factor, ςA, form of RNA polymerase.

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TAF7L modulates brown adipose tissue formation

eLife ◽

10.7554/elife.02811 ◽

2014 ◽

Vol 3 ◽

Cited By ~ 12

Author(s):

Haiying Zhou ◽

Bo Wan ◽

Ivan Grubisic ◽

Tommy Kaplan ◽

Robert Tjian

Keyword(s):

Adipose Tissue ◽

Brown Adipose Tissue ◽

Core Promoter ◽

Uncoupling Protein ◽

Dna Looping ◽

Chromatin Interactions ◽

Brown Adipose ◽

Important Regulator

Brown adipose tissue (BAT) plays an essential role in metabolic homeostasis by dissipating energy via thermogenesis through uncoupling protein 1 (UCP1). Previously, we reported that the TATA-binding protein associated factor 7L (TAF7L) is an important regulator of white adipose tissue (WAT) differentiation. In this study, we show that TAF7L also serves as a molecular switch between brown fat and muscle lineages in vivo and in vitro. In adipose tissue, TAF7L-containing TFIID complexes associate with PPARγ to mediate DNA looping between distal enhancers and core promoter elements. Our findings suggest that the presence of the tissue-specific TAF7L subunit in TFIID functions to promote long-range chromatin interactions during BAT lineage specification.

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Abrogation of Neuraminidase Reduces Biofilm Formation, Capsule Biosynthesis, and Virulence of Porphyromonas gingivalis

Infection and Immunity ◽

10.1128/iai.05773-11 ◽

2011 ◽

Vol 80 (1) ◽

pp. 3-13 ◽

Cited By ~ 27

Author(s):

Chen Li ◽

Kurniyati ◽

Bo Hu ◽

Jiang Bian ◽

Jianlan Sun ◽

...

Keyword(s):

Porphyromonas Gingivalis ◽

Biofilm Formation ◽

Adult Population ◽

Transcriptional Analysis ◽

Wild Type ◽

Content Type ◽

Multiple Organs ◽

Biochemical Analyses

ABSTRACTThe oral bacteriumPorphyromonas gingivalisis a key etiological agent of human periodontitis, a prevalent chronic disease that affects up to 80% of the adult population worldwide.P. gingivalisexhibits neuraminidase activity. However, the enzyme responsible for this activity, its biochemical features, and its role in the physiology and virulence ofP. gingivalisremain elusive. In this report, we found thatP. gingivalisencodes a neuraminidase, PG0352 (SiaPg). Transcriptional analysis showed thatPG0352is monocistronic and is regulated by a sigma70-like promoter. Biochemical analyses demonstrated that SiaPgis an exo-α-neuraminidase that cleaves glycosidic-linked sialic acids. Cryoelectron microscopy and tomography analyses revealed that thePG0352deletion mutant (ΔPG352) failed to produce an intact capsule layer. Compared to the wild type,in vitrostudies showed that ΔPG352 formed less biofilm and was less resistant to killing by the host complement.In vivostudies showed that while the wild type caused a spreading type of infection that affected multiple organs and all infected mice were killed, ΔPG352 only caused localized infection and all animals survived. Taken together, these results demonstrate that SiaPgis an important virulence factor that contributes to the biofilm formation, capsule biosynthesis, and pathogenicity ofP. gingivalis, and it can potentially serve as a new target for developing therapeutic agents againstP. gingivalisinfection.

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Estrogen-inducible binding of a nuclear factor to the vitellogenin upstream region

Molecular and Cellular Biology ◽

10.1128/mcb.8.10.4557-4560.1988 ◽

1988 ◽

Vol 8 (10) ◽

pp. 4557-4560

Author(s):

O Bakker ◽

J N Philipsen ◽

B C Hennis ◽

G Ab

Keyword(s):

Dimethyl Sulfate ◽

Upstream Region ◽

Nuclear Factor ◽

Base Pairs ◽

Exonuclease Iii ◽

Factor I ◽

Nuclear Factor I ◽

Vitellogenin Gene

The estrogen-dependent binding of a protein to the upstream region of the chicken vitellogenin gene was detected by using in vivo dimethyl sulfate, genomic DNase I, and in vitro exonuclease III footprinting. The site is located between base pairs -848 and -824, and its sequence resembles that of the nuclear factor I binding site. The results suggest that a nuclear factor binding to this site is involved in the regulation of the vitellogenin gene.

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Participation of the upstream region of the fibroin gene in the formation of transcription complex in vitro

Molecular and Cellular Biology ◽

10.1128/mcb.6.11.3928-3933.1986 ◽

1986 ◽

Vol 6 (11) ◽

pp. 3928-3933

Author(s):

M Tsuda ◽

S Hirose ◽

Y Suzuki

Keyword(s):

Complex Formation ◽

Specific Interaction ◽

Inhibitory Effect ◽

Silk Gland ◽

Upstream Region ◽

Fibroin Gene ◽

Transcription Complexes ◽

Posterior Silk Gland

The addition of exogenous histones has an inhibitory effect on fibroin gene transcription in posterior silk gland extracts. The histones probably disturb a process in complex formation, because when transcription complexes were constructed by preincubation of the templates with the extracts, the inhibitory effect of histones was greatly reduced. Transcription of a fibroin gene construct, pFb5' delta-238, having the upstream region beyond the TATA box was relatively less inhibited than that of pFb5' delta-44 lacking the upstream region. This tendency toward differential inhibition was observed in the silk gland extracts but not in a HeLa cell extract and persisted even after complex formation in the silk gland extracts, suggesting a specific interaction of the upstream region with some factors in the extracts. The complexes formed on pFb5' delta-44 are probably more susceptible to the inhibitory effect of histones. On the basis of these results we propose a participation of the upstream region of the fibroin gene in the formation of stable transcription complexes at the promoter through an interaction with specific factors in the silk gland. Since the transcription-enhancing effect via the upstream region is augmented at a high histone/DNA ratio, it may mimic the in vivo situation in which the fibroin gene can be transcribed in the posterior silk gland even in the presence of excess suppressive materials.

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Delimiting regulatory sequences of the Drosophila melanogaster Ddc gene

Molecular and Cellular Biology ◽

10.1128/mcb.6.12.4548-4557.1986 ◽

1986 ◽

Vol 6 (12) ◽

pp. 4548-4557

Author(s):

J Hirsh ◽

B A Morgan ◽

S B Scholnick

Keyword(s):

Drosophila Melanogaster ◽

Germ Line ◽

Regulatory Elements ◽

P Element ◽

Developmental Expression ◽

Upstream Region ◽

Regulatory Sequences ◽

Flanking Sequences

We delimited sequences necessary for in vivo expression of the Drosophila melanogaster dopa decarboxylase gene Ddc. The expression of in vitro-altered genes was assayed following germ line integration via P-element vectors. Sequences between -209 and -24 were necessary for normally regulated expression, although genes lacking these sequences could be expressed at 10 to 50% of wild-type levels at specific developmental times. These genes showed components of normal developmental expression, which suggests that they retain some regulatory elements. All Ddc genes lacking the normal immediate 5'-flanking sequences were grossly deficient in larval central nervous system expression. Thus, this upstream region must contain at least one element necessary for this expression. A mutated Ddc gene without a normal TATA boxlike sequence used the normal RNA start points, indicating that this sequences is not required for start point specificity.

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