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1.
BMC Genomics ; 25(1): 630, 2024 Jun 24.
Artículo en Inglés | MEDLINE | ID: mdl-38914936

RESUMEN

Deep Mutational Scanning (DMS) assays are powerful tools to study sequence-function relationships by measuring the effects of thousands of sequence variants on protein function. During a DMS experiment, several technical artefacts might distort non-linearly the functional score obtained, potentially biasing the interpretation of the results. We therefore tested several technical parameters in the deepPCA workflow, a DMS assay for protein-protein interactions, in order to identify technical sources of non-linearities. We found that parameters common to many DMS assays such as amount of transformed DNA, timepoint of harvest and library composition can cause non-linearities in the data. Designing experiments in a way to minimize these non-linear effects will improve the quantification and interpretation of mutation effects.


Asunto(s)
Mutación , Flujo de Trabajo , Proteínas/metabolismo , Proteínas/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Mapeo de Interacción de Proteínas/métodos , Análisis Mutacional de ADN/métodos , Unión Proteica
2.
Nucleic Acids Res ; 48(13): 7265-7278, 2020 07 27.
Artículo en Inglés | MEDLINE | ID: mdl-32544229

RESUMEN

DNA2 is an essential nuclease-helicase implicated in DNA repair, lagging-strand DNA synthesis, and the recovery of stalled DNA replication forks (RFs). In Saccharomyces cerevisiae, dna2Δ inviability is reversed by deletion of the conserved helicase PIF1 and/or DNA damage checkpoint-mediator RAD9. It has been suggested that Pif1 drives the formation of long 5'-flaps during Okazaki fragment maturation, and that the essential function of Dna2 is to remove these intermediates. In the absence of Dna2, 5'-flaps are thought to accumulate on the lagging strand, resulting in DNA damage-checkpoint arrest and cell death. In line with Dna2's role in RF recovery, we find that the loss of Dna2 results in severe chromosome under-replication downstream of endogenous and exogenous RF-stalling. Importantly, unfaithful chromosome replication in Dna2-mutant cells is exacerbated by Pif1, which triggers the DNA damage checkpoint along a pathway involving Pif1's ability to promote homologous recombination-coupled replication. We propose that Dna2 fulfils its essential function by promoting RF recovery, facilitating replication completion while suppressing excessive RF restart by recombination-dependent replication (RDR) and checkpoint activation. The critical nature of Dna2's role in controlling the fate of stalled RFs provides a framework to rationalize the involvement of DNA2 in Seckel syndrome and cancer.


Asunto(s)
ADN Helicasas/metabolismo , Replicación del ADN , Enfermedades Genéticas Congénitas/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Puntos de Control del Ciclo Celular , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , ADN , Daño del ADN , ADN Helicasas/genética , Humanos , Mutación , Saccharomyces cerevisiae , Proteínas de Saccharomyces cerevisiae/genética
3.
Nat Commun ; 10(1): 2535, 2019 06 10.
Artículo en Inglés | MEDLINE | ID: mdl-31182712

RESUMEN

Rif1 is involved in telomere homeostasis, DNA replication timing, and DNA double-strand break (DSB) repair pathway choice from yeast to human. The molecular mechanisms that enable Rif1 to fulfill its diverse roles remain to be determined. Here, we demonstrate that Rif1 is S-acylated within its conserved N-terminal domain at cysteine residues C466 and C473 by the DHHC family palmitoyl acyltransferase Pfa4. Rif1 S-acylation facilitates the accumulation of Rif1 at DSBs, the attenuation of DNA end-resection, and DSB repair by non-homologous end-joining (NHEJ). These findings identify S-acylation as a posttranslational modification regulating DNA repair. S-acylated Rif1 mounts a localized DNA-damage response proximal to the inner nuclear membrane, revealing a mechanism of compartmentalized DSB repair pathway choice by sequestration of a fatty acylated repair factor at the inner nuclear membrane.


Asunto(s)
Roturas del ADN de Doble Cadena , Reparación del ADN por Unión de Extremidades , Proteínas Represoras/genética , Proteínas de Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/genética , Proteínas de Unión a Telómeros/genética , Acilación , Reparación del ADN , Membrana Nuclear/metabolismo , Proteínas Represoras/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas de Unión a Telómeros/metabolismo
4.
Nat Struct Mol Biol ; 24(7): 588-595, 2017 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-28604726

RESUMEN

In yeast, Rif1 is part of the telosome, where it inhibits telomerase and checkpoint signaling at chromosome ends. In mammalian cells, Rif1 is not telomeric, but it suppresses DNA end resection at chromosomal breaks, promoting repair by nonhomologous end joining (NHEJ). Here, we describe crystal structures for the uncharacterized and conserved ∼125-kDa N-terminal domain of Rif1 from Saccharomyces cerevisiae (Rif1-NTD), revealing an α-helical fold shaped like a shepherd's crook. We identify a high-affinity DNA-binding site in the Rif1-NTD that fully encases DNA as a head-to-tail dimer. Engagement of the Rif1-NTD with telomeres proved essential for checkpoint control and telomere length regulation. Unexpectedly, Rif1-NTD also promoted NHEJ at DNA breaks in yeast, revealing a conserved role of Rif1 in DNA repair. We propose that tight associations between the Rif1-NTD and DNA gate access of processing factors to DNA ends, enabling Rif1 to mediate diverse telomere maintenance and DNA repair functions.


Asunto(s)
Reparación del ADN por Unión de Extremidades , Proteínas de Unión al ADN/química , Proteínas de Unión al ADN/metabolismo , Proteínas Represoras/química , Proteínas Represoras/metabolismo , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas de Unión a Telómeros/química , Proteínas de Unión a Telómeros/metabolismo , Telómero/metabolismo , Sitios de Unión , Cristalografía por Rayos X , ADN/metabolismo , Modelos Moleculares , Unión Proteica , Conformación Proteica , Multimerización de Proteína , Saccharomyces cerevisiae/enzimología
5.
Nat Commun ; 7: 13157, 2016 10 25.
Artículo en Inglés | MEDLINE | ID: mdl-27779184

RESUMEN

Cells have evolved mechanisms to protect, restart and repair perturbed replication forks, allowing full genome duplication, even under replication stress. Interrogating the interplay between nuclease-helicase Dna2 and Holliday junction (HJ) resolvase Yen1, we find the Dna2 helicase activity acts parallel to homologous recombination (HR) in promoting DNA replication and chromosome detachment at mitosis after replication fork stalling. Yen1, but not the HJ resolvases Slx1-Slx4 and Mus81-Mms4, safeguards chromosome segregation by removing replication intermediates that escape Dna2. Post-replicative DNA damage checkpoint activation in Dna2 helicase-defective cells causes terminal G2/M arrest by precluding Yen1-dependent repair, whose activation requires progression into anaphase. These findings explain the exquisite replication stress sensitivity of Dna2 helicase-defective cells, and identify a non-canonical role for Yen1 in the processing of replication intermediates that is distinct from HJ resolution. The involvement of Dna2 helicase activity in completing replication may have implications for DNA2-associated pathologies, including cancer and Seckel syndrome.


Asunto(s)
ADN Helicasas/genética , Replicación del ADN , Regulación Fúngica de la Expresión Génica , Resolvasas de Unión Holliday/genética , Proteínas de Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/genética , Segregación Cromosómica , Cromosomas Fúngicos/química , Cromosomas Fúngicos/metabolismo , ADN Helicasas/metabolismo , ADN Cruciforme/genética , ADN Cruciforme/metabolismo , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Endodesoxirribonucleasas/genética , Endodesoxirribonucleasas/metabolismo , Endonucleasas/genética , Endonucleasas/metabolismo , Endonucleasas de ADN Solapado/genética , Endonucleasas de ADN Solapado/metabolismo , Puntos de Control de la Fase G2 del Ciclo Celular/genética , Resolvasas de Unión Holliday/metabolismo , Recombinación Homóloga , Mitosis , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo
6.
DNA Repair (Amst) ; 33: 17-23, 2015 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-26068713

RESUMEN

PBY1 continues to be linked with DNA repair through functional genomics studies in yeast. Using the yeast knockout (YKO) strain collection, high-throughput genetic interaction screens have identified a large set of negative interactions between PBY1 and genes involved in genome stability. In drug sensitivity screens, the YKO collection pby1Δ strain exhibits a sensitivity profile typical for genes involved in DNA replication and repair. We show that these findings are not related to loss of Pby1. On the basis of genetic interaction profile similarity, we pinpoint disruption of Holliday junction resolvase Mus81-Mms4 as the mutation responsible for DNA repair phenotypes currently ascribed to pby1. The finding that Pby1 is not a DNA repair factor reconciles discrepancies in the data available for PBY1, and indirectly supports a role for Pby1 in mRNA metabolism. Data that has been collected using the YKO collection pby1Δ strain confirms and expands the chemical-genetic interactome of MUS81-MMS4.


Asunto(s)
Reparación del ADN , ADN Cruciforme/metabolismo , Proteínas de Unión al ADN/metabolismo , Endonucleasas/metabolismo , Endonucleasas de ADN Solapado/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/metabolismo , Factores de Transcripción/metabolismo , Cromosomas Fúngicos/metabolismo , Daño del ADN , Epistasis Genética , Técnicas de Inactivación de Genes , Mutación/genética , Fenotipo , ARN Mensajero/genética , ARN Mensajero/metabolismo
8.
J Clin Invest ; 124(2): 742-54, 2014 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-24401275

RESUMEN

High levels of mammalian target of rapamycin complex 1 (mTORC1) activity in malignant gliomas promote tumor progression, suggesting that targeting mTORC1 has potential as a therapeutic strategy. Remarkably, clinical trials in patients with glioma revealed that rapamycin analogs (rapalogs) have limited efficacy, indicating activation of resistance mechanisms. Targeted depletion of MAPK-interacting Ser/Thr kinase 1 (MNK1) sensitizes glioma cells to the mTORC1 inhibitor rapamycin through an indistinct mechanism. Here, we analyzed how MNK1 and mTORC1 signaling pathways regulate the assembly of translation initiation complexes, using the cap analog m7GTP to enrich for initiation complexes in glioma cells followed by mass spectrometry-based quantitative proteomics. Association of eukaryotic translation initiation factor 4E (eIF4E) with eIF4E-binding protein 1 (4EBP1) was regulated by the mTORC1 pathway, whereas pharmacological blocking of MNK activity by CGP57380 or MNK1 knockdown, along with mTORC1 inhibition by RAD001, increased 4EBP1 binding to eIF4E. Furthermore, combined MNK1 and mTORC1 inhibition profoundly inhibited 4EBP1 phosphorylation at Ser65, protein synthesis and proliferation in glioma cells, and reduced tumor growth in an orthotopic glioblastoma (GBM) mouse model. Immunohistochemical analysis of GBM samples revealed increased 4EBP1 phosphorylation. Taken together, our data indicate that rapalog-activated MNK1 signaling promotes glioma growth through regulation of 4EBP1 and indicate a molecular cross-talk between the mTORC1 and MNK1 pathways that has potential to be exploited therapeutically.


Asunto(s)
Neoplasias Encefálicas/tratamiento farmacológico , Factor 4E Eucariótico de Iniciación/metabolismo , Glioma/tratamiento farmacológico , Complejos Multiproteicos/metabolismo , Proteínas Serina-Treonina Quinasas/metabolismo , Sirolimus/uso terapéutico , Serina-Treonina Quinasas TOR/metabolismo , Compuestos de Anilina/química , Animales , Neoplasias Encefálicas/metabolismo , Línea Celular Tumoral , Femenino , Regulación Neoplásica de la Expresión Génica , Glioma/metabolismo , Humanos , Inmunohistoquímica , Diana Mecanicista del Complejo 1 de la Rapamicina , Ratones , Ratones Noqueados , Ratones Desnudos , Trasplante de Neoplasias , Fosforilación , Unión Proteica , Biosíntesis de Proteínas , Purinas/química , Transducción de Señal , Sirolimus/análogos & derivados
9.
EMBO J ; 31(14): 3183-97, 2012 Jul 18.
Artículo en Inglés | MEDLINE | ID: mdl-22588082

RESUMEN

Protein O-fucosylation is a post-translational modification found on serine/threonine residues of thrombospondin type 1 repeats (TSR). The fucose transfer is catalysed by the protein O-fucosyltransferase 2 (POFUT2) and >40 human proteins contain the TSR consensus sequence for POFUT2-dependent fucosylation. To better understand O-fucosylation on TSR, we carried out a structural and functional analysis of human POFUT2 and its TSR substrate. Crystal structures of POFUT2 reveal a variation of the classical GT-B fold and identify sugar donor and TSR acceptor binding sites. Structural findings are correlated with steady-state kinetic measurements of wild-type and mutant POFUT2 and TSR and give insight into the catalytic mechanism and substrate specificity. By using an artificial mini-TSR substrate, we show that specificity is not primarily encoded in the TSR protein sequence but rather in the unusual 3D structure of a small part of the TSR. Our findings uncover that recognition of distinct conserved 3D fold motifs can be used as a mechanism to achieve substrate specificity by enzymes modifying completely folded proteins of very wide sequence diversity and biological function.


Asunto(s)
Fucosiltransferasas/química , Pliegue de Proteína , Cristalografía por Rayos X , Fucosa/química , Fucosa/genética , Fucosa/metabolismo , Fucosiltransferasas/genética , Fucosiltransferasas/metabolismo , Glicosilación , Humanos , Estructura Terciaria de Proteína , Secuencias Repetitivas de Aminoácido , Relación Estructura-Actividad
10.
Am J Hum Genet ; 85(1): 76-86, 2009 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-19576565

RESUMEN

Alpha-dystroglycanopathies such as Walker Warburg syndrome represent an important subgroup of the muscular dystrophies that have been related to defective O-mannosylation of alpha-dystroglycan. In many patients, the underlying genetic etiology remains unsolved. Isolated muscular dystrophy has not been described in the congenital disorders of glycosylation (CDG) caused by N-linked protein glycosylation defects. Here, we present a genetic N-glycosylation disorder with muscular dystrophy in the group of CDG type I. Extensive biochemical investigations revealed a strongly reduced dolichol-phosphate-mannose (Dol-P-Man) synthase activity. Sequencing of the three DPM subunits and complementation of DPM3-deficient CHO2.38 cells showed a pathogenic p.L85S missense mutation in the strongly conserved coiled-coil domain of DPM3 that tethers catalytic DPM1 to the ER membrane. Cotransfection experiments in CHO cells showed a reduced binding capacity of DPM3(L85S) for DPM1. Investigation of the four Dol-P-Man-dependent glycosylation pathways in the ER revealed strongly reduced O-mannosylation of alpha-dystroglycan in a muscle biopsy, thereby explaining the clinical phenotype of muscular dystrophy. This mild Dol-P-Man biosynthesis defect due to DPM3 mutations is a cause for alpha-dystroglycanopathy, thereby bridging the congenital disorders of glycosylation with the dystroglycanopathies.


Asunto(s)
Monofosfato de Dolicol Manosa/metabolismo , Manosiltransferasas/genética , Proteínas de la Membrana/genética , Distrofias Musculares/genética , Distrofias Musculares/metabolismo , Distroglicanos/metabolismo , Femenino , Glicosilación , Humanos
11.
Biometals ; 22(2): 211-23, 2009 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-18690415

RESUMEN

The effects of changes in macrophage iron status, induced by single or multiple iron injections, iron depletion or pregnancy, on both immune function and mRNA expression of genes involved in iron influx and egress have been evaluated. Macrophages isolated from iron deficient rats, or pregnant rats at day 21 of gestation, either supplemented with a single dose of iron dextran, 10 mg, at the commencement of pregnancy, or not, showed significant increases of macrophage ferroportin mRNA expression, which was paralleled by significant decreases in hepatic Hamp mRNA expression. IRP activity in macrophages was not significantly altered by iron status or the inducement of pregnancy +/- a single iron supplement. Macrophage immune function was significantly altered by iron supplementation and pregnancy. Iron supplementation, alone or combined with pregnancy, increased the activities of both NADPH oxidase and nuclear factor kappa B (NFkappaB). In contrast, the imposition of pregnancy reduced the ability of these parameters to respond to an inflammatory stimuli. Increasing iron status, if only marginally, will reduce the ability of macrophages to mount a sustained response to inflammation as well as altering iron homeostatic mechanisms.


Asunto(s)
Hierro/toxicidad , Macrófagos/citología , Alveolos Pulmonares/metabolismo , Animales , Femenino , Homeostasis , Sistema Inmunológico , Inflamación , Macrófagos/metabolismo , NADPH Oxidasas/metabolismo , FN-kappa B/metabolismo , Óxido Nítrico Sintasa/metabolismo , Embarazo , Preñez , Ratas , Ratas Wistar
12.
J Biol Chem ; 281(48): 36742-51, 2006 Dec 01.
Artículo en Inglés | MEDLINE | ID: mdl-17032646

RESUMEN

Thrombospondin type 1 repeats (TSRs) are biologically important domains of extracellular proteins. They are modified with a unique Glcbeta1,3Fucalpha1-O-linked disaccharide on either serine or threonine residues. Here we identify the putative glycosyltransferase, B3GTL, as the beta1,3-glucosyltransferase involved in the biosynthesis of this disaccharide. This enzyme is conserved from Caenorhabditis elegans to man and shares 28% sequence identity with Fringe, the beta1,3-N-acetylglucosaminyltransferase that modifies O-linked fucosyl residues in proteins containing epidermal growth factor-like domains, such as Notch. beta1,3-Glucosyltransferase glucosylates properly folded TSR-fucose but not fucosylated epidermal growth factor-like domain or the non-fucosylated modules. Specifically, the glucose is added in a beta1,3-linkage to the fucose in TSR. The activity profiles of beta1,3-glucosyltransferase and protein O-fucosyltransferase 2, the enzyme that carries out the first step in TSR O-fucosylation, superimpose in endoplasmic reticulum subfractions obtained by density gradient centrifugation. Both enzymes are soluble proteins that efficiently modify properly folded TSR modules. The identification of the beta1,3-glucosyltransferase gene allows us to manipulate the formation of the rare Glcbeta1,3Fucalpha1 structure to investigate its biological function.


Asunto(s)
Disacáridos/química , Glucosiltransferasas/química , Trombospondinas/química , Animales , Caenorhabditis elegans , Centrifugación por Gradiente de Densidad , Retículo Endoplásmico/metabolismo , Factor de Crecimiento Epidérmico/química , Fucosa/química , Glucosiltransferasas/metabolismo , Humanos , Péptidos/química , Ratas , Espectrometría de Masa por Ionización de Electrospray , Especificidad por Sustrato
13.
Mol Cell Proteomics ; 1(1): 11-8, 2002 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-12096136

RESUMEN

The final chemical structure of a newly synthesized protein is often only attained after further covalent modification. Ideally, a comprehensive proteome analysis includes this aspect, a task that is complicated by our incomplete knowledge of the range of possible modifications and often by the lack of suitable analysis methods. Here we present two recently discovered, unusual forms of protein glycosylation, i.e. C-mannosylation and O-fucosylation. Their analysis by a combined mass spectrometric approach is illustrated with peptides from the thrombospondin type 1 repeats (TSRs) of the recombinant axonal guidance protein F-spondin. Nano-electrospray ionization tandem-mass spectrometry of isolated peptides showed that eight of ten Trp residues in the TSRs of F-spondin are C-mannosylated. O-Fucosylation sites were determined by a recently established nano-electrospray ionization quadrupole time-of-flight tandem-mass spectrometry approach. Four of five TSRs carry the disaccharide Hex-dHex-O-Ser/Thr in close proximity to the C-mannosylation sites. In analogy to thrombospondin-1, we assume this to be Glc-Fuc-O-Ser/Thr. Our current knowledge of these glycosylations will be discussed.


Asunto(s)
Fucosa/metabolismo , Glicopéptidos/química , Sustancias de Crecimiento , Manosa/metabolismo , Espectrometría de Masas/métodos , Moléculas de Adhesión de Célula Nerviosa/metabolismo , Péptidos , Trombospondina 1/metabolismo , Secuencias de Aminoácidos , Proteínas de la Matriz Extracelular , Glicosilación , Humanos , Procesamiento Proteico-Postraduccional , Proteínas Recombinantes de Fusión/química , Trombospondina 1/química
14.
Extremophiles ; 6(2): 103-10, 2002 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-12013430

RESUMEN

A novel methanogen, Methanosarcina baltica GS1-AT, DSM 14042, JCM 11281, was isolated from sediment at a depth of 241 m in the Gotland Deep of the Baltic Sea. Cells were irregular, monopolar monotrichous flagellated cocci 1.5-3 microm in diameter often occurring in pairs or tetrads. The catabolic substrates used included methanol, methylated amines, and acetate, but not formate or H2/CO2. Growth was observed in a temperature range between 4 degrees and 27 degrees C with an optimum at 25 degrees C. The doubling time with methanol as substrate was 84 h at 25 degrees C, 120 h at 9 degrees C, and 167 h at 4 degrees C. The doubling time with acetate as substrate was 252 h at 25 degrees C and 425 h at 20 degrees C. After the transfer of methanol-grown cultures, long lag phases were observed that lasted 15-20 days at 25 degrees C and 25 days at 4 degrees -9 degrees C. The NaCl optimum for growth was 2%-4%, and the fastest growth occurred within a pH range of 6.5-7.5. Analysis of the 16S rDNA sequence revealed that the strain was phylogenetically related to Methanosarcina. The sequence similarity to described species of <95.7% and its physiological properties distinguished strain GS1-A(T) from all described species of the genus Methanosarcina.


Asunto(s)
Methanosarcina/aislamiento & purificación , Secuencia de Bases , Concentración de Iones de Hidrógeno , Metanol/metabolismo , Methanosarcina/genética , Methanosarcina/crecimiento & desarrollo , Methanosarcina/metabolismo , Filogenia , ARN de Archaea/genética , ARN Ribosómico 16S/genética , Agua de Mar/microbiología , Suecia , Temperatura
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