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1.
Microorganisms ; 11(2)2023 Jan 25.
Article in English | MEDLINE | ID: mdl-36838276

ABSTRACT

The increasing amounts of municipal solid waste and their management in landfills caused an increase in the production of leachate, a liquid formed by the percolation of rainwater through the waste. Leachate creates serious problems to municipal wastewater treatment plants; indeed, its high levels of ammonia are toxic for bacterial cells and drastically reduce the biological removal of nitrogen by activated sludge. In the present work, we studied, using a metagenomic approach based on next-generation sequencing (NGS), the microbial composition of sludge in the municipal wastewater treatment plant of Porto Sant'Elpidio (Italy). Through activated sludge enrichment experiments based on the Repetitive Re-Inoculum Assay, we were able to select and identify a minimal bacterial community capable of degrading high concentrations of ammonium (NH4+-N ≅ 350 mg/L) present in a leachate-based medium. The analysis of NGS data suggests that seven families of bacteria (Alcaligenaceae, Nitrosomonadaceae, Caulobacteraceae, Xanthomonadaceae, Rhodanobacteraceae, Comamonadaceae and Chitinophagaceae) are mainly responsible for ammonia oxidation. Furthermore, we isolated from the enriched sludge three genera (Klebsiella sp., Castellaniella sp. and Acinetobacter sp.) capable of heterotrophic nitrification coupled with aerobic denitrification. These bacteria released a trace amount of both nitrite and nitrate possibly transforming ammonia into gaseous nitrogen. Our findings represent the starting point to produce an optimized microorganisms's mixture for the biological removal of ammonia contained in leachate.

2.
Cancers (Basel) ; 14(16)2022 Aug 22.
Article in English | MEDLINE | ID: mdl-36011047

ABSTRACT

The advent of trastuzumab has significantly improved the prognosis of HER2-positive (HER2+) breast cancer patients; nevertheless, drug resistance limits its clinical benefit. Anti-HER2 active immunotherapy represents an attractive alternative strategy, but effective immunization needs to overcome the patient's immune tolerance against the self-HER2. Phage display technology, taking advantage of phage intrinsic immunogenicity, permits one to generate effective cancer vaccines able to break immune tolerance to self-antigens. In this study, we demonstrate that both preventive and therapeutic vaccination with M13 bacteriophages, displaying the extracellular (EC) and transmembrane (TM) domains of human HER2 or its Δ16HER2 splice variant on their surface (ECTM and Δ16ECTM phages), delayed mammary tumor onset and reduced tumor growth rate and multiplicity in ∆16HER2 transgenic mice, which are tolerant to human ∆16HER2. This antitumor protection correlated with anti-HER2 antibody production. The molecular mechanisms underlying the anticancer effect of vaccine-elicited anti-HER2 antibodies were analyzed in vitro against BT-474 human breast cancer cells, sensitive or resistant to trastuzumab. Immunoglobulins (IgG) purified from immune sera reduced cell viability mainly by impairing ERK phosphorylation and reactivating retinoblastoma protein function in both trastuzumab-sensitive and -resistant BT-474 cells. In conclusion, we demonstrated that phage-based HER2 vaccines impair mammary cancer onset and progression, opening new perspectives for HER2+ breast cancer treatment.

3.
Microorganisms ; 8(10)2020 Oct 10.
Article in English | MEDLINE | ID: mdl-33050410

ABSTRACT

Second messenger nucleotides, such as guanosine penta- or tetra-phosphate, commonly referred to as (p)ppGpp, are powerful signaling molecules, used by all bacteria to fine-tune cellular metabolism in response to nutrient availability. Indeed, under nutritional starvation, accumulation of (p)ppGpp reduces cell growth, inhibits stable RNAs synthesis, and selectively up- or down- regulates the expression of a large number of genes. Here, we show that the E. coli hns promoter responds to intracellular level of (p)ppGpp. hns encodes the DNA binding protein H-NS, one of the major components of bacterial nucleoid. Currently, H-NS is viewed as a global regulator of transcription in an environment-dependent mode. Combining results from relA (ppGpp synthetase) and spoT (ppGpp synthetase/hydrolase) null mutants with those from an inducible plasmid encoded RelA system, we have found that hns expression is inversely correlated with the intracellular concentration of (p)ppGpp, particularly in exponential phase of growth. Furthermore, we have reproduced in an in vitro system the observed in vivo (p)ppGpp-mediated transcriptional repression of hns promoter. Electrophoretic mobility shift assays clearly demonstrated that this unusual nucleotide negatively affects the stability of RNA polymerase-hns promoter complex. Hence, these findings demonstrate that the hns promoter is subjected to an RNA polymerase-mediated down-regulation by increased intracellular levels of (p)ppGpp.

4.
Pharmacol Res ; 161: 105123, 2020 11.
Article in English | MEDLINE | ID: mdl-32822867

ABSTRACT

Breast cancer (BC) is the most common cancer in women and, among different BC subtypes, triple negative (TN) and human epidermal growth factor receptor 2 (HER2)-positive BCs have the worst prognosis. In this study, we investigated the anticancer activity of the root ethanolic and hexane extracts from Lithospermum erythrorhizon, a traditional Chinese herbal medicine known also as tzu ts'ao or tzu-ken, against in vitro and in vivo models of TNBC and HER2-positive BC. Treatment with L. erythrorhizon root extracts resulted in a dose-dependent inhibition of BC cell viability and in a significant reduction of the growth of TNBC cells transplanted in syngeneic mice. Acetylshikonin, a naphthoquinone, was identified as the main bioactive component in extracts and was responsible for the observed antitumor activity, being able to decrease BC cell viability and to interfere with autochthonous mammary carcinogenesis in Δ16HER2 transgenic mice. Acetylshikonin anticancer effect depends on its ability to act as a potent inhibitor of dihydrofolate reductase (DHFR), to down-regulate key mediators governing cancer growth and progression, such as HER2, Src and STAT3, and to induce apoptosis by caspase-3 activation. The accumulation of acetylshikonin in blood samples as well as in brain, kidney, liver and tumor tissues was also investigated by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) highlighting that L. erythrorhizon treatment is effective in delivering the active compound into the target tissues. These results provide evidence that L. erythrorhizon extract and in particular its main component acetylshikonin are effective against aggressive BC subtypes and reveal new acetylshikonin mechanisms of action.


Subject(s)
Anthraquinones/pharmacology , Antineoplastic Agents/pharmacology , Breast Neoplasms/prevention & control , Folic Acid Antagonists/pharmacology , Lithospermum , Receptor, ErbB-2/metabolism , Tetrahydrofolate Dehydrogenase/metabolism , Animals , Anthraquinones/isolation & purification , Anthraquinones/pharmacokinetics , Antineoplastic Agents/isolation & purification , Antineoplastic Agents/pharmacokinetics , Apoptosis/drug effects , Breast Neoplasms/enzymology , Breast Neoplasms/genetics , Breast Neoplasms/pathology , Cell Line, Tumor , Cell Proliferation/drug effects , Female , Folic Acid Antagonists/isolation & purification , Folic Acid Antagonists/pharmacokinetics , Humans , Lithospermum/chemistry , Mice, Transgenic , Plant Roots , Receptor, ErbB-2/genetics , Signal Transduction , Tissue Distribution , Tumor Burden/drug effects , Xenograft Model Antitumor Assays
5.
FASEB J ; 33(12): 13228-13240, 2019 12.
Article in English | MEDLINE | ID: mdl-31560576

ABSTRACT

tRNA-derived fragments (tRFs) have been defined as a novel class of small noncoding RNAs. tRFs have been reported to be deregulated in cancer, but their biologic function remains to be fully understood. We have identified a new tRF (named tRF3E), derived from mature tRNAGlu, that is specifically expressed in healthy mammary glands but not in breast cancer (BC). Consistently, tRF3E levels significantly decrease in the blood of patients with epidermal growth factor receptor 2 (HER2)-positive BC reflecting tumor status (control > early cancer > metastatic cancer). tRF3E down-regulation was recapitulated in Δ16HER2 transgenic mice, representing a BC preclinical model. Pulldown assays, used to search for proteins capable to selectively bind tRF3E, have shown that this tRF specifically interacts with nucleolin (NCL), an RNA-binding protein overexpressed in BC and able to repress the translation of p53 mRNA. The binding properties of NCL-tRF3E complex, predicted in silico and analyzed by EMSA assays, are congruent with a competitive displacement of p53 mRNA by tRF3E, leading to an increased p53 expression and consequently to a modulation of cancer cell growth. Here, we provide evidence that tRF3E plays an important role in the pathogenesis of BC displaying tumor-suppressor functions through a NCL-mediated mechanism.-Falconi, M., Giangrossi, M., Elexpuru Zabaleta, M., Wang, J., Gambini, V., Tilio, M., Bencardino, D., Occhipinti, S., Belletti, B., Laudadio, E., Galeazzi, R., Marchini, C., Amici, A. A novel 3'-tRNAGlu-derived fragment acts as a tumor suppressor in breast cancer by targeting nucleolin.


Subject(s)
Breast Neoplasms/metabolism , Phosphoproteins/metabolism , RNA, Transfer, Glu/metabolism , RNA-Binding Proteins/metabolism , Animals , Blotting, Western , Breast Neoplasms/genetics , Electrophoretic Mobility Shift Assay , Gene Expression Regulation, Neoplastic/genetics , Gene Expression Regulation, Neoplastic/physiology , Humans , Mice , Mice, Transgenic , Phosphoproteins/genetics , RNA, Transfer, Glu/genetics , RNA-Binding Proteins/genetics , Reverse Transcriptase Polymerase Chain Reaction , Nucleolin
6.
Sci Rep ; 7(1): 13169, 2017 10 13.
Article in English | MEDLINE | ID: mdl-29030601

ABSTRACT

Wheat amylase/trypsin bi-functional inhibitors (ATIs) are protein stimulators of innate immune response, with a recently established role in promoting both gastrointestinal and extra-gastrointestinal inflammatory syndromes. These proteins have been reported to trigger downstream intestinal inflammation upon activation of TLR4, a member of the Toll-like family of proteins that activates signalling pathways and induces the expression of immune and pro-inflammatory genes. In this study, we demonstrated the ability of ATI to directly interact with TLR4 with nanomolar affinity, and we kinetically and structurally characterized the interaction between these macromolecules by means of a concerted approach based on surface plasmon resonance binding analyses and computational studies. On the strength of these results, we designed an oligopeptide capable of preventing the formation of the complex between ATI and the receptor.


Subject(s)
Biosensing Techniques , Plant Proteins/metabolism , Toll-Like Receptor 4/metabolism , Triticum/metabolism , Trypsin Inhibitors/metabolism , Protein Binding , Surface Plasmon Resonance
7.
Front Microbiol ; 8: 650, 2017.
Article in English | MEDLINE | ID: mdl-28458662

ABSTRACT

VirF is the master activator of virulence genes of Shigella and its expression is required for the invasion of the human intestinal mucosa by pathogenic bacteria. VirF was shown to directly activate the transcription of virB and icsA, which encode two essential proteins involved in the pathogenicity process, by binding their promoter regions. In this study, we demonstrate by band shift, enzymatic probing and cross-linking experiments that VirF, in addition to DNA, can also bind the icsA transcript and RnaG, an antisense non-coding small RNA that promotes the premature termination of icsA mRNA through a transcriptional attenuation mechanism. Furthermore, we show that VirF binds in vitro also other species of RNAs, although with lower specificity. The existence of VirF-RnaG and VirF-icsA mRNA complexes is confirmed in a pulldown assay carried out under experimental conditions that very close reproduce the in vivo conditions and that allows immobilized VirF to "fish" out RnaG and icsA mRNA from a total RNA extract. The VirF binding sites identified on both icsA mRNA and RnaG contain a 13 nucleotides stretch (5'-UUUUaGYcUuUau-3') that is the RNA-converted consensus sequence previously proposed for the VirF-DNA interaction. Band-shift assays with a synthetic RNA molecule whose sequence perfectly matches the consensus indicate that this signature plays a key role also in the VirF-RNA interaction, in particular when exposed in a stem-loop structure. To further explore the icsA-RnaG-VirF regulatory system, we developed an in vitro test (RNA-RNA Pairing Assay) in which pairing between icsA mRNA and synthetic RNAs that reproduce the individual stem-loop motifs of RnaG, was analyzed in the presence of VirF. This assay shows that this protein can prevent the formation of the kissing complex, defined as the initial nucleation points for RNA heteroduplex formation, between RnaG and icsA mRNA. Consistently, VirF alleviates the RnaG-mediated repression of icsA transcription in vitro. Therefore VirF, by hindering the icsA transcript-RnaG interaction, exhibits an activity opposed to that usually displayed by proteins, which generally assist the RNA-RNA interaction; this quite uncommon and new function and the regulatory implications of VirF as a potential RNA-binding protein are discussed.

8.
Front Mol Biosci ; 3: 61, 2016.
Article in English | MEDLINE | ID: mdl-27747215

ABSTRACT

Shigella is a highly adapted human pathogen, mainly found in the developing world and causing a severe enteric syndrome. The highly sophisticated infectious strategy of Shigella banks on the capacity to invade the intestinal epithelial barrier and cause its inflammatory destruction. The cellular pathogenesis and clinical presentation of shigellosis are the sum of the complex action of a large number of bacterial virulence factors mainly located on a large virulence plasmid (pINV). The expression of pINV genes is controlled by multiple environmental stimuli through a regulatory cascade involving proteins and sRNAs encoded by both the pINV and the chromosome. The primary regulator of the virulence phenotype is VirF, a DNA-binding protein belonging to the AraC family of transcriptional regulators. The virF gene, located on the pINV, is expressed only within the host, mainly in response to the temperature transition occurring when the bacterium transits from the outer environment to the intestinal milieu. VirF then acts as anti-H-NS protein and directly activates the icsA and virB genes, triggering the full expression of the invasion program of Shigella. In this review we will focus on the structure of VirF, on its sophisticated regulation, and on its role as major player in the path leading from the non-invasive to the invasive phenotype of Shigella. We will address also the involvement of VirF in mechanisms aimed at withstanding adverse conditions inside the host, indicating that this protein is emerging as a global regulator whose action is not limited to virulence systems. Finally, we will discuss recent observations conferring VirF the potential of a novel antibacterial target for shigellosis.

9.
Front Mol Biosci ; 3: 19, 2016.
Article in English | MEDLINE | ID: mdl-27252944

ABSTRACT

CspA, the most characterized member of the csp gene family of Escherichia coli, is highly expressed not only in response to cold stress, but also during the early phase of growth at 37°C. Here, we investigate at molecular level the antagonistic role played by the nucleoid proteins FIS and H-NS in the regulation of cspA expression under non-stress conditions. By means of both probing experiments and immunological detection, we demonstrate in vitro the existence of binding sites for these proteins on the cspA regulatory region, in which FIS and H-NS bind simultaneously to form composite DNA-protein complexes. While the in vitro promoter activity of cspA is stimulated by FIS and repressed by H-NS, a compensatory effect is observed when both proteins are added in the transcription assay. Consistently with these findings, inactivation of fis and hns genes reversely affect the in vivo amount of cspA mRNA. In addition, by means of strains expressing a high level of the alarmone guanosine tetraphosphate ((p)ppGpp) and in vitro transcription assays, we show that the cspA promoter is sensitive to (p)ppGpp inhibition. The (p)ppGpp-mediated expression of fis and hns genes is also analyzed, thus clarifying some aspects of the regulatory loop governing cspA transcription.

10.
PLoS One ; 10(8): e0136744, 2015.
Article in English | MEDLINE | ID: mdl-26313003

ABSTRACT

The polyamine profile of Shigella, the etiological agent of bacillary dysentery in humans, differs markedly from that of E. coli, its innocuous commensal ancestor. Pathoadaptive mutations such as the loss of cadaverine and the increase of spermidine favour the full expression of the virulent phenotype of Shigella. Spermidine levels affect the expression of the MdtJI complex, a recently identified efflux pump belonging to the small multi-drug resistance family of transporters. In the present study, we have addressed the regulation of the mdtJI operon in Shigella by asking which factors influence its expression as compared to E. coli. In particular, after identifying the mdtJI promoter by primer extension analysis, in vivo transcription assays and gel-retardation experiments were carried out to get insight on the silencing of mdtJI in E. coli. The results indicate that H-NS, a major nucleoid protein, plays a key role in repressing the mdtJI operon by direct binding to the regulatory region. In the Shigella background mdtJI expression is increased by the high levels of spermidine typically found in this microorganism and by VirF, the plasmid-encoded regulator of the Shigella virulence regulatory cascade. We also show that the expression of mdtJI is stimulated by bile components. Functional analyses reveal that MdtJI is able to promote the excretion of putrescine, the spermidine precursor. This leads us to consider the MdtJI complex as a possible safety valve allowing Shigella to maintain spermidine to a level optimally suited to survival within infected macrophages and, at the same time, prevent toxicity due to spermidine over-accumulation.


Subject(s)
Bacterial Proteins/metabolism , Gene Expression Regulation, Bacterial , Interferon Regulatory Factors/genetics , Polyamines/metabolism , Shigella flexneri/genetics , Viral Proteins/genetics , Bacterial Proteins/genetics , Carrier Proteins/genetics , Carrier Proteins/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Fimbriae Proteins/genetics , Fimbriae Proteins/metabolism , Interferon Regulatory Factors/metabolism , Operon , Plasmids/genetics , Promoter Regions, Genetic , Putrescine/metabolism , Shigella flexneri/metabolism , Shigella flexneri/pathogenicity , Spermidine/metabolism , Viral Proteins/metabolism
11.
Cell Signal ; 26(2): 352-62, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24280125

ABSTRACT

Increasing evidence supports the theory that tumor growth, homeostasis, and recurrence are dependent on a small subset of cells with stem cell properties, redefined cancer initiating cells (CICs) or cancer stem cells. Bone morphogenetic proteins (BMPs) are involved in cell-fate specification during embryogenesis, in the maintenance of developmental potency in adult stem cells and may contribute to sustain CIC populations in breast carcinoma. Using the mouse A17 cell model previously related to mesenchymal cancer stem cells and displaying properties of CICs, we investigated the role of BMPs in the control of breast cancer cell plasticity. We showed that an autocrine activation of BMP signaling is crucial for the maintenance of mesenchymal stem cell phenotype and tumorigenic potential of A17 cells. Pharmacological inhibition of BMP signaling cascade by Dorsomorphin resulted in the acquisition of epithelial-like traits by A17 cells, including expression of Citokeratin-18 and E-cadherin, through downregulation of Snail and Slug transcriptional factors and Cyclooxygenase-2 (COX2) expression, and in the loss of their stem-features and self-renewal ability. This phenotypic switch compromised A17 cell motility, invasiveness and in vitro tumor growth. These results reveal that BMPs are key molecules at the crossroad between stemness and cancer.


Subject(s)
Bone Morphogenetic Proteins/metabolism , Neoplastic Stem Cells/drug effects , Pyrazoles/pharmacology , Pyrimidines/pharmacology , Signal Transduction/drug effects , Animals , Bone Morphogenetic Protein 4/pharmacology , Bone Morphogenetic Protein Receptors, Type I/metabolism , Bone Morphogenetic Protein Receptors, Type II/metabolism , Breast Neoplasms/metabolism , Breast Neoplasms/pathology , Cell Line, Tumor , Cell Movement/drug effects , Cell Survival/drug effects , Cyclooxygenase 2/genetics , Cyclooxygenase 2/metabolism , Epithelial-Mesenchymal Transition/drug effects , Female , Gene Expression Regulation/drug effects , Humans , Inhibitor of Differentiation Protein 1/metabolism , Mice , Neoplastic Stem Cells/cytology , Neoplastic Stem Cells/metabolism , Phenotype , Pyrazoles/chemistry , Pyrimidines/chemistry
12.
Nucleic Acids Res ; 39(18): 8122-34, 2011 Oct.
Article in English | MEDLINE | ID: mdl-21724612

ABSTRACT

The icsA gene of Shigella encodes a structural protein involved in colonization of the intestinal mucosa by bacteria. This gene is expressed upon invasion of the host and is controlled by a complex regulatory circuit involving the nucleoid protein H-NS, the AraC-like transcriptional activator VirF, and a 450 nt antisense RNA (RnaG) acting as transcriptional attenuator. We investigated on the interplay of these factors at the molecular level. DNase I footprints reveal that both H-NS and VirF bind to a region including the icsA and RnaG promoters. H-NS is shown to repress icsA transcription at 30°C but not at 37°C, suggesting a significant involvement of this protein in the temperature-regulated expression of icsA. We also demonstrate that VirF directly stimulates icsA transcription and is able to alleviate H-NS repression in vitro. According to these results, icsA expression is derepressed in hns- background and overexpressed when VirF is provided in trans. Moreover, we find that RnaG-mediated transcription attenuation depends on 80 nt at its 5'-end, a stretch carrying the antisense region. Bases engaged in the initial contact leading to sense-antisense pairing have been identified using synthetic RNA and DNA oligonucleotides designed to rebuild and mutagenize the two stem-loop motifs of the antisense region.


Subject(s)
Bacterial Proteins/genetics , Bacterial Proteins/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Gene Expression Regulation, Bacterial , RNA, Antisense/metabolism , Trans-Activators/metabolism , Transcription Factors/genetics , Base Sequence , Binding Sites , Molecular Sequence Data , Promoter Regions, Genetic , RNA, Antisense/chemistry , RNA, Bacterial/chemistry , RNA, Bacterial/metabolism , Transcription, Genetic , Virulence Factors/genetics
13.
Diagn Microbiol Infect Dis ; 70(3): 387-94, 2011 Jul.
Article in English | MEDLINE | ID: mdl-21683270

ABSTRACT

The constitutive or inducible macrolide-lincosamide-streptogramin (MLS) phenotype of 30 erm(B)-positive Streptococcus pyogenes isolates was determined by different methods and under various growth conditions and correlated to the sequence of the 5'-untranslated regions of erm(B). The MLS phenotype of one-third of the isolates could not be classified. In liquid medium, some of these isolates responded to induction only during the logarithmic phase of growth, while others expressed clindamycin resistance even under noninducing conditions. By increasing the growth rate, we observed a shift from a constitutive towards an inducible pattern of resistance. All data were confirmed by analysis of the 23S rRNA methylation level. The erm(B)-5'-untranslated region was 99% similar in sequence. In erm(B)-positive S. pyogenes, the MLS phenotype is strongly influenced by culture conditions and control of its expression does not depend exclusively on the sequence of the erm(B)-5'-untranslated region.


Subject(s)
Anti-Bacterial Agents/pharmacology , Bacterial Proteins/metabolism , Drug Resistance, Bacterial , Lincosamides/pharmacology , Macrolides/pharmacology , Streptococcus pyogenes/drug effects , Streptogramin B/pharmacology , 5' Untranslated Regions , Adolescent , Bacterial Proteins/genetics , Child , Child, Preschool , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , Humans , Infant , Infant, Newborn , Methylation , Microbial Sensitivity Tests/methods , RNA, Ribosomal, 23S/metabolism , Sequence Analysis, DNA , Sequence Homology, Nucleic Acid , Streptococcal Infections/microbiology , Streptococcus pyogenes/genetics , Streptococcus pyogenes/isolation & purification
14.
J Lipid Res ; 52(5): 897-907, 2011 May.
Article in English | MEDLINE | ID: mdl-21357570

ABSTRACT

Hydroxy-3-methyl-glutaryl-CoA reductase (HMGR) is the rate-controlling enzyme of cholesterol synthesis, and owing to its biological and pharmacological relevance, researchers have investigated several compounds capable of modulating its activity with the hope of developing new hypocholesterolemic drugs. In particular, polyphenol-rich extracts were extensively tested for their cholesterol-lowering effect as alternatives, or adjuvants, to the conventional statin therapies, but a full understanding of the mechanism of their action has yet to be reached. Our work reports on a detailed kinetic and equilibrium study on the modulation of HMGR by the most-abundant catechin in green tea, epigallocatechin-3-gallate (EGCG). Using a concerted approach involving spectrophotometric, optical biosensor, and chromatographic analyses, molecular docking, and site-directed mutagenesis on the cofactor site of HMGR, we have demonstrated that EGCG potently inhibits the in vitro activity of HMGR (K(i) in the nanomolar range) by competitively binding to the cofactor site of the reductase. Finally, we evaluated the effect of combined EGCG-statin administration.


Subject(s)
Catechin/analogs & derivatives , Hydroxymethylglutaryl CoA Reductases/metabolism , Hydroxymethylglutaryl-CoA Reductase Inhibitors/pharmacology , Recombinant Proteins/metabolism , Biosensing Techniques , Catechin/pharmacology , Computational Biology , Enzyme Activation/drug effects , Enzyme Assays , Humans , Hydroxymethylglutaryl CoA Reductases/genetics , Microsomes, Liver/metabolism , Recombinant Proteins/genetics
15.
Nucleic Acids Res ; 38(10): 3362-75, 2010 Jun.
Article in English | MEDLINE | ID: mdl-20129941

ABSTRACT

The virulence gene icsA of Shigella flexneri encodes an invasion protein crucial for host colonization by pathogenic bacteria. Within the intergenic region virA-icsA, we have discovered a new gene that encodes a non-translated antisense RNA (named RnaG), transcribed in cis on the complementary strand of icsA. In vitro transcription assays show that RnaG promotes premature termination of transcription of icsA mRNA. Transcriptional inhibition is also observed in vivo by monitoring the expression profile in Shigella by real-time polymerase chain reaction and when RnaG is provided in trans. Chemical and enzymatic probing of the leader region of icsA mRNA either free or bound to RnaG indicate that upon hetero-duplex formation an intrinsic terminator, leading to transcription block, is generated on the nascent icsA mRNA. Mutations in the hairpin structure of the proposed terminator impair the RnaG mediated-regulation of icsA transcription. This study represents the first evidence of transcriptional attenuation mechanism caused by a small RNA in Gram-negative bacteria. We also present data on the secondary structure of the antisense region of RnaG. In addition, alternatively silencing icsA and RnaG promoters, we find that transcription from the strong RnaG promoter reduces the activity of the weak convergent icsA promoter through the transcriptional interference regulation.


Subject(s)
Bacterial Proteins/genetics , DNA-Binding Proteins/genetics , Gene Expression Regulation, Bacterial , RNA, Antisense/metabolism , Shigella flexneri/genetics , Transcription Factors/genetics , Transcription, Genetic , Bacterial Proteins/biosynthesis , DNA-Binding Proteins/biosynthesis , Down-Regulation , Promoter Regions, Genetic , RNA, Antisense/chemistry , RNA, Antisense/genetics , Shigella flexneri/pathogenicity , Transcription Factors/biosynthesis , Virulence Factors/biosynthesis , Virulence Factors/genetics
16.
J Mol Biol ; 355(2): 169-74, 2006 Jan 13.
Article in English | MEDLINE | ID: mdl-16303134

ABSTRACT

The nucleoid-associated transcriptional repressor H-NS forms both dimers and tetramers in vivo. Two types of two-hybrid systems, one capable of detecting protein dimerization and the other protein tetramerization, have been used to determine whether environmental changes could affect the oligomerization capacity of this protein in the cell. Increasing the temperature from 37 degrees C to 48 degrees C and changing the pH between 4.0 and 9.0 did not influence either dimerization or tetramerization, whereas lowering the temperature below 25 degrees C and increasing osmolarity were found to reduce the formation of H-NS tetramers, which are the active form of this protein, without affecting dimerization. These findings provide a rationale to explain the induction of H-NS expression during cold-shock, suggest a mechanism contributing to derepressing osmotic-shock genes transcriptionally regulated by H-NS and indicate that changes of the oligomerization properties of H-NS do not play a role in the H-NS and temperature-dependent control of virulence gene expression.


Subject(s)
Bacterial Proteins/metabolism , DNA-Binding Proteins/metabolism , Escherichia coli Proteins/metabolism , Escherichia coli/metabolism , Repressor Proteins/metabolism , Cold Temperature , Dimerization , Escherichia coli/genetics , Gene Expression Regulation, Bacterial , Hydrogen-Ion Concentration , Osmotic Pressure , Temperature , Two-Hybrid System Techniques
17.
EMBO J ; 24(16): 2896-905, 2005 Aug 17.
Article in English | MEDLINE | ID: mdl-16052211

ABSTRACT

Two types of two-hybrid systems demonstrate that the transcriptional repressor, nucleoid-associated protein H-NS (histone-like, nucleoid structuring protein) forms dimers and tetramers in vivo, the latter being the active form of the protein. The H-NS 'protein oligomerization' domain (N-domain) is unable to oligomerize in the absence of the intradomain linker while the 'DNA-binding' C-domain clearly displays a protein-protein interaction capacity, which contributes to H-NS tetramerization and which is lost following Pro115 mutation. Linker deletion or substitution with KorB linker abolishes H-NS oligomerization. A model describing H-NS dimerization and tetramerization based on all available data and suggesting the existence in the tetramer of a bundle of four alpha-helices, each contributed by an H-NS monomer, is presented.


Subject(s)
Bacterial Proteins/metabolism , DNA-Binding Proteins/metabolism , Models, Molecular , Repressor Proteins/metabolism , Bacterial Proteins/genetics , DNA-Binding Proteins/genetics , Dimerization , Escherichia coli , Mutation/genetics , Oligonucleotides , Plasmids/genetics , Protein Structure, Tertiary
18.
J Biol Chem ; 280(22): 21498-505, 2005 Jun 03.
Article in English | MEDLINE | ID: mdl-15795232

ABSTRACT

One of the most efficient systems of acid resistance in Escherichia coli, the gad system, is based on the coordinated action of two isoforms of glutamate decarboxylase (GadA and GadB) and of a specific glutamate/gamma-aminobutyrate antiporter (GadC). The gadA/BC genes, activated in response to acid stress and in stationary phase cells, are subjected to complex circuits of regulation involving sigma70, sigmaS, cAMP receptor protein, H-NS, EvgAS, TorRS, GadE, GadX, GadW, and YdeO. Herein, we provide evidence that the nucleoid-associated protein H-NS directly functions as repressor of gadA, one of the structural genes, and gadX, a regulatory gene encoding one of the primary activators of the gad system. Band shift and DNase I footprints reveal that H-NS indeed binds to specific sites in the promoter regions of gadA and gadX and represses the transcription of these genes both in an in vitro system and in vivo. Moreover, we show that a maltose-binding protein MalE-GadX fusion is able to stimulate the promoter activity of gadA/BC, thus indicating that GadX is by itself able to up-regulate the gad genes and that a functional competition between H-NS and GadX takes place at the gadA promoter. Altogether, our results indicate that H-NS directly inhibits gadA and gadX transcription and, by controlling the intracellular level of the activator GadX, indirectly affects the expression of the whole gad system.


Subject(s)
AraC Transcription Factor/physiology , Bacterial Proteins/physiology , DNA-Binding Proteins/physiology , Escherichia coli Proteins/physiology , Escherichia coli/enzymology , Glutamate Decarboxylase/metabolism , AraC Transcription Factor/genetics , Bacterial Proteins/genetics , Base Sequence , Binding Sites , Binding, Competitive , DNA/chemistry , DNA Primers/chemistry , DNA, Superhelical , DNA-Binding Proteins/genetics , Deoxyribonuclease I/metabolism , Dose-Response Relationship, Drug , Escherichia coli/metabolism , Escherichia coli Proteins/genetics , Lac Operon , Molecular Sequence Data , Mutation , Plasmids/metabolism , Promoter Regions, Genetic , Protein Binding , Protein Isoforms , RNA, Messenger/metabolism , Recombinant Fusion Proteins/metabolism , Sequence Homology, Nucleic Acid , Temperature , Up-Regulation , beta-Galactosidase/metabolism
19.
Mol Microbiol ; 51(2): 523-37, 2004 Jan.
Article in English | MEDLINE | ID: mdl-14756791

ABSTRACT

In the human enteropathogen Shigella transcription of virF, the primary regulator of the invasion functions, is strictly temperature-dependent and is antagonistically mediated by H-NS and FIS, which bind to specific sites on the virF promoter. Here we report on the relevance of DNA geometry to the thermoregulation of virF and demonstrate that the virF promoter hosts a major DNA bend halfway between two H-NS sites. The bent region has been mutagenized in vitro to mimic temperature-induced changes of DNA curvature. Functional analysis of curvature mutants and of promoter constructs in which the two H-NS sites are phased-out by a half-helix turn reveals that modifying the spatial relationships between these sites severely affects the interaction of H-NS with the virF promoter, as well as its in vivo and in vitro temperature-dependent activity. The role of promoter curvature as thermosensor is also compatible with the present observation that, with increasing temperature, the virF bending centre moves downstream at a rate having its maximum around the transition temperature, abruptly unmasking a binding site for the transcriptional activator FIS.


Subject(s)
DNA, Bacterial/chemistry , DNA, Bacterial/genetics , Promoter Regions, Genetic/genetics , Shigella/genetics , Shigella/pathogenicity , Base Sequence , DNA Primers , Escherichia coli/genetics , Models, Genetic , Molecular Sequence Data , Mutagenesis, Site-Directed , Nucleic Acid Conformation , Plasmids/genetics , Polymerase Chain Reaction , Restriction Mapping , Sequence Alignment , Sequence Homology, Nucleic Acid
20.
Res Microbiol ; 153(7): 461-8, 2002 Sep.
Article in English | MEDLINE | ID: mdl-12405354

ABSTRACT

The contribution of histone-like proteins to the transcriptional regulation of virulence gene networks is a common feature among pathogenic bacteria. In this article we review current knowledge about the regulative role of major histone-like proteins in the silencing/activation of the invasivity phenotype of Shigella, the etiological agent of bacillary dissentery.


Subject(s)
Bacterial Proteins/metabolism , DNA-Binding Proteins/metabolism , Escherichia coli Proteins , Gene Expression Regulation, Bacterial , Regulon , Shigella/pathogenicity , Bacterial Proteins/genetics , DNA-Binding Proteins/genetics , Dysentery, Bacillary/microbiology , Humans , Plasmids , Virulence
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