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1.
Cell ; 161(5): 1074-1088, 2015 May 21.
Artículo en Inglés | MEDLINE | ID: mdl-26000483

RESUMEN

Microbial pathogens infect host cells by delivering virulence factors (effectors) that interfere with defenses. In plants, intracellular nucleotide-binding/leucine-rich repeat receptors (NLRs) detect specific effector interference and trigger immunity by an unknown mechanism. The Arabidopsis-interacting NLR pair, RRS1-R with RPS4, confers resistance to different pathogens, including Ralstonia solanacearum bacteria expressing the acetyltransferase effector PopP2. We show that PopP2 directly acetylates a key lysine within an additional C-terminal WRKY transcription factor domain of RRS1-R that binds DNA. This disrupts RRS1-R DNA association and activates RPS4-dependent immunity. PopP2 uses the same lysine acetylation strategy to target multiple defense-promoting WRKY transcription factors, causing loss of WRKY-DNA binding and transactivating functions needed for defense gene expression and disease resistance. Thus, RRS1-R integrates an effector target with an NLR complex at the DNA to switch a potent bacterial virulence activity into defense gene activation.


Asunto(s)
Arabidopsis/inmunología , Acetiltransferasas/metabolismo , Arabidopsis/microbiología , Proteínas de Arabidopsis/metabolismo , ADN/metabolismo , Modelos Moleculares , Proteínas de Plantas/metabolismo , Ralstonia solanacearum/enzimología , Ralstonia solanacearum/metabolismo , Ralstonia solanacearum/patogenicidad , Factores de Transcripción/metabolismo
2.
Nature ; 625(7994): 366-376, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-38093015

RESUMEN

Sexual reproduction of Toxoplasma gondii, confined to the felid gut, remains largely uncharted owing to ethical concerns regarding the use of cats as model organisms. Chromatin modifiers dictate the developmental fate of the parasite during its multistage life cycle, but their targeting to stage-specific cistromes is poorly described1,2. Here we found that the transcription factors AP2XII-1 and AP2XI-2 operate during the tachyzoite stage, a hallmark of acute toxoplasmosis, to silence genes necessary for merozoites, a developmental stage critical for subsequent sexual commitment and transmission to the next host, including humans. Their conditional and simultaneous depletion leads to a marked change in the transcriptional program, promoting a full transition from tachyzoites to merozoites. These in vitro-cultured pre-gametes have unique protein markers and undergo typical asexual endopolygenic division cycles. In tachyzoites, AP2XII-1 and AP2XI-2 bind DNA as heterodimers at merozoite promoters and recruit MORC and HDAC3 (ref. 1), thereby limiting chromatin accessibility and transcription. Consequently, the commitment to merogony stems from a profound epigenetic rewiring orchestrated by AP2XII-1 and AP2XI-2. Successful production of merozoites in vitro paves the way for future studies on Toxoplasma sexual development without the need for cat infections and holds promise for the development of therapies to prevent parasite transmission.


Asunto(s)
Gatos , Técnicas In Vitro , Estadios del Ciclo de Vida , Toxoplasma , Animales , Gatos/parasitología , Humanos , Cromatina/genética , Cromatina/metabolismo , Modelos Animales de Enfermedad , Epigénesis Genética , Técnicas In Vitro/métodos , Estadios del Ciclo de Vida/genética , Merozoítos/genética , Proteínas Nucleares/metabolismo , Regiones Promotoras Genéticas/genética , Proteínas Protozoarias/genética , Proteínas Protozoarias/metabolismo , Toxoplasma/genética , Toxoplasma/crecimiento & desarrollo , Toxoplasma/fisiología , Toxoplasmosis/genética , Toxoplasmosis/parasitología , Toxoplasmosis/transmisión , Transcripción Genética
3.
Cell ; 157(7): 1698-711, 2014 Jun 19.
Artículo en Inglés | MEDLINE | ID: mdl-24910301

RESUMEN

Germline-specific Piwi-interacting RNAs (piRNAs) protect animal genomes against transposons and are essential for fertility. piRNAs targeting active transposons are amplified by the ping-pong cycle, which couples Piwi endonucleolytic slicing of target RNAs to biogenesis of new piRNAs. Here, we describe the identification of a transient Amplifier complex that mediates biogenesis of secondary piRNAs in insect cells. Amplifier is nucleated by the DEAD box RNA helicase Vasa and contains the two Piwi proteins participating in the ping-pong loop, the Tudor protein Qin/Kumo and antisense piRNA guides. These components assemble on the surface of Vasa's helicase domain, which functions as an RNA clamp to anchor Amplifier onto transposon transcripts. We show that ATP-dependent RNP remodeling by Vasa facilitates transfer of 5' sliced piRNA precursors between ping-pong partners, and loss of this activity causes sterility in Drosophila. Our results reveal the molecular basis for the small RNA amplification that confers adaptive immunity against transposons.


Asunto(s)
Bombyx/metabolismo , Proteínas de Insectos/metabolismo , ARN Interferente Pequeño/metabolismo , Adenosina Trifosfato/metabolismo , Animales , Bombyx/genética , Línea Celular , ARN Helicasas DEAD-box/genética , ARN Helicasas DEAD-box/metabolismo , Elementos Transponibles de ADN , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Femenino , Proteínas de Insectos/genética , Mutación , Ovario/citología , Ovario/metabolismo
4.
Mol Cell ; 73(6): 1162-1173.e5, 2019 03 21.
Artículo en Inglés | MEDLINE | ID: mdl-30712990

RESUMEN

The MHC class I antigen presentation system enables T cell immunosurveillance of cancers and viruses. A substantial fraction of the immunopeptidome derives from rapidly degraded nascent polypeptides (DRiPs). By knocking down each of the 80 ribosomal proteins, we identified proteins that modulate peptide generation without altering source protein expression. We show that 60S ribosomal proteins L6 (RPL6) and RPL28, which are adjacent on the ribosome, play opposite roles in generating an influenza A virus-encoded peptide. Depleting RPL6 decreases ubiquitin-dependent peptide presentation, whereas depleting RPL28 increases ubiquitin-dependent and -independent peptide presentation. 40S ribosomal protein S28 (RPS28) knockdown increases total peptide supply in uninfected cells by increasing DRiP synthesis from non-canonical translation of "untranslated" regions and non-AUG start codons and sensitizes tumor cells for T cell targeting. Our findings raise the possibility of modulating immunosurveillance by pharmaceutical targeting ribosomes.


Asunto(s)
Presentación de Antígeno , Antígenos de Histocompatibilidad Clase I/biosíntesis , Proteínas Ribosómicas/metabolismo , Subunidades Ribosómicas Grandes de Eucariotas/metabolismo , Subunidades Ribosómicas Pequeñas de Eucariotas/metabolismo , Linfocitos T/metabolismo , Animales , Línea Celular Tumoral , Técnicas de Cocultivo , Células HEK293 , Antígenos de Histocompatibilidad Clase I/inmunología , Interacciones Huésped-Patógeno , Humanos , Vigilancia Inmunológica , Virus de la Influenza A/inmunología , Virus de la Influenza A/patogenicidad , Melanoma/inmunología , Melanoma/metabolismo , Ratones Endogámicos C57BL , Ratones Transgénicos , Proteínas Ribosómicas/genética , Subunidades Ribosómicas Grandes de Eucariotas/genética , Subunidades Ribosómicas Pequeñas de Eucariotas/genética , Neoplasias Cutáneas/inmunología , Neoplasias Cutáneas/metabolismo , Linfocitos T/inmunología , Linfocitos T/virología
5.
Development ; 150(21)2023 11 01.
Artículo en Inglés | MEDLINE | ID: mdl-37818613

RESUMEN

The transcriptional co-regulator SIN3 influences gene expression through multiple interactions that include histone deacetylases. Haploinsufficiency and mutations in SIN3 are the underlying cause of Witteveen-Kolk syndrome and related intellectual disability and autism syndromes, emphasizing its key role in development. However, little is known about the diversity of its interactions and functions in developmental processes. Here, we show that loss of SIN-3, the single SIN3 homolog in Caenorhabditis elegans, results in maternal-effect sterility associated with de-regulation of the germline transcriptome, including de-silencing of X-linked genes. We identify at least two distinct SIN3 complexes containing specific histone deacetylases and show that they differentially contribute to fertility. Single-cell, single-molecule fluorescence in situ hybridization reveals that in sin-3 mutants the X chromosome becomes re-expressed prematurely and in a stochastic manner in individual germ cells, suggesting a role for SIN-3 in its silencing. Furthermore, we identify histone residues whose acetylation increases in the absence of SIN-3. Together, this work provides a powerful framework for the in vivo study of SIN3 and associated proteins.


Asunto(s)
Proteínas de Caenorhabditis elegans , Caenorhabditis elegans , Histona Desacetilasas , Complejo Correpresor Histona Desacetilasa y Sin3 , Animales , Caenorhabditis elegans/genética , Caenorhabditis elegans/metabolismo , Células Germinativas/metabolismo , Histona Desacetilasas/genética , Histona Desacetilasas/metabolismo , Histonas/metabolismo , Hibridación Fluorescente in Situ , Cromosoma X/metabolismo , Proteínas de Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/metabolismo , Complejo Correpresor Histona Desacetilasa y Sin3/genética , Complejo Correpresor Histona Desacetilasa y Sin3/metabolismo
6.
Genes Dev ; 32(3-4): 283-296, 2018 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-29440262

RESUMEN

Meiotic crossover formation requires the stabilization of early recombination intermediates by a set of proteins and occurs within the environment of the chromosome axis, a structure important for the regulation of meiotic recombination events. The molecular mechanisms underlying and connecting crossover recombination and axis localization are elusive. Here, we identified the ZZS (Zip2-Zip4-Spo16) complex, required for crossover formation, which carries two distinct activities: one provided by Zip4, which acts as hub through physical interactions with components of the chromosome axis and the crossover machinery, and the other carried by Zip2 and Spo16, which preferentially bind branched DNA molecules in vitro. We found that Zip2 and Spo16 share structural similarities to the structure-specific XPF-ERCC1 nuclease, although it lacks endonuclease activity. The XPF domain of Zip2 is required for crossover formation, suggesting that, together with Spo16, it has a noncatalytic DNA recognition function. Our results suggest that the ZZS complex shepherds recombination intermediates toward crossovers as a dynamic structural module that connects recombination events to the chromosome axis. The identification of the ZZS complex improves our understanding of the various activities required for crossover implementation and is likely applicable to other organisms, including mammals.


Asunto(s)
Proteínas Cromosómicas no Histona/metabolismo , Intercambio Genético , Proteínas de Unión al ADN/metabolismo , Meiosis/genética , Proteínas Asociadas a Microtúbulos/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas Cromosómicas no Histona/química , Cromosomas Fúngicos , ADN/química , ADN/metabolismo , Roturas del ADN de Doble Cadena , Proteínas de Unión al ADN/química , Endodesoxirribonucleasas/metabolismo , Proteínas Asociadas a Microtúbulos/química , Dominios Proteicos , Proteínas de Saccharomyces cerevisiae/química
7.
PLoS Pathog ; 19(11): e1011417, 2023 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-37983287

RESUMEN

Successful subversion of translation initiation factors eIF4E determines the infection success of potyviruses, the largest group of viruses affecting plants. In the natural variability of many plant species, resistance to potyvirus infection is provided by polymorphisms at eIF4E that renders them inadequate for virus hijacking but still functional in translation initiation. In crops where such natural resistance alleles are limited, the genetic inactivation of eIF4E has been proposed for the engineering of potyvirus resistance. However, recent findings indicate that knockout eIF4E alleles may be deleterious for plant health and could jeopardize resistance efficiency in comparison to functional resistance proteins. Here, we explored the cause of these adverse effects by studying the role of the Arabidopsis eIF4E1, whose inactivation was previously reported as conferring resistance to the potyvirus clover yellow vein virus (ClYVV) while also promoting susceptibility to another potyvirus turnip mosaic virus (TuMV). We report that eIF4E1 is required to maintain global plant translation and to restrict TuMV accumulation during infection, and its absence is associated with a favoured virus multiplication over host translation. Furthermore, our findings show that, in the absence of eIF4E1, infection with TuMV results in the production of a truncated eIFiso4G1 protein. Finally, we demonstrate a role for eIFiso4G1 in TuMV accumulation and in supporting plant fitness during infection. These findings suggest that eIF4E1 counteracts the hijacking of the plant translational apparatus during TuMV infection and underscore the importance of preserving the functionality of translation initiation factors eIF4E when implementing potyvirus resistance strategies.


Asunto(s)
Proteínas de Arabidopsis , Arabidopsis , Potyvirus , Arabidopsis/metabolismo , Factor 4E Eucariótico de Iniciación/genética , Factor 4E Eucariótico de Iniciación/metabolismo , Potyvirus/fisiología , Plantas Modificadas Genéticamente/metabolismo , Enfermedades de las Plantas/genética , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Factor 4G Eucariótico de Iniciación/metabolismo
8.
Mol Cell ; 66(1): 89-101.e8, 2017 Apr 06.
Artículo en Inglés | MEDLINE | ID: mdl-28366643

RESUMEN

Histone replacement by transition proteins (TPs) and protamines (Prms) constitutes an essential step for the successful production of functional male gametes, yet nothing is known on the underlying functional interplay between histones, TPs, and Prms. Here, by studying spermatogenesis in the absence of a spermatid-specific histone variant, H2A.L.2, we discover a fundamental mechanism involved in the transformation of nucleosomes into nucleoprotamines. H2A.L.2 is synthesized at the same time as TPs and enables their loading onto the nucleosomes. TPs do not displace histones but rather drive the recruitment and processing of Prms, which are themselves responsible for histone eviction. Altogether, the incorporation of H2A.L.2 initiates and orchestrates a series of successive transitional states that ultimately shift to the fully compacted genome of the mature spermatozoa. Hence, the current view of histone-to-nucleoprotamine transition should be revisited and include an additional step with H2A.L.2 assembly prior to the action of TPs and Prms.


Asunto(s)
Ensamble y Desensamble de Cromatina , Cromatina/metabolismo , Histonas/metabolismo , Nucleosomas/metabolismo , Protaminas/metabolismo , Espermatogénesis , Espermatozoides/metabolismo , Animales , Células COS , Chlorocebus aethiops , Cromatina/genética , Proteínas Cromosómicas no Histona/genética , Proteínas Cromosómicas no Histona/metabolismo , Biología Computacional , Bases de Datos Genéticas , Fertilidad , Regulación del Desarrollo de la Expresión Génica , Predisposición Genética a la Enfermedad , Genoma , Histonas/deficiencia , Histonas/genética , Infertilidad Masculina/genética , Infertilidad Masculina/metabolismo , Infertilidad Masculina/patología , Infertilidad Masculina/fisiopatología , Masculino , Ratones de la Cepa 129 , Ratones Noqueados , Nucleosomas/genética , Fenotipo , Espermatogénesis/genética , Espermatozoides/patología , Transfección
9.
EMBO J ; 39(10): e102935, 2020 05 18.
Artículo en Inglés | MEDLINE | ID: mdl-31930742

RESUMEN

Magnesium homeostasis is essential for life and depends on magnesium transporters, whose activity and ion selectivity need to be tightly controlled. Rhomboid intramembrane proteases pervade the prokaryotic kingdom, but their functions are largely elusive. Using proteomics, we find that Bacillus subtilis rhomboid protease YqgP interacts with the membrane-bound ATP-dependent processive metalloprotease FtsH and cleaves MgtE, the major high-affinity magnesium transporter in B. subtilis. MgtE cleavage by YqgP is potentiated in conditions of low magnesium and high manganese or zinc, thereby protecting B. subtilis from Mn2+ /Zn2+ toxicity. The N-terminal cytosolic domain of YqgP binds Mn2+ and Zn2+ ions and facilitates MgtE cleavage. Independently of its intrinsic protease activity, YqgP acts as a substrate adaptor for FtsH, a function that is necessary for degradation of MgtE. YqgP thus unites protease and pseudoprotease function, hinting at the evolutionary origin of rhomboid pseudoproteases such as Derlins that are intimately involved in eukaryotic ER-associated degradation (ERAD). Conceptually, the YqgP-FtsH system we describe here is analogous to a primordial form of "ERAD" in bacteria and exemplifies an ancestral function of rhomboid-superfamily proteins.


Asunto(s)
ATPasas Asociadas con Actividades Celulares Diversas/metabolismo , Bacillus subtilis/metabolismo , Endopeptidasas/metabolismo , Proteínas de la Membrana/metabolismo , Bacillus subtilis/crecimiento & desarrollo , Proteínas Bacterianas/metabolismo , Regulación Bacteriana de la Expresión Génica , Proteómica/métodos
10.
J Cell Sci ; 135(15)2022 08 01.
Artículo en Inglés | MEDLINE | ID: mdl-35621049

RESUMEN

Acetyl-CoA participates in post-translational modification of proteins and in central carbon and lipid metabolism in several cell compartments. In mammals, acetyl-CoA transporter 1 (AT1, also known as SLC33A1) facilitates the flux of cytosolic acetyl-CoA into the endoplasmic reticulum (ER), enabling the acetylation of proteins of the secretory pathway, in concert with the activity of dedicated acetyltransferases such as NAT8. However, the involvement of the ER acetyl-CoA pool in acetylation of ER-transiting proteins in Apicomplexa is unknown. Here, we identified homologs of AT1 and NAT8 in Toxoplasma gondii and Plasmodium berghei parasites. Proteome-wide analyses revealed widespread N-terminal acetylation of secreted proteins in both species. Such extensive acetylation of N-terminally processed proteins has not been observed previously in any other organism. Deletion of AT1 homologs in both T. gondii and P. berghei resulted in considerable reductions in parasite fitness. In P. berghei, AT1 was found to be important for growth of asexual blood stages, production of female gametocytes and male gametocytogenesis, implying its requirement for parasite transmission. In the absence of AT1, lysine acetylation and N-terminal acetylation in T. gondii remained globally unaltered, suggesting an uncoupling between the role of AT1 in development and active acetylation occurring along the secretory pathway.


Asunto(s)
Parásitos , Toxoplasma , Acetilcoenzima A/metabolismo , Acetilación , Animales , Retículo Endoplásmico/metabolismo , Femenino , Masculino , Mamíferos/metabolismo , Parásitos/metabolismo , Procesamiento Proteico-Postraduccional , Proteoma/metabolismo , Toxoplasma/genética , Toxoplasma/metabolismo
11.
Cell Commun Signal ; 22(1): 158, 2024 03 04.
Artículo en Inglés | MEDLINE | ID: mdl-38439036

RESUMEN

BACKGROUND: BMP9 and BMP10 are two major regulators of vascular homeostasis. These two ligands bind with high affinity to the endothelial type I kinase receptor ALK1, together with a type II receptor, leading to the direct phosphorylation of the SMAD transcription factors. Apart from this canonical pathway, little is known. Interestingly, mutations in this signaling pathway have been identified in two rare cardiovascular diseases, hereditary hemorrhagic telangiectasia and pulmonary arterial hypertension. METHODS: To get an overview of the signaling pathways modulated by BMP9 and BMP10 stimulation in endothelial cells, we employed an unbiased phosphoproteomic-based strategy. Identified phosphosites were validated by western blot analysis and regulated targets by RT-qPCR. Cell cycle analysis was analyzed by flow cytometry. RESULTS: Large-scale phosphoproteomics revealed that BMP9 and BMP10 treatment induced a very similar phosphoproteomic profile. These BMPs activated a non-canonical transcriptional SMAD-dependent MAPK pathway (MEKK4/P38). We were able to validate this signaling pathway and demonstrated that this activation required the expression of the protein GADD45ß. In turn, activated P38 phosphorylated the heat shock protein HSP27 and the endocytosis protein Eps15 (EGF receptor pathway substrate), and regulated the expression of specific genes (E-selectin, hyaluronan synthase 2 and cyclooxygenase 2). This study also highlighted the modulation in phosphorylation of proteins involved in transcriptional regulation (phosphorylation of the endothelial transcription factor ERG) and cell cycle inhibition (CDK4/6 pathway). Accordingly, we found that BMP10 induced a G1 cell cycle arrest and inhibited the mRNA expression of E2F2, cyclinD1 and cyclinA1. CONCLUSIONS: Overall, our phosphoproteomic screen identified numerous proteins whose phosphorylation state is impacted by BMP9 and BMP10 treatment, paving the way for a better understanding of the molecular mechanisms regulated by BMP signaling in vascular diseases.


Asunto(s)
Proteínas Morfogenéticas Óseas , Células Endoteliales , Puntos de Control del Ciclo Celular , Fosforilación , Puntos de Control de la Fase G1 del Ciclo Celular
12.
Nucleic Acids Res ; 50(21): 12425-12443, 2022 11 28.
Artículo en Inglés | MEDLINE | ID: mdl-36447390

RESUMEN

Human pre-mRNA processing relies on multi-subunit macromolecular complexes, which recognize specific RNA sequence elements essential for assembly and activity. Canonical pre-mRNA processing proceeds via the recognition of a polyadenylation signal (PAS) and a downstream sequence element (DSE), and produces polyadenylated mature mRNAs, while replication-dependent (RD) histone pre-mRNA processing requires association with a stem-loop (SL) motif and a histone downstream element (HDE), and produces cleaved but non-polyadenylated mature mRNAs. H2AC18 mRNA, a specific H2A RD histone pre-mRNA, can be processed to give either a non-polyadenylated mRNA, ending at the histone SL, or a polyadenylated mRNA. Here, we reveal how H2AC18 captures the two human pre-mRNA processing complexes in a mutually exclusive mode by overlapping a canonical PAS (AAUAAA) sequence element with a HDE. Disruption of the PAS sequence on H2AC18 pre-mRNA prevents recruitment of the canonical complex in vitro, without affecting the histone machinery. This shows how the relative position of cis-acting elements in histone pre-mRNAs allows the selective recruitment of distinct human pre-mRNA complexes, thereby expanding the capability to regulate 3' processing and polyadenylation.


Asunto(s)
Histonas , Precursores del ARN , Humanos , Precursores del ARN/genética , Precursores del ARN/metabolismo , Histonas/genética , Histonas/metabolismo , Poliadenilación , Factores de Escisión y Poliadenilación de ARNm/genética , ARN Mensajero/genética , ARN Mensajero/metabolismo
13.
J Cell Sci ; 134(11)2021 06 01.
Artículo en Inglés | MEDLINE | ID: mdl-34100550

RESUMEN

Goldberg-Shprintzen disease (GOSHS) is a rare microcephaly syndrome accompanied by intellectual disability, dysmorphic facial features, peripheral neuropathy and Hirschsprung disease. It is associated with recessive mutations in the gene encoding kinesin family member 1-binding protein (KIF1BP, also known as KIFBP). The encoded protein regulates axon microtubules dynamics, kinesin attachment and mitochondrial biogenesis, but it is not clear how its loss could lead to microcephaly. We identified KIF1BP in the interactome of citron kinase (CITK, also known as CIT), a protein produced by the primary hereditary microcephaly 17 (MCPH17) gene. KIF1BP and CITK interact under physiological conditions in mitotic cells. Similar to CITK, KIF1BP is enriched at the midbody ring and is required for cytokinesis. The association between KIF1BP and CITK can be influenced by CITK activity, and the two proteins may antagonize each other for their midbody localization. KIF1BP knockdown decreases microtubule stability, increases KIF23 midbody levels and impairs midbody localization of KIF14, as well as of chromosome passenger complex. These data indicate that KIF1BP is a CITK interactor involved in midbody maturation and abscission, and suggest that cytokinesis failure may contribute to the microcephaly phenotype observed in GOSHS.


Asunto(s)
Anomalías Craneofaciales , Enfermedad de Hirschsprung , Citocinesis/genética , Células HeLa , Humanos , Huso Acromático
14.
J Cell Sci ; 134(2)2021 01 25.
Artículo en Inglés | MEDLINE | ID: mdl-33495358

RESUMEN

Upon activation by different transmembrane receptors, the same signaling protein can induce distinct cellular responses. A way to decipher the mechanisms of such pleiotropic signaling activity is to directly manipulate the decision-making activity that supports the selection between distinct cellular responses. We developed an optogenetic probe (optoSRC) to control SRC signaling, an example of a pleiotropic signaling node, and we demonstrated its ability to generate different acto-adhesive structures (lamellipodia or invadosomes) upon distinct spatio-temporal control of SRC kinase activity. The occurrence of each acto-adhesive structure was simply dictated by the dynamics of optoSRC nanoclusters in adhesive sites, which were dependent on the SH3 and Unique domains of the protein. The different decision-making events regulated by optoSRC dynamics induced distinct downstream signaling pathways, which we characterized using time-resolved proteomic and network analyses. Collectively, by manipulating the molecular mobility of SRC kinase activity, these experiments reveal the pleiotropy-encoding mechanism of SRC signaling.


Asunto(s)
Citoesqueleto , Proteómica , Transducción de Señal , Familia-src Quinasas , Animales , Células Cultivadas , Simulación de Dinámica Molecular , Fosforilación , Dominios Homologos src , Familia-src Quinasas/genética , Familia-src Quinasas/metabolismo
15.
Hepatology ; 76(5): 1345-1359, 2022 11.
Artículo en Inglés | MEDLINE | ID: mdl-35253915

RESUMEN

BACKGROUND AND AIMS: Netrin-1 displays protumoral properties, though the pathological contexts and processes involved in its induction remain understudied. The liver is a major model of inflammation-associated cancer development, leading to HCC. APPROACH AND RESULTS: A panel of cell biology and biochemistry approaches (reverse transcription quantitative polymerase chain reaction, reporter assays, run-on, polysome fractionation, cross linking immunoprecipitation, filter binding assay, subcellular fractionation, western blotting, immunoprecipitation, stable isotope labeling by amino acids in cell culture) on in vitro-grown primary hepatocytes, human liver cell lines, mouse samples and clinical samples was used. We identify netrin-1 as a hepatic inflammation-inducible factor and decipher its mode of activation through an exhaustive eliminative approach. We show that netrin-1 up-regulation relies on a hitherto unknown mode of induction, namely its exclusive translational activation. This process includes the transfer of NTN1 (netrin-1) mRNA to the endoplasmic reticulum and the direct interaction between the Staufen-1 protein and this transcript as well as netrin-1 mobilization from its cell-bound form. Finally, we explore the impact of a phase 2 clinical trial-tested humanized anti-netrin-1 antibody (NP137) in two distinct, toll-like receptor (TLR) 2/TLR3/TLR6-dependent, hepatic inflammatory mouse settings. We observe a clear anti-inflammatory activity indicating the proinflammatory impact of netrin-1 on several chemokines and Ly6C+ macrophages. CONCLUSIONS: These results identify netrin-1 as an inflammation-inducible factor in the liver through an atypical mechanism as well as its contribution to hepatic inflammation.


Asunto(s)
Carcinoma Hepatocelular , Neoplasias Hepáticas , Ratones , Humanos , Animales , Receptor Toll-Like 2 , Factores de Crecimiento Nervioso/metabolismo , Receptor Toll-Like 3 , Receptor Toll-Like 6 , Proteínas Supresoras de Tumor/metabolismo , Inflamación/metabolismo , Antiinflamatorios , ARN Mensajero , Aminoácidos , Receptores de Netrina
16.
Proc Natl Acad Sci U S A ; 117(32): 19168-19177, 2020 08 11.
Artículo en Inglés | MEDLINE | ID: mdl-32719135

RESUMEN

The emergence of superbugs developing resistance to antibiotics and the resurgence of microbial infections have led scientists to start an antimicrobial arms race. In this context, we have previously identified an active RiPP, the Ruminococcin C1, naturally produced by Ruminococcus gnavus E1, a symbiont of the healthy human intestinal microbiota. This RiPP, subclassified as a sactipeptide, requires the host digestive system to become active against pathogenic Clostridia and multidrug-resistant strains. Here we report its unique compact structure on the basis of four intramolecular thioether bridges with reversed stereochemistry introduced posttranslationally by a specific radical-SAM sactisynthase. This structure confers to the Ruminococcin C1 important clinical properties including stability to digestive conditions and physicochemical treatments, a higher affinity for bacteria than simulated intestinal epithelium, a valuable activity at therapeutic doses on a range of clinical pathogens, mediated by energy resources disruption, and finally safety for human gut tissues.


Asunto(s)
Antibacterianos/química , Antibacterianos/farmacología , Clostridiales/química , Péptidos/química , Péptidos/farmacología , Antibacterianos/aislamiento & purificación , Infecciones Bacterianas/tratamiento farmacológico , Infecciones Bacterianas/microbiología , Humanos , Mucosa Intestinal/efectos de los fármacos , Mucosa Intestinal/microbiología , Péptidos/aislamiento & purificación
17.
Proteomics ; 22(22): e2200155, 2022 11.
Artículo en Inglés | MEDLINE | ID: mdl-36168874

RESUMEN

Diatoms are one of the largest groups in phytoplankton biodiversity. Understanding their response to nitrogen variations, present from micromolar to near-zero levels in oceans and fresh waters, is essential to comprehend their ecological success. Nitrogen starvation is used in biotechnological processes, to trigger the remodeling of carbon metabolism in the direction of fatty acids and triacylglycerol synthesis. We evaluated whole proteome changes in Phaeodactylum tricornutum after 7 days of cultivation with 5.5-mM nitrate (+N) or without any nitrogen source (-N). On a total of 3768 proteins detected in biological replicates, our analysis pointed to 384 differentially abundant proteins (DAP). Analysis of proteins of lower abundance in -N revealed an arrest of amino acid and protein syntheses, a remodeling of nitrogen metabolism, and a decrease of the proteasome abundance suggesting a decline in unselective whole-proteome decay. Analysis of proteins of higher abundance revealed the setting up of a general nitrogen scavenging system dependent on deaminases. The increase of a plastid palmitoyl-ACP desaturase appeared as a hallmark of carbon metabolism rewiring in the direction of fatty acid and triacylglycerol synthesis. This dataset is also valuable to select gene candidates for improved biotechnological properties.


Asunto(s)
Diatomeas , Diatomeas/genética , Diatomeas/metabolismo , Proteoma/metabolismo , Nitrógeno/metabolismo , Proteómica , Carbono/metabolismo , Ácidos Grasos/metabolismo , Triglicéridos
18.
Mol Hum Reprod ; 28(2)2022 02 04.
Artículo en Inglés | MEDLINE | ID: mdl-35150275

RESUMEN

Histone-to-protamine transition is an essential step in the generation of fully functional spermatozoa in various mammalian species. In human and mouse, one of the two protamine-encoding genes produces a precursor pre-protamine 2 (pre-PRM2) protein, which is then processed and assembled. Here, we design an original approach based on the generation of pre-PRM2-specific antibodies to visualize the unprocessed pre-PRM2 by microscopy, flow cytometry and immunoblotting. Using mouse models with characterized failures in histone-to-protamine replacement, we show that pre-PRM2 retention is tightly linked to impaired nucleosome disassembly. Additionally, in elongating/condensing spermatids, we observe that pre-PRM2 and transition protein are co-expressed spatiotemporally, and their physical interaction suggests that these proteins act simultaneously rather than successively during histone replacement. By using our anti-human pre-PRM2 antibody, we also measured pre-PRM2 retention rates in the spermatozoa from 49 men of a series of infertile couples undergoing ICSI, which shed new light on the debated relation between pre-PRM2 retention and sperm parameters. Finally, by monitoring 2-pronuclei embryo formation following ICSI, we evaluated the fertilization ability of the sperm in these 49 patients. Our results suggest that the extent of pre-PRM2 retention in sperm, rather than pre-PRM2 accumulation per se, is associated with fertilization failure. Hence, anti-pre-PRM2 antibodies are valuable tools that could be used in routine monitoring of sperm parameters in fertility clinics, as well as in experimental research programmes to better understand the obscure process of histone-to-protamine transition.


Asunto(s)
Histonas , Inyecciones de Esperma Intracitoplasmáticas , Animales , Femenino , Histonas/metabolismo , Humanos , Masculino , Mamíferos , Ratones , Protaminas/metabolismo , Espermatozoides/metabolismo
19.
Bioinformatics ; 37(17): 2770-2771, 2021 Sep 09.
Artículo en Inglés | MEDLINE | ID: mdl-33538793

RESUMEN

SUMMARY: Many factors can influence results in clinical research, in particular bias in the distribution of samples prior to biochemical preparation. Well Plate Maker is a user-friendly application to design single- or multiple-well plate assays. It allows multiple group experiments to be randomized and therefore helps to reduce possible batch effects. Although primarily fathered to optimize the design of clinical sample analysis by high throughput mass spectrometry (e.g. proteomics or metabolomics), it includes multiple options to limit edge-of-plate effects, to incorporate control samples or to limit cross-contamination. It thus fits the constraints of many experimental fields. AVAILABILITY AND IMPLEMENTATION: Well Plate Maker is implemented in R and available at Bioconductor repository (https://bioconductor.org/packages/wpm) under the open source Artistic 2.0 license. In addition to classical scripting, it can be used through a graphical user interface, developed with Shiny technology.

20.
PLoS Pathog ; 16(11): e1008593, 2020 11.
Artículo en Inglés | MEDLINE | ID: mdl-33180834

RESUMEN

Despite the existence of a preventive vaccine, chronic infection with Hepatitis B virus (HBV) affects more than 250 million people and represents a major global cause of hepatocellular carcinoma (HCC) worldwide. Current clinical treatments, in most of cases, do not eliminate viral genome that persists as a DNA episome in the nucleus of hepatocytes and constitutes a stable template for the continuous expression of viral genes. Several studies suggest that, among viral factors, the HBV core protein (HBc), well-known for its structural role in the cytoplasm, could have critical regulatory functions in the nucleus of infected hepatocytes. To elucidate these functions, we performed a proteomic analysis of HBc-interacting host-factors in the nucleus of differentiated HepaRG, a surrogate model of human hepatocytes. The HBc interactome was found to consist primarily of RNA-binding proteins (RBPs), which are involved in various aspects of mRNA metabolism. Among them, we focused our studies on SRSF10, a RBP that was previously shown to regulate alternative splicing (AS) in a phosphorylation-dependent manner and to control stress and DNA damage responses, as well as viral replication. Functional studies combining SRSF10 knockdown and a pharmacological inhibitor of SRSF10 phosphorylation (1C8) showed that SRSF10 behaves as a restriction factor that regulates HBV RNAs levels and that its dephosphorylated form is likely responsible for the anti-viral effect. Surprisingly, neither SRSF10 knock-down nor 1C8 treatment modified the splicing of HBV RNAs but rather modulated the level of nascent HBV RNA. Altogether, our work suggests that in the nucleus of infected cells HBc interacts with multiple RBPs that regulate viral RNA metabolism. Our identification of SRSF10 as a new anti-HBV restriction factor offers new perspectives for the development of new host-targeted antiviral strategies.


Asunto(s)
Carcinoma Hepatocelular/virología , Proteínas de Ciclo Celular/metabolismo , Virus de la Hepatitis B/fisiología , Hepatitis B/virología , Neoplasias Hepáticas/virología , Proteínas Represoras/metabolismo , Factores de Empalme Serina-Arginina/metabolismo , Proteínas del Núcleo Viral/metabolismo , Proteínas de Ciclo Celular/genética , Virus de la Hepatitis B/genética , Hepatocitos/virología , Humanos , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Fosforilación , Proteómica , ARN Viral/metabolismo , Proteínas de Unión al ARN/genética , Proteínas de Unión al ARN/metabolismo , Proteínas Represoras/genética , Factores de Empalme Serina-Arginina/genética , Proteínas del Núcleo Viral/genética , Replicación Viral
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