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1.
Cell Rep ; 42(10): 113199, 2023 10 31.
Article in English | MEDLINE | ID: mdl-37804508

ABSTRACT

PARP-1 activation at DNA damage sites leads to the synthesis of long poly(ADP-ribose) (PAR) chains, which serve as a signal for DNA repair. Here we show that FUS, an RNA-binding protein, is specifically directed to PAR through its RNA recognition motif (RRM) to increase PAR synthesis by PARP-1 in HeLa cells after genotoxic stress. Using a structural approach, we also identify specific residues located in the FUS RRM, which can be PARylated by PARP-1 to control the level of PAR synthesis. Based on the results of this work, we propose a model in which, following a transcriptional arrest that releases FUS from nascent mRNA, FUS can be recruited by PARP-1 activated by DNA damage to stimulate PAR synthesis. We anticipate that this model offers new perspectives to understand the role of FET proteins in cancers and in certain neurodegenerative diseases such as amyotrophic lateral sclerosis.


Subject(s)
DNA Damage , Poly Adenosine Diphosphate Ribose , Poly(ADP-ribose) Polymerases , RNA-Binding Protein FUS , Humans , DNA Repair , HeLa Cells , Poly (ADP-Ribose) Polymerase-1/genetics , Poly (ADP-Ribose) Polymerase-1/metabolism , Poly Adenosine Diphosphate Ribose/metabolism , Poly(ADP-ribose) Polymerase Inhibitors , Poly(ADP-ribose) Polymerases/genetics , Poly(ADP-ribose) Polymerases/metabolism , RNA Recognition Motif , RNA-Binding Protein FUS/genetics , RNA-Binding Protein FUS/metabolism
2.
Sci Rep ; 13(1): 7772, 2023 05 13.
Article in English | MEDLINE | ID: mdl-37179431

ABSTRACT

FUS is an RNA-binding protein involved in familiar forms of ALS and FTLD that also assembles into fibrillar cytoplasmic aggregates in some neurodegenerative diseases without genetic causes. The self-adhesive prion-like domain in FUS generates reversible condensates via the liquid-liquid phase separation process (LLPS) whose maturation can lead to the formation of insoluble fibrillar aggregates in vitro, consistent with the appearance of cytoplasmic inclusions in ageing neurons. Using a single-molecule imaging approach, we reveal that FUS can assemble into nanofibrils at concentrations in the nanomolar range. These results suggest that the formation of fibrillar aggregates of FUS could occur in the cytoplasm at low concentrations of FUS, below the critical ones required to trigger the liquid-like condensate formation. Such nanofibrils may serve as seeds for the formation of pathological inclusions. Interestingly, the fibrillation of FUS at low concentrations is inhibited by its binding to mRNA or after the phosphorylation of its prion-like domain, in agreement with previous models.


Subject(s)
Amyotrophic Lateral Sclerosis , Neurodegenerative Diseases , Prions , Humans , RNA, Messenger/metabolism , Prions/metabolism , Neurodegenerative Diseases/metabolism , Cytoplasm/metabolism , Phosphorylation , RNA-Binding Protein FUS/metabolism , Amyotrophic Lateral Sclerosis/metabolism
3.
Elife ; 122023 01 18.
Article in English | MEDLINE | ID: mdl-36651723

ABSTRACT

RNA-protein interactions (RPIs) are promising targets for developing new molecules of therapeutic interest. Nevertheless, challenges arise from the lack of methods and feedback between computational and experimental techniques during the drug discovery process. Here, we tackle these challenges by developing a drug screening approach that integrates chemical, structural and cellular data from both advanced computational techniques and a method to score RPIs in cells for the development of small RPI inhibitors; and we demonstrate its robustness by targeting Y-box binding protein 1 (YB-1), a messenger RNA-binding protein involved in cancer progression and resistance to chemotherapy. This approach led to the identification of 22 hits validated by molecular dynamics (MD) simulations and nuclear magnetic resonance (NMR) spectroscopy of which 11 were found to significantly interfere with the binding of messenger RNA (mRNA) to YB-1 in cells. One of our leads is an FDA-approved poly(ADP-ribose) polymerase 1 (PARP-1) inhibitor. This work shows the potential of our integrative approach and paves the way for the rational development of RPI inhibitors.


Subject(s)
Neoplasms , RNA , Humans , Molecular Dynamics Simulation , Drug Discovery , RNA, Messenger/genetics , Y-Box-Binding Protein 1/genetics , Y-Box-Binding Protein 1/metabolism
4.
Elife ; 102021 09 07.
Article in English | MEDLINE | ID: mdl-34490845

ABSTRACT

TDP-43 is a nuclear RNA-binding protein that forms neuronal cytoplasmic inclusions in two major neurodegenerative diseases, ALS and FTLD. While the self-assembly of TDP-43 by its structured N-terminal and intrinsically disordered C-terminal domains has been widely studied, the mechanism by which mRNA preserves TDP-43 solubility in the nucleus has not been addressed. Here, we demonstrate that tandem RNA recognition motifs of TDP-43 bind to long GU-repeats in a cooperative manner through intermolecular interactions. Moreover, using mutants whose cooperativity is impaired, we found that the cooperative binding of TDP-43 to mRNA may be critical to maintain the solubility of TDP-43 in the nucleus and the miscibility of TDP-43 in cytoplasmic stress granules. We anticipate that the knowledge of a higher order assembly of TDP-43 on mRNA may clarify its role in intron processing and provide a means of interfering with the cytoplasmic aggregation of TDP-43.


Subject(s)
Cytoplasmic Granules , DNA-Binding Proteins/metabolism , RNA-Binding Proteins/metabolism , RNA/metabolism , DNA-Binding Proteins/genetics , Escherichia coli , Humans , RNA Recognition Motif , RNA-Binding Proteins/genetics
5.
Cell Mol Life Sci ; 74(12): 2319-2332, 2017 06.
Article in English | MEDLINE | ID: mdl-28168443

ABSTRACT

Type 2 phosphatidic acid phosphatases (PAP2s) can be either soluble or integral membrane enzymes. In bacteria, integral membrane PAP2s play major roles in the metabolisms of glycerophospholipids, undecaprenyl-phosphate (C55-P) lipid carrier and lipopolysaccharides. By in vivo functional experiments and biochemical characterization we show that the membrane PAP2 coded by the Bacillus subtilis yodM gene is the principal phosphatidylglycerol phosphate (PGP) phosphatase of B. subtilis. We also confirm that this enzyme, renamed bsPgpB, has a weaker activity on C55-PP. Moreover, we solved the crystal structure of bsPgpB at 2.25 Å resolution, with tungstate (a phosphate analog) in the active site. The structure reveals two lipid chains in the active site vicinity, allowing for PGP substrate modeling and molecular dynamic simulation. Site-directed mutagenesis confirmed the residues important for substrate specificity, providing a basis for predicting the lipids preferentially dephosphorylated by membrane PAP2s.


Subject(s)
Bacillus subtilis/enzymology , Cell Membrane/enzymology , Phosphatidate Phosphatase/chemistry , Phosphatidate Phosphatase/metabolism , Bacillus subtilis/genetics , Catalytic Domain , Crystallography, X-Ray , Escherichia coli/metabolism , Genes, Bacterial , Genetic Complementation Test , Models, Molecular , Mutagenesis, Site-Directed , Phosphatidate Phosphatase/genetics , Phosphatidylglycerols/metabolism , Solubility , Substrate Specificity
6.
Invest. clín ; 57(2): 158-175, jun. 2016. ilus, tab
Article in English | LILACS | ID: biblio-841108

ABSTRACT

It was designed and characterized a reporter system to be captured by antibodies bound to ELISA plates. The system was designed with the rK346 from Leishmania infantum, a highly antigenic and specific protein. The rK346 was coupled to the horseradish peroxidase C (HRPc) from Armoracia rusticana using glutaraldehyde or sulfo-SMCC. Glutaraldehyde conjugation was performed in two steps. Separation of conjugates was carried out using a Sepharose S-200 in size exclusion chromatography (SEC); fractions were analyzed via HRPc activity and through ELISA plates sensitized with polyclonal anti-rK346 IgG purified from rabbit serum. A heterogeneous population of conjugates rK346-HRPc was obtained with molecular weights ranging between 109.7 ± 16.5 to 67.6 ± 10.1 kDa; with rK346-HRPc stoichiometries of 1:2; 2:1; 3:1; and 2:2. Conjugation using sulfo-SMCC was carried out first by introducing -SH groups onto the HRPc using the SATA reagent and the antigen was modified with sulfo-SMCC during 45 min. Separation and analysis of conjugates was performed similarly as with glutaraldehyde, resulting in a heterogeneous population of conjugates rK346-HRPc with molecular weights between 150.5 ± 22.6 to 80.0 ± 12.0 kDa; with rK346-HRPC stoichiometries of 2:1; 1:2; 2:2; and 1:3, with an increased conjugation efficiency in comparison with glutaraldehyde. This enables sulfo-SMCC to be used as a potential reagent for coupling the antigen to the HRPc, to design an economic, specific and easy method to apply as a reporter system, available to assess individuals at risk and/or at early and late stages of visceral leishmaniasis.


Se diseñó y caracterizó un sistema reportero para ser capturado por anticuerpos enlazados a placas de ELISA. El sistema fue diseñado con una proteína altamente antigénica y específica, la rK346 de Leishmania infantum. La rK346 fue acoplada a la peroxidasa C de rábano picante (HRPc) de Armoracia rusticana usando glutaraldehido o sulfo-SMCC. La conjugación con glutaraldehido fue realizada en dos pasos. La separación de los conjugados fue llevada a cabo a través de una cromatografía de exclusión molecular sefarosa S-200 (CES), las fracciones fueron analizadas midiendo la actividad HRPc y por placas ELISA sensibilizadas con inmunoglobulina G policlonal anti-rK346, purificada desde suero de conejo. Se obtuvo una población heterogénea de conjugados rK346-HRPc en un rango de pesos moleculares entre 109,7 ± 16,5 a 67,6 ± 10,1 kDa; con estequiometria rK346-HRPc de 1:2; 2:1; 3:1; y 2:2. La conjugación usando sulfo-SMCC se llevó a cabo primero introduciendo grupos -SH en la HRPc usando el reactivo SATA; el antígeno se modificó con sulfo-SMCC. La separación y el análisis de los conjugados se realizaron de forma similar que con el glutaraldehido, resultando en una población heterogénea de conjugados rK346-HRPc con un rango de pesos moleculares entre 150,5 ± 22,6 a 80,0 ± 12,0 kDa; con estequiometria rK346-HRPC de 2:1; 1:2; 2:2 y 1:3, y con una eficiencia de conjugación incrementada en comparación con glutaraldehido. De esta forma, se habilitó al sulfo-SMCC como un reactivo potencial para acoplar antígenos a la HRPc, como método para el diseño de un sistema reportero económico, especifico y fácil de aplicar, útil en la evaluación de individuos en riesgo y/o en estados tempranos o avanzados de leishmaniasis visceral.


Subject(s)
Antibodies, Protozoan/isolation & purification , Leishmania infantum/immunology , Horseradish Peroxidase , Antigens, Protozoan , Immunoconjugates
7.
Invest Clin ; 57(2): 158-175, 2016 Jun.
Article in English | MEDLINE | ID: mdl-28429896

ABSTRACT

It was designed and characterized a reporter system to be captured by an- tibodies bound to ELISA plates. The system was designed with the rK346 from Leishmania infantum, a highly antigenic and specific protein. The rK346 was coupled to the horseradish peroxidase C (HRPc) from Armoracia rusticana using glutaraldehyde or sulfo-SMCC. Gluta- raldehyde conjugation was performed in two steps. Separation of conjugates was carried out using a Sepharose S-200 in size exclusion chromatography (SEC); fractions were analyzed via HRPc activity and through ELISA plates sensitized with polyclonal anti-rK346 IgG puri- fied from rabbit serum. A heterogeneous population of conjugates rK346-HRPc was obtained with molecular weights ranging between 109.7 ± 16.5 to 67.6 ± 10.1 kDa; with rK346-HRPe stoichiometries of 1:2; 2:1; 3:1; and 2:2. Conjugation using sulfo-SMCC was carried out first by introducing -SH groups onto the HRPc using the SATA reagent and the antigen was modi- fied with sulfo-SMCC during 45 min. Separation and analysis of conjugates was performed similarly as with glutaraldehyde, resulting in a heterogeneous population of conjugates rK346- HRPc with molecular weights between 150.5 ± 22.6 to 80.0 ± 12.0 kDa; with rK346-HRPC stoichiometries of 2:1; 1:2; 2:2; and 1:3, with an increased conjugation efficiency in compari- son with glutaraldehyde. This enables sulfo-SMCC to be used as a potential reagent for cou- pling the antigen to the HRPc, to design an economic, specific and easy method to apply as a reporter system, available to assess individuals at risk and/or at early and late stages of visceral leishmaniasis.


Subject(s)
Antibodies, Protozoan/isolation & purification , Antigens, Protozoan , Horseradish Peroxidase , Leishmania infantum/immunology , Immunoconjugates
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