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1.
Cell ; 169(7): 1240-1248.e23, 2017 Jun 15.
Artículo en Inglés | MEDLINE | ID: mdl-28622509

RESUMEN

Drug-resistant bacterial pathogens pose an urgent public-health crisis. Here, we report the discovery, from microbial-extract screening, of a nucleoside-analog inhibitor that inhibits bacterial RNA polymerase (RNAP) and exhibits antibacterial activity against drug-resistant bacterial pathogens: pseudouridimycin (PUM). PUM is a natural product comprising a formamidinylated, N-hydroxylated Gly-Gln dipeptide conjugated to 6'-amino-pseudouridine. PUM potently and selectively inhibits bacterial RNAP in vitro, inhibits bacterial growth in culture, and clears infection in a mouse model of Streptococcus pyogenes peritonitis. PUM inhibits RNAP through a binding site on RNAP (the NTP addition site) and mechanism (competition with UTP for occupancy of the NTP addition site) that differ from those of the RNAP inhibitor and current antibacterial drug rifampin (Rif). PUM exhibits additive antibacterial activity when co-administered with Rif, exhibits no cross-resistance with Rif, and exhibits a spontaneous resistance rate an order-of-magnitude lower than that of Rif. PUM is a highly promising lead for antibacterial therapy.


Asunto(s)
Antibacterianos/aislamiento & purificación , Antibacterianos/farmacología , ARN Polimerasas Dirigidas por ADN/antagonistas & inhibidores , Streptomyces/química , Animales , Antibacterianos/química , Bacterias/clasificación , Bacterias/efectos de los fármacos , Bacterias/crecimiento & desarrollo , ARN Polimerasas Dirigidas por ADN/química , Farmacorresistencia Bacteriana , Femenino , Células HeLa , Humanos , Ratones , Ratones Endogámicos ICR , Microbiología del Suelo , Infecciones Estreptocócicas/tratamiento farmacológico , Streptococcus pyogenes/efectos de los fármacos , Transcripción Genética/efectos de los fármacos
2.
Nucleic Acids Res ; 52(15): 8661-8674, 2024 Aug 27.
Artículo en Inglés | MEDLINE | ID: mdl-38989620

RESUMEN

Binding gene-wide single-stranded nucleic acids to surface-immobilized complementary probes is an important but challenging process for biophysical studies and diagnostic applications. The challenge comes from the conformational dynamics of the long chain that affects its accessibility and weakens its hybridization to the probes. We investigated the binding of bacteriophage genome M13mp18 on several different 20-mer probes immobilized on the surface of a multi-spot, label-free biosensor, and observed that only a few of them display strong binding capability with dissociation constant as low as 10 pM. Comparing experimental data and computational analysis of the M13mp18 chain structural features, we found that the capturing performance of a specific probe is directly related to the multiplicity of binding sites on the genomic strand, and poorly connected with the predicted secondary and tertiary structure. We show that a model of weak cooperativity of transient bonds is compatible with the measured binding kinetics and accounts for the enhancement of probe capturing observed when more than 20 partial pairings with binding free energy lower than -10 kcal mol-1 are present. This mechanism provides a specific pattern of response of a genomic strand on a panel of properly selected oligomer probe sequences.


Asunto(s)
ADN de Cadena Simple , ADN de Cadena Simple/metabolismo , ADN de Cadena Simple/química , Sitios de Unión , Cinética , Conformación de Ácido Nucleico , Bacteriófago M13/genética , Bacteriófago M13/metabolismo , ADN Viral/metabolismo , ADN Viral/química , ADN Viral/genética , Técnicas Biosensibles/métodos , Hibridación de Ácido Nucleico , Sondas de ADN/química , Termodinámica
3.
Small ; 19(32): e2300947, 2023 08.
Artículo en Inglés | MEDLINE | ID: mdl-37060208

RESUMEN

Rapid detection of whole virus particles in biological or environmental samples represents an unmet need for the containment of infectious diseases. Here, an optical device enabling the enumeration of single virion particles binding on antibody or aptamers immobilized on a surface with anti-reflective coating is described. In this regime, nanoparticles adhering to the sensor surface provide localized contributions to the reflected field that become detectable because of their mixing with the interfering waves in the reflection direction. Thus, these settings are exploited to realize a scan-free, label-free, micro-array-type digital assay on a disposable cartridge, in which the virion counting takes place in wide field-of-view imaging. With this approach we could quantify, by enumeration, different variants of SARS-CoV-2 virions interacting with antibodies and aptamers immobilized on different spots. For all tested variants, the aptamers showed larger affinity but lower specificity relative to the antibodies. It is found that the combination of different probes on the same surface enables increasing specificity of detection and dynamic range.


Asunto(s)
Aptámeros de Nucleótidos , Técnicas Biosensibles , COVID-19 , Humanos , SARS-CoV-2 , Técnicas Biosensibles/métodos , Anticuerpos , Virión
4.
Nucleic Acids Res ; 49(22): 12785-12804, 2021 12 16.
Artículo en Inglés | MEDLINE | ID: mdl-34871443

RESUMEN

Genome instability is a condition characterized by the accumulation of genetic alterations and is a hallmark of cancer cells. To uncover new genes and cellular pathways affecting endogenous DNA damage and genome integrity, we exploited a Synthetic Genetic Array (SGA)-based screen in yeast. Among the positive genes, we identified VID22, reported to be involved in DNA double-strand break repair. vid22Δ cells exhibit increased levels of endogenous DNA damage, chronic DNA damage response activation and accumulate DNA aberrations in sequences displaying high probabilities of forming G-quadruplexes (G4-DNA). If not resolved, these DNA secondary structures can block the progression of both DNA and RNA polymerases and correlate with chromosome fragile sites. Vid22 binds to and protects DNA at G4-containing regions both in vitro and in vivo. Loss of VID22 causes an increase in gross chromosomal rearrangement (GCR) events dependent on G-quadruplex forming sequences. Moreover, the absence of Vid22 causes defects in the correct maintenance of G4-DNA rich elements, such as telomeres and mtDNA, and hypersensitivity to the G4-stabilizing ligand TMPyP4. We thus propose that Vid22 is directly involved in genome integrity maintenance as a novel regulator of G4 metabolism.


Asunto(s)
G-Cuádruplex , Inestabilidad Genómica , Proteínas de la Membrana/fisiología , Proteínas de Saccharomyces cerevisiae/fisiología , Aberraciones Cromosómicas , Daño del ADN , Genoma Fúngico , Proteínas de la Membrana/genética , Proteínas de la Membrana/metabolismo , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Homeostasis del Telómero
5.
Mikrochim Acta ; 188(4): 143, 2021 03 28.
Artículo en Inglés | MEDLINE | ID: mdl-33774708

RESUMEN

A microfluidic, label-free optical sensor for water pollutants, which is based on a packed micro-column of microspheres with refractive index similar to that of water, is presented. The perfluoropolyether microspheres are synthetized by membrane emulsification followed by UV irradiation. The microfluidic channel hosting the packed column is transparent when filled with pure water as a consequence of refractive index matching, whereas it scatters light in presence of compounds with lipophilic moieties that spontaneously adsorb on the fluorinated microspheres. The device is characterized by investigating the response to cationic and anionic surfactants. Both the signal growth rate and the recovery rate measured during washing with water depend on the type and concentration of the compounds. The cationic surfactants tested display a larger signal increase, linearly scaling with concentration. A limit of detection of 1 µM is obtained in the current configuration. The water index-matched microspheres enable to access an additional analytical parameter, that is the propagation velocity of the scattering signal along the column. This parameter is also found to scale linearly with concentration, hence providing a complementary analytical tool sensitive to the adhesion kinetics.


Asunto(s)
Técnicas Analíticas Microfluídicas/métodos , Microesferas , Compuestos de Amonio Cuaternario/análisis , Dodecil Sulfato de Sodio/análisis , Tensoactivos/análisis , Contaminantes Químicos del Agua/análisis , Adsorción , Polímeros de Fluorocarbono/química , Dispositivos Laboratorio en un Chip , Técnicas Analíticas Microfluídicas/instrumentación , Compuestos de Amonio Cuaternario/química , Refractometría , Dodecil Sulfato de Sodio/química , Tensoactivos/química , Contaminantes Químicos del Agua/química
6.
Int J Mol Sci ; 22(8)2021 Apr 07.
Artículo en Inglés | MEDLINE | ID: mdl-33916983

RESUMEN

Transcription factors regulate gene activity by binding specific regions of genomic DNA thanks to a subtle interplay of specific and nonspecific interactions that is challenging to quantify. Here, we exploit Reflective Phantom Interface (RPI), a label-free biosensor based on optical reflectivity, to investigate the binding of the N-terminal domain of Gal4, a well-known gene regulator, to double-stranded DNA fragments containing or not its consensus sequence. The analysis of RPI-binding curves provides interaction strength and kinetics and their dependence on temperature and ionic strength. We found that the binding of Gal4 to its cognate site is stronger, as expected, but also markedly slower. We performed a combined analysis of specific and nonspecific binding-equilibrium and kinetics-by means of a simple model based on nested potential wells and found that the free energy gap between specific and nonspecific binding is of the order of one kcal/mol only. We investigated the origin of such a small value by performing all-atom molecular dynamics simulations of Gal4-DNA interactions. We found a strong enthalpy-entropy compensation, by which the binding of Gal4 to its cognate sequence entails a DNA bending and a striking conformational freezing, which could be instrumental in the biological function of Gal4.


Asunto(s)
Proteínas de Unión al ADN/química , ADN/química , Proteínas de Saccharomyces cerevisiae/química , Factores de Transcripción/química , Algoritmos , Secuencia de Bases , Sitios de Unión , ADN/metabolismo , Proteínas de Unión al ADN/metabolismo , Cinética , Modelos Moleculares , Modelos Teóricos , Conformación Molecular , Unión Proteica , Proteínas de Saccharomyces cerevisiae/metabolismo , Relación Estructura-Actividad , Factores de Transcripción/metabolismo
7.
Biophys J ; 119(5): 989-1001, 2020 09 01.
Artículo en Inglés | MEDLINE | ID: mdl-32738217

RESUMEN

Hybridization of complementary single strands of DNA represents a very effective natural molecular recognition process widely exploited for diagnostic, biotechnology, and nanotechnology applications. A common approach relies on the immobilization on a surface of single-stranded DNA probes that bind complementary targets in solution. However, despite the deep knowledge on DNA interactions in bulk solution, the modeling of the same interactions on a surface are still challenging and perceived as strongly system dependent. Here, we show that a two-dimensional analysis of the kinetics of hybridization, performed at different target concentrations and probe surface densities by a label-free optical biosensor, reveals peculiar features inconsistent with an ideal Langmuir-like behavior. We propose a simple non-Langmuir kinetic model accounting for an enhanced electrostatic repulsion originating from the surface immobilization of nucleic acids and for steric hindrance close to full hybridization of the surface probes. The analysis of the kinetic data by the model enables quantifying the repulsive potential at the surface, as well as retrieving the kinetic parameters of isolated probes. We show that the strength and the kinetics of hybridization at large probe density can be improved by a three-dimensional immobilization strategy of probe strands with a double-stranded linker.


Asunto(s)
ADN de Cadena Simple , ADN , ADN/genética , Sondas de ADN , Cinética , Hibridación de Ácido Nucleico
8.
BMC Microbiol ; 17(1): 81, 2017 04 04.
Artículo en Inglés | MEDLINE | ID: mdl-28376742

RESUMEN

BACKGROUND: Polynucleotide phosphorylase (PNPase, encoded by pnp) is generally thought of as an enzyme dedicated to RNA metabolism. The pleiotropic effects of PNPase deficiency is imputed to altered processing and turnover of mRNAs and small RNAs, which in turn leads to aberrant gene expression. However, it has long since been known that this enzyme may also catalyze template-independent polymerization of dNDPs into ssDNA and the reverse phosphorolytic reaction. Recently, PNPase has been implicated in DNA recombination, repair, mutagenesis and resistance to genotoxic agents in diverse bacterial species, raising the possibility that PNPase may directly, rather than through control of gene expression, participate in these processes. RESULTS: In this work we present evidence that in Escherichia coli PNPase enhances both homologous recombination upon P1 transduction and error prone DNA repair of double strand breaks induced by zeocin, a radiomimetic agent. Homologous recombination does not require PNPase phosphorolytic activity and is modulated by its RNA binding domains whereas error prone DNA repair of zeocin-induced DNA damage is dependent on PNPase catalytic activity and cannot be suppressed by overexpression of RNase II, the other major enzyme (encoded by rnb) implicated in exonucleolytic RNA degradation. Moreover, E. coli pnp mutants are more sensitive than the wild type to zeocin. This phenotype depends on PNPase phosphorolytic activity and is suppressed by rnb, thus suggesting that zeocin detoxification may largely depend on RNA turnover. CONCLUSIONS: Our data suggest that PNPase may participate both directly and indirectly through regulation of gene expression to several aspects of DNA metabolism such as recombination, DNA repair and resistance to genotoxic agents.


Asunto(s)
Reparación del ADN , Escherichia coli/enzimología , Escherichia coli/genética , Regulación Enzimológica de la Expresión Génica , Recombinación Homóloga , Polirribonucleótido Nucleotidiltransferasa/genética , Polirribonucleótido Nucleotidiltransferasa/metabolismo , Bleomicina/farmacología , Daño del ADN , ADN de Cadena Simple/metabolismo , Escherichia coli/efectos de los fármacos , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Exorribonucleasas/metabolismo , Regulación Bacteriana de la Expresión Génica , Mutagénesis , Mutación , Unión Proteica , Estabilidad del ARN , ARN Bacteriano , ARN Mensajero/metabolismo
9.
J Bacteriol ; 197(11): 1931-8, 2015 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-25825432

RESUMEN

UNLABELLED: The complex posttranscriptional regulation mechanism of the Escherichia coli pnp gene, which encodes the phosphorolytic exoribonuclease polynucleotide phosphorylase (PNPase), involves two endoribonucleases, namely, RNase III and RNase E, and PNPase itself, which thus autoregulates its own expression. The models proposed for pnp autoregulation posit that the target of PNPase is a mature pnp mRNA previously processed at its 5' end by RNase III, rather than the primary pnp transcript (RNase III-dependent models), and that PNPase activity eventually leads to pnp mRNA degradation by RNase E. However, some published data suggest that pnp expression may also be regulated through a PNPase-dependent, RNase III-independent mechanism. To address this issue, we constructed isogenic Δpnp rnc(+) and Δpnp Δrnc strains with a chromosomal pnp-lacZ translational fusion and measured ß-galactosidase activity in the absence and presence of PNPase expressed by a plasmid. Our results show that PNPase also regulates its own expression via a reversible RNase III-independent pathway acting upstream from the RNase III-dependent branch. This pathway requires the PNPase RNA binding domains KH and S1 but not its phosphorolytic activity. We suggest that the RNase III-independent autoregulation of PNPase occurs at the level of translational repression, possibly by competition for pnp primary transcript between PNPase and the ribosomal protein S1. IMPORTANCE: In Escherichia coli, polynucleotide phosphorylase (PNPase, encoded by pnp) posttranscriptionally regulates its own expression. The two models proposed so far posit a two-step mechanism in which RNase III, by cutting the leader region of the pnp primary transcript, creates the substrate for PNPase regulatory activity, eventually leading to pnp mRNA degradation by RNase E. In this work, we provide evidence supporting an additional pathway for PNPase autogenous regulation in which PNPase acts as a translational repressor independently of RNase III cleavage. Our data make a new contribution to the understanding of the regulatory mechanism of pnp mRNA, a process long since considered a paradigmatic example of posttranscriptional regulation at the level of mRNA stability.


Asunto(s)
Regulación hacia Abajo , Proteínas de Escherichia coli/metabolismo , Escherichia coli/enzimología , Regulación Enzimológica de la Expresión Génica , Polirribonucleótido Nucleotidiltransferasa/genética , Biosíntesis de Proteínas , Ribonucleasa III/metabolismo , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Regulación Bacteriana de la Expresión Génica , Polirribonucleótido Nucleotidiltransferasa/metabolismo , Ribonucleasa III/genética
10.
Front Immunol ; 15: 1323406, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38476234

RESUMEN

Both viral infection and vaccination affect the antibody repertoire of a person. Here, we demonstrate that the analysis of serum antibodies generates information not only on the virus type that caused the infection but also on the specific virus variant. We developed a rapid multiplex assay providing a fingerprint of serum antibodies against five different SARS-CoV-2 variants based on a microarray of virus antigens immobilized on the surface of a label-free reflectometric biosensor. We analyzed serum from the plasma of convalescent subjects and vaccinated volunteers and extracted individual antibody profiles of both total immunoglobulin Ig and IgA fractions. We found that Ig level profiles were strongly correlated with the specific variant of infection or vaccination and that vaccinated subjects displayed a larger quantity of total Ig and a lower fraction of IgA relative to the population of convalescent unvaccinated subjects.


Asunto(s)
COVID-19 , SARS-CoV-2 , Humanos , Inmunoglobulinas , Inmunoglobulina A
11.
Pediatr Infect Dis J ; 43(5): 454-456, 2024 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-38190639

RESUMEN

We report the first case of significant fetal myocardial involvement associated with maternal SARS-CoV-2 infection, in which restoration of cardiac function at birth was noted. The demonstration of previous infection was supported by the quantification of humoral response in child and mother, in particular the presence of anti-N antibodies and through the detection of specific antibodies against the BA.4/5 variant.


Asunto(s)
COVID-19 , Miocarditis , Niño , Femenino , Humanos , Miocarditis/etiología , COVID-19/complicaciones , SARS-CoV-2 , Anticuerpos , Madres , Anticuerpos Antivirales
12.
Nucleic Acids Res ; 39(21): 9250-61, 2011 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-21859751

RESUMEN

Bacillus subtilis pnpA gene product, polynucleotide phosphorylase (PNPase), is involved in double-strand break (DSB) repair via homologous recombination (HR) or non-homologous end-joining (NHEJ). RecN is among the first responders to localize at the DNA DSBs, with PNPase facilitating the formation of a discrete RecN focus per nucleoid. PNPase, which co-purifies with RecA and RecN, was able to degrade single-stranded (ss) DNA with a 3' → 5' polarity in the presence of Mn(2+) and low inorganic phosphate (Pi) concentration, or to extend a 3'-OH end in the presence dNDP · Mn(2+). Both PNPase activities were observed in evolutionarily distant bacteria (B. subtilis and Escherichia coli), suggesting conserved functions. The activity of PNPase was directed toward ssDNA degradation or polymerization by manipulating the Pi/dNDPs concentrations or the availability of RecA or RecN. In its dATP-bound form, RecN stimulates PNPase-mediated polymerization. ssDNA phosphorolysis catalyzed by PNPase is stimulated by RecA, but inhibited by SsbA. Our findings suggest that (i) the PNPase degradative and polymerizing activities might play a critical role in the transition from DSB sensing to end resection via HR and (ii) by blunting a 3'-tailed duplex DNA, in the absence of HR, B. subtilis PNPase might also contribute to repair via NHEJ.


Asunto(s)
Proteínas Bacterianas/metabolismo , ADN de Cadena Simple/metabolismo , ADN Polimerasa Dirigida por ADN/metabolismo , Exodesoxirribonucleasas/metabolismo , Polirribonucleótido Nucleotidiltransferasa/metabolismo , Bacillus subtilis/enzimología , Enzimas de Restricción del ADN/metabolismo , Nucleótidos de Desoxiadenina/metabolismo , Escherichia coli/enzimología , Manganeso/química , Rec A Recombinasas/metabolismo
13.
BMC Microbiol ; 12: 270, 2012 Nov 21.
Artículo en Inglés | MEDLINE | ID: mdl-23171129

RESUMEN

BACKGROUND: Transition from planktonic cells to biofilm is mediated by production of adhesion factors, such as extracellular polysaccharides (EPS), and modulated by complex regulatory networks that, in addition to controlling production of adhesion factors, redirect bacterial cell metabolism to the biofilm mode. RESULTS: Deletion of the pnp gene, encoding polynucleotide phosphorylase, an RNA processing enzyme and a component of the RNA degradosome, results in increased biofilm formation in Escherichia coli. This effect is particularly pronounced in the E. coli strain C-1a, in which deletion of the pnp gene leads to strong cell aggregation in liquid medium. Cell aggregation is dependent on the EPS poly-N-acetylglucosamine (PNAG), thus suggesting negative regulation of the PNAG biosynthetic operon pgaABCD by PNPase. Indeed, pgaABCD transcript levels are higher in the pnp mutant. Negative control of pgaABCD expression by PNPase takes place at mRNA stability level and involves the 5'-untranslated region of the pgaABCD transcript, which serves as a cis-element regulating pgaABCD transcript stability and translatability. CONCLUSIONS: Our results demonstrate that PNPase is necessary to maintain bacterial cells in the planktonic mode through down-regulation of pgaABCD expression and PNAG production.


Asunto(s)
Acetilglucosamina/metabolismo , Biopelículas/crecimiento & desarrollo , Escherichia coli/fisiología , Regulación Bacteriana de la Expresión Génica , Polirribonucleótido Nucleotidiltransferasa/metabolismo , ARN Bacteriano/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Eliminación de Gen , Perfilación de la Expresión Génica , Polirribonucleótido Nucleotidiltransferasa/genética , Estabilidad del ARN
14.
Microorganisms ; 9(5)2021 May 07.
Artículo en Inglés | MEDLINE | ID: mdl-34067197

RESUMEN

Escherichia coli C is a strong biofilm producer in comparison to E. coli K-12 laboratory strains due to higher expression of the pgaABCD operon encoding the enzymes for the biosynthesis of the extracellular polysaccharide poly-ß-1,6-N-acetylglucosamine (PNAG). The pgaABCD operon is negatively regulated at the post-transcriptional level by two factors, namely CsrA, a conserved RNA-binding protein controlling multiple pathways, and the RNA exonuclease polynucleotide phosphorylase (PNPase). In this work, we investigated the molecular bases of different PNAG production in C-1a and MG1655 strains taken as representative of E. coli C and K-12 strains, respectively. We found that pgaABCD operon expression is significantly lower in MG1655 than in C-1a; consistently, CsrA protein levels were much higher in MG1655. In contrast, we show that the negative effect exerted by PNPase on pgaABCD expression is much stronger in C-1a than in MG1655. The amount of CsrA and of the small RNAs CsrB, CsrC, and McaS sRNAs regulating CsrA activity is dramatically different in the two strains, whereas PNPase level is similar. Finally, the compensatory regulation acting between CsrB and CsrC in MG1655 does not occur in E. coli C. Our results suggest that PNPase preserves CsrA-dependent regulation by indirectly modulating csrA expression.

15.
Polymers (Basel) ; 13(22)2021 Nov 11.
Artículo en Inglés | MEDLINE | ID: mdl-34833198

RESUMEN

The physical-chemical properties of the surface of DNA microarrays and biosensors play a fundamental role in their performance, affecting the signal's amplitude and the strength and kinetics of binding. We studied how the interaction parameters vary for hybridization of complementary 23-mer DNA, when the probe strands are immobilized on different copolymers, which coat the surface of an optical, label-free biosensor. Copolymers of N, N-dimethylacrylamide bringing either a different type or density of sites for covalent immobilization of DNA probes, or different backbone charges, were used to functionalize the surface of a Reflective Phantom Interface multispot biosensor made of a glass prism with a silicon dioxide antireflective layer. By analyzing the kinetic hybridization curves at different probe surface densities and target concentrations in solution, we found that all the tested coatings displayed a common association kinetics of about 9 × 104 M-1·s-1 at small probe density, decreasing by one order of magnitude close to the surface saturation of probes. In contrast, both the yield of hybridization and the dissociation kinetics, and hence the equilibrium constant, depend on the type of copolymer coating. Nearly doubled signal amplitudes, although equilibrium dissociation constant was as large as 4 nM, were obtained by immobilizing the probe via click chemistry, whereas amine-based immobilization combined with passivation with diamine carrying positive charges granted much slower dissociation kinetics, yielding an equilibrium dissociation constant as low as 0.5 nM. These results offer quantitative criteria for an optimal selection of surface copolymer coatings, depending on the application.

16.
RNA ; 14(11): 2417-29, 2008 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-18824515

RESUMEN

The exoribonuclease polynucleotide phosphorylase (PNPase, encoded by pnp) is a major player in bacterial RNA decay. In Escherichia coli, PNPase expression is post-transcriptionally regulated at the level of mRNA stability. The primary transcript is very efficiently processed by the endonuclease RNase III at a specific site and the processed pnp mRNA is rapidly degraded in a PNPase-dependent manner. While investigating the PNPase autoregulation mechanism we found, by UV-cross-linking experiments, that the ribosomal protein S1 in crude extracts binds to the pnp-mRNA leader region. We assayed the potential role of S1 protein in pnp gene regulation by modulating S1 expression from depletion to overexpression. We found that S1 depletion led to a sharp decrease of the amount of pnp and other tested mRNAs, as detected by Northern blotting, whereas S1 overexpression caused a strong stabilization of pnp and the other transcripts. Surprisingly, mRNA stabilization depended on PNPase, as it was not observed in a pnp deletion strain. PNPase-dependent stabilization, however, was not detected by chemical decay assay of bulk mRNA. Overall, our data suggest that PNPase exonucleolytic activity may be modulated by the translation potential of the target mRNAs and that, upon ribosomal protein S1 overexpression, PNPase protects from degradation a set of full-length mRNAs. It thus appears that a single mRNA species may be differentially targeted to either decay or PNPase-dependent stabilization, thus preventing its depletion in conditions of fast turnover.


Asunto(s)
Proteínas de Escherichia coli/metabolismo , Escherichia coli/enzimología , Polirribonucleótido Nucleotidiltransferasa/metabolismo , Estabilidad del ARN , ARN Mensajero/metabolismo , Proteínas Ribosómicas/metabolismo , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Regulación Bacteriana de la Expresión Génica , Regulación Enzimológica de la Expresión Génica , Polirribonucleótido Nucleotidiltransferasa/genética , Unión Proteica , ARN Bacteriano/metabolismo , Proteínas Ribosómicas/genética
17.
J Bacteriol ; 191(6): 1738-48, 2009 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-19136586

RESUMEN

The Escherichia coli polynucleotide phosphorylase (PNPase; encoded by pnp), a phosphorolytic exoribonuclease, posttranscriptionally regulates its own expression at the level of mRNA stability and translation. Its primary transcript is very efficiently processed by RNase III, an endonuclease that makes a staggered double-strand cleavage about in the middle of a long stem-loop in the 5'-untranslated region. The processed pnp mRNA is then rapidly degraded in a PNPase-dependent manner. Two non-mutually exclusive models have been proposed to explain PNPase autogenous regulation. The earlier one suggested that PNPase impedes translation of the RNase III-processed pnp mRNA, thus exposing the transcript to degradative pathways. More recently, this has been replaced by the current model, which maintains that PNPase would simply degrade the promoter proximal small RNA generated by the RNase III endonucleolytic cleavage, thus destroying the double-stranded structure at the 5' end that otherwise stabilizes the pnp mRNA. In our opinion, however, the first model was not completely ruled out. Moreover, the RNA decay pathway acting upon the pnp mRNA after disruption of the 5' double-stranded structure remained to be determined. Here we provide additional support to the current model and show that the RNase III-processed pnp mRNA devoid of the double-stranded structure at its 5' end is not translatable and is degraded by RNase E in a PNPase-independent manner. Thus, the role of PNPase in autoregulation is simply to remove, in concert with RNase III, the 5' fragment of the cleaved structure that both allows translation and prevents the RNase E-mediated PNPase-independent degradation of the pnp transcript.


Asunto(s)
Proteínas de Escherichia coli/genética , Escherichia coli/enzimología , Regulación Bacteriana de la Expresión Génica , Polirribonucleótido Nucleotidiltransferasa/genética , Endorribonucleasas/genética , Endorribonucleasas/metabolismo , Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Regulación Enzimológica de la Expresión Génica , Polirribonucleótido Nucleotidiltransferasa/metabolismo , Biosíntesis de Proteínas , Estabilidad del ARN , ARN Bacteriano/genética , ARN Bacteriano/metabolismo , Ribonucleasa III/genética , Ribonucleasa III/metabolismo
18.
Sci Rep ; 8(1): 977, 2018 01 17.
Artículo en Inglés | MEDLINE | ID: mdl-29343682

RESUMEN

C1-inhibitor is a serine protease inhibitor (serpin) controlling complement and contact system activation. Gene mutations result in reduced C1-inhibitor functional plasma level causing hereditary angioedema, a life-threatening disorder. Despite a stable defect, the clinical expression of hereditary angioedema is unpredictable, and the molecular mechanism underlying this variability remains undisclosed. Here we report functional and structural studies on the Arg378Cys C1-inhibitor mutant found in a patient presenting reduced C1-inhibitor levels, episodically undergoing normalization. Expression studies resulted in a drop in mutant C1-innhibitor secretion compared to wild-type. Notwithstanding, the purified proteins had similar features. Thermal denaturation experiments showed a comparable denaturation profile, but the mutant thermal stability decays when tested in conditions reproducing intracellular crowding.Our findings suggest that once correctly folded, the Arg378Cys C1-inhibitor is secreted as an active, although quite unstable, monomer. However, it could bear a folding defect, occasionally promoting protein oligomerization and interfering with the secretion process, thus accounting for its plasma level variability. This defect is exacerbated by the nature of the mutation since the acquired cysteine leads to the formation of non-functional homodimers through inter-molecular disulphide bonding. All the proposed phenomena could be modulated by specific environmental conditions, rendering this mutant exceptionally vulnerable to mild stress.


Asunto(s)
Proteínas Inactivadoras del Complemento 1/deficiencia , Herencia/genética , Angioedema/genética , Femenino , Humanos , Persona de Mediana Edad , Mutación/genética
19.
Wiley Interdiscip Rev RNA ; 7(2): 241-58, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-26750178

RESUMEN

Polynucleotide phosphorylase (PNPase) is an exoribonuclease that catalyzes the processive phosphorolytic degradation of RNA from the 3'-end. The enzyme catalyzes also the reverse reaction of polymerization of nucleoside diphosphates that has been implicated in the generation of heteropolymeric tails at the RNA 3'-end. The enzyme is widely conserved and plays a major role in RNA decay in both Gram-negative and Gram-positive bacteria. Moreover, it participates in maturation and quality control of stable RNA. PNPase autoregulates its own expression at post-transcriptional level through a complex mechanism that involves the endoribonuclease RNase III and translation control. The activity of PNPase is modulated in an intricate and still unclear manner by interactions with small molecules and recruitment in different multiprotein complexes. Not surprisingly, given the wide spectrum of PNPase substrates, PNPase-defective mutations in different bacterial species have pleiotropic effects and perturb the execution of genetic programs involving drastic changes in global gene expression such as biofilm formation, growth at suboptimal temperatures, and virulence.


Asunto(s)
Bacterias/enzimología , Polirribonucleótido Nucleotidiltransferasa/metabolismo , Adaptación Biológica , Bacterias/genética , Catálisis , Activación Enzimática , Regulación Bacteriana de la Expresión Génica , Regulación Enzimológica de la Expresión Génica , Complejos Multiproteicos/metabolismo , Polirribonucleótido Nucleotidiltransferasa/química , Polirribonucleótido Nucleotidiltransferasa/genética , Unión Proteica , Procesamiento Postranscripcional del ARN , Estabilidad del ARN , Relación Estructura-Actividad
20.
Mol Immunol ; 71: 123-130, 2016 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-26895475

RESUMEN

Hereditary angioedema due to C1-inhibitor deficiency (C1-INH-HAE) is an autosomal dominant disease caused by mutations in the SERPING1 gene. A Jordanian family, including 14 individuals with C1-INH-HAE clinical symptoms, was studied. In the propositus and his parents, SERPING1 had four mutations leading to amino acid substitutions. Two are known polymorphic variants (c.167T>C; p.Val34Ala and c.1438G>A; p.Val458Met), the others are newly described. One (c.203C>T; p.Thr46Ile) is located in the N-terminal domain of the C1-inhibitor protein and segregates with angioedema symptoms in the family. The other (c.800C>T; p.Ala245Val) belongs to the serpin domain, and derives from the unaffected father. DNA from additional 24 family members were screened for c.203C>T mutation in the target gene. All individuals heterozygous for the c.203C>T mutation had antigenic and functional plasma levels of C1-inhibitor below 50% of normal, confirming the diagnosis of type I C1-INH-HAE. Angioedema symptoms were present in 14 of 16 subjects carrier for the c.203T allele. Among these subjects, those carrying the c.800T variation had more severe and frequent symptoms than subjects without this mutation. This family-based study provides the first evidence that multiple amino acid substitutions in SERPING1 could influence C1-INH-HAE phenotype.


Asunto(s)
Proteínas Inactivadoras del Complemento 1/genética , Angioedema Hereditario Tipos I y II/genética , Adolescente , Adulto , Western Blotting , Niño , Preescolar , Proteína Inhibidora del Complemento C1 , Análisis Mutacional de ADN , Femenino , Genotipo , Humanos , Jordania , Masculino , Persona de Mediana Edad , Mutación Missense , Linaje , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Adulto Joven
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