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1.
Mol Cell ; 83(7): 1075-1092.e9, 2023 04 06.
Artículo en Inglés | MEDLINE | ID: mdl-36868228

RESUMEN

A multitude of histone chaperones are required to support histones from their biosynthesis until DNA deposition. They cooperate through the formation of histone co-chaperone complexes, but the crosstalk between nucleosome assembly pathways remains enigmatic. Using exploratory interactomics, we define the interplay between human histone H3-H4 chaperones in the histone chaperone network. We identify previously uncharacterized histone-dependent complexes and predict the structure of the ASF1 and SPT2 co-chaperone complex, expanding the role of ASF1 in histone dynamics. We show that DAXX provides a unique functionality to the histone chaperone network, recruiting histone methyltransferases to promote H3K9me3 catalysis on new histone H3.3-H4 prior to deposition onto DNA. Hereby, DAXX provides a molecular mechanism for de novo H3K9me3 deposition and heterochromatin assembly. Collectively, our findings provide a framework for understanding how cells orchestrate histone supply and employ targeted deposition of modified histones to underpin specialized chromatin states.


Asunto(s)
Chaperonas de Histonas , Histonas , Humanos , Histonas/metabolismo , Chaperonas de Histonas/genética , Chaperonas de Histonas/metabolismo , Nucleosomas/genética , Proteínas de Ciclo Celular/metabolismo , ADN , Chaperonas Moleculares/genética , Chaperonas Moleculares/metabolismo , Proteínas Co-Represoras/genética , Proteínas Co-Represoras/metabolismo
2.
Mol Cell ; 73(6): 1191-1203.e6, 2019 03 21.
Artículo en Inglés | MEDLINE | ID: mdl-30824373

RESUMEN

Protein transport into the nucleus is mediated by transport receptors. Import of highly charged proteins, such as histone H1 and ribosomal proteins, requires a dimer of two transport receptors. In this study, we determined the cryo-EM structure of the Imp7:Impß:H1.0 complex, showing that the two importins form a cradle that accommodates the linker histone. The H1.0 globular domain is bound to Impß, whereas the acidic loops of Impß and Imp7 chaperone the positively charged C-terminal tail. Although it remains disordered, the H1 tail serves as a zipper that closes and stabilizes the structure through transient non-specific interactions with importins. Moreover, we found that the GGxxF and FxFG motifs in the Imp7 C-terminal tail are essential for Imp7:Impß dimerization and H1 import, resembling importin interaction with nucleoporins, which, in turn, promote complex disassembly. The architecture of many other complexes might be similarly defined by rapidly exchanging electrostatic interactions mediated by disordered regions.


Asunto(s)
Núcleo Celular/metabolismo , Histonas/metabolismo , Carioferinas/metabolismo , Transporte Activo de Núcleo Celular , Animales , Sitios de Unión , Núcleo Celular/genética , Núcleo Celular/ultraestructura , Microscopía por Crioelectrón , Humanos , Carioferinas/genética , Carioferinas/ultraestructura , Modelos Moleculares , Complejos Multiproteicos , Mutación , Proteínas de Complejo Poro Nuclear/metabolismo , Unión Proteica , Dominios y Motivos de Interacción de Proteínas , Electricidad Estática , Relación Estructura-Actividad , Proteínas de Xenopus/genética , Proteínas de Xenopus/metabolismo , Xenopus laevis , beta Carioferinas/genética , beta Carioferinas/metabolismo , Proteína de Unión al GTP ran/metabolismo
3.
Circulation ; 143(3): 254-266, 2021 01 19.
Artículo en Inglés | MEDLINE | ID: mdl-33167684

RESUMEN

BACKGROUND: Acute infection is a well-established risk factor of cardiovascular inflammation increasing the risk for a cardiovascular complication within the first weeks after infection. However, the nature of the processes underlying such aggravation remains unclear. Lipopolysaccharide derived from Gram-negative bacteria is a potent activator of circulating immune cells including neutrophils, which foster inflammation through discharge of neutrophil extracellular traps (NETs). Here, we use a model of endotoxinemia to link acute infection and subsequent neutrophil activation with acceleration of vascular inflammation Methods: Acute infection was mimicked by injection of a single dose of lipopolysaccharide into hypercholesterolemic mice. Atherosclerosis burden was studied by histomorphometric analysis of the aortic root. Arterial myeloid cell adhesion was quantified by intravital microscopy. RESULTS: Lipopolysaccharide treatment rapidly enhanced atherosclerotic lesion size by expansion of the lesional myeloid cell accumulation. Lipopolysaccharide treatment led to the deposition of NETs along the arterial lumen, and inhibition of NET release annulled lesion expansion during endotoxinemia, thus suggesting that NETs regulate myeloid cell recruitment. To study the mechanism of monocyte adhesion to NETs, we used in vitro adhesion assays and biophysical approaches. In these experiments, NET-resident histone H2a attracted monocytes in a receptor-independent, surface charge-dependent fashion. Therapeutic neutralization of histone H2a by antibodies or by in silico designed cyclic peptides enables us to reduce luminal monocyte adhesion and lesion expansion during endotoxinemia. CONCLUSIONS: Our study shows that NET-associated histone H2a mediates charge-dependent monocyte adhesion to NETs and accelerates atherosclerosis during endotoxinemia.


Asunto(s)
Aterosclerosis/metabolismo , Adhesión Celular/fisiología , Endotoxemia/metabolismo , Monocitos/metabolismo , Electricidad Estática , Animales , Aterosclerosis/inducido químicamente , Aterosclerosis/patología , Adhesión Celular/efectos de los fármacos , Endotoxemia/inducido químicamente , Endotoxemia/patología , Trampas Extracelulares/metabolismo , Humanos , Lipopolisacáridos/toxicidad , Ratones , Ratones Endogámicos C57BL , Ratones Transgénicos , Monocitos/efectos de los fármacos , Monocitos/patología
4.
Proteomics ; 20(10): e2000007, 2020 05.
Artículo en Inglés | MEDLINE | ID: mdl-32267065

RESUMEN

Targeted proteomics depends on the availability of stable isotope labeled (SIL) peptide standards, which for absolute protein quantification need to be absolutely quantified. In the present study, three new approaches for absolute quantification of SIL peptides are developed. All approaches rely on a quantification tag (Qtag) with a specific UV absorption. The Qtag is attached to the peptide during synthesis and is removed by tryptic digestion under standard proteomics workflow conditions. While one quantification method (method A) is designed to allow the fast and economic production of absolutely quantified SIL peptides, two other methods (methods B and C) are developed to enable the straightforward re-quantification of SIL peptides after reconstitution to control and monitor known problems related to peptide solubility, precipitation, and adhesion to vials. All methods yield consistent results when compared to each other and when compared to quantification by amino acid analysis. The precise quantitation methods are used to characterize the in vivo specificity of the H3 specific histone methyltransferase EZH2.


Asunto(s)
Marcaje Isotópico/normas , Péptidos/aislamiento & purificación , Proteínas/genética , Proteómica/normas , Aminoácidos/genética , Humanos , Espectrometría de Masas , Péptidos/química , Péptidos/genética , Proteínas/química , Rayos Ultravioleta
5.
Nucleic Acids Res ; 45(W1): W276-W284, 2017 07 03.
Artículo en Inglés | MEDLINE | ID: mdl-28498958

RESUMEN

The molecular understanding of cellular processes requires the identification and characterization of the involved protein complexes. Affinity-purification and mass spectrometric analysis (AP-MS) are performed on a routine basis to detect proteins assembled in complexes. In particular, protein abundances obtained by quantitative mass spectrometry and direct protein contacts detected by crosslinking and mass spectrometry (XL-MS) provide complementary datasets for revealing the composition, topology and interactions of modules in a protein network. Here, we aim to combine quantitative and connectivity information by a webserver tool in order to infer protein complexes. In a first step, modeling protein abundances and functional annotations from Gene Ontology (GO) results in a network which, in a second step, is integrated with connectivity data from XL-MS analysis in order to complement and validate the protein complexes in the network. The output of our integrative approach is a quantitative protein interaction map which is supplemented with topological information of the detected protein complexes. compleXView is built up by two independent modules which are dedicated to the analysis of label-free AP-MS data and to the visualization of the detected complexes in a network together with crosslink-derived distance restraints. compleXView is available to all users without login requirements at http://xvis.genzentrum.lmu.de/compleXView.


Asunto(s)
Complejos Multiproteicos/metabolismo , Mapeo de Interacción de Proteínas/métodos , Programas Informáticos , Internet , Espectrometría de Masas , Complejos Multiproteicos/química , Mapas de Interacción de Proteínas , Proteína Fosfatasa 2/metabolismo
6.
Proteomics ; 16(3): 437-47, 2016 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-26593131

RESUMEN

Histone posttranslational modifications and histone variants control the epigenetic regulation of gene expression and affect a wide variety of biological processes. A complex pattern of such modifications and variants defines the identity of cells within complex organ systems and can therefore be used to characterize cells at a molecular level. However, their detection and identification in situ has been limited so far due to lack of specificity, selectivity, and availability of antihistone antibodies. Here, we describe a novel MALDI imaging MS based workflow, which enables us to detect and characterize histones by their intact mass and their correlation with cytological properties of the tissue using novel statistical and image analysis tools. The workflow allows us to characterize the in situ distribution of the major histone variants and their modification in the mouse brain. This new analysis tool is particularly useful for the investigation of expression patterns of the linker histone H1 variants for which suitable antibodies are so far not available.


Asunto(s)
Encéfalo/metabolismo , Cromatina/química , Epigénesis Genética , Histonas/genética , Procesamiento Proteico-Postraduccional , Acetilación , Animales , Encéfalo/ultraestructura , Química Encefálica , Cromatina/metabolismo , Histonas/metabolismo , Masculino , Metilación , Ratones , Imagen Molecular/métodos , Fosforilación , Análisis de Componente Principal , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción/métodos , Biología de Sistemas/instrumentación , Biología de Sistemas/métodos
7.
Mol Syst Biol ; 9: 648, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-23511206

RESUMEN

To understand the structure and function of large molecular machines, accurate knowledge of their stoichiometry is essential. In this study, we developed an integrated targeted proteomics and super-resolution microscopy approach to determine the absolute stoichiometry of the human nuclear pore complex (NPC), possibly the largest eukaryotic protein complex. We show that the human NPC has a previously unanticipated stoichiometry that varies across cancer cell types, tissues and in disease. Using large-scale proteomics, we provide evidence that more than one third of the known, well-defined nuclear protein complexes display a similar cell type-specific variation of their subunit stoichiometry. Our data point to compositional rearrangement as a widespread mechanism for adapting the functions of molecular machines toward cell type-specific constraints and context-dependent needs, and highlight the need of deeper investigation of such structural variants.


Asunto(s)
Proteínas de Complejo Poro Nuclear/análisis , Proteínas de Complejo Poro Nuclear/química , Poro Nuclear/química , Poro Nuclear/metabolismo , Calibración , Línea Celular , Humanos , Espectrometría de Masas/métodos , Microscopía/métodos , Proteínas de Complejo Poro Nuclear/metabolismo , Proteómica/métodos
8.
Nat Genet ; 55(9): 1567-1578, 2023 09.
Artículo en Inglés | MEDLINE | ID: mdl-37666988

RESUMEN

Modified parental histones are segregated symmetrically to daughter DNA strands during replication and can be inherited through mitosis. How this may sustain the epigenome and cell identity remains unknown. Here we show that transmission of histone-based information during DNA replication maintains epigenome fidelity and embryonic stem cell plasticity. Asymmetric segregation of parental histones H3-H4 in MCM2-2A mutants compromised mitotic inheritance of histone modifications and globally altered the epigenome. This included widespread spurious deposition of repressive modifications, suggesting elevated epigenetic noise. Moreover, H3K9me3 loss at repeats caused derepression and H3K27me3 redistribution across bivalent promoters correlated with misexpression of developmental genes. MCM2-2A mutation challenged dynamic transitions in cellular states across the cell cycle, enhancing naïve pluripotency and reducing lineage priming in G1. Furthermore, developmental competence was diminished, correlating with impaired exit from pluripotency. Collectively, this argues that epigenetic inheritance of histone modifications maintains a correctly balanced and dynamic chromatin landscape able to support mammalian cell differentiation.


Asunto(s)
Epigenoma , Histonas , Animales , Histonas/genética , Cromatina/genética , Células Madre Embrionarias , Mitosis , Mamíferos
9.
Biomark Res ; 10(1): 43, 2022 Jun 10.
Artículo en Inglés | MEDLINE | ID: mdl-35681175

RESUMEN

BACKGROUND: Immunotherapy of acute myeloid leukemia has experienced considerable advances, however novel target antigens continue to be sought after. To this end, unbiased approaches for surface protein detection are limited and integration with other data types, such as gene expression and somatic mutational burden, are poorly utilized. The Cell Surface Capture technology provides an unbiased, discovery-driven approach to map the surface proteins on cells of interest. Yet, direct utilization of primary patient samples has been limited by the considerable number of viable cells needed. METHODS: Here, we optimized the Cell Surface Capture protocol to enable direct interrogation of primary patient samples and applied our optimized protocol to a set of samples from patients with acute myeloid leukemia (AML) to generate the AML surfaceome. We then further curated this AML surfaceome to exclude antigens expressed on healthy tissues and integrated mutational burden data from hematologic cancers to further enrich for targets which are likely to be essential to leukemia biology. Finally, we validated our findings in a separate cohort of AML patient samples. RESULTS: Our protocol modifications allowed us to double the yield in identified proteins and increased the specificity from 54 to 80.4% compared to previous approaches. Using primary AML patient samples, we were able to identify a total of 621 surface proteins comprising the AML surfaceome. We integrated this data with gene expression and mutational burden data to curate a set of robust putative target antigens. Seventy-six proteins were selected as potential candidates for further investigation of which we validated the most promising novel candidate markers, and identified CD148, ITGA4 and Integrin beta-7 as promising targets in AML. Integrin beta-7 showed the most promising combination of expression in patient AML samples, and low or absent expression on healthy hematopoietic tissue. CONCLUSION: Taken together, we demonstrate the feasibility of a highly optimized surfaceome detection method to interrogate the entire AML surfaceome directly from primary patient samples and integrate this data with gene expression and mutational burden data to achieve a robust, multiomic target identification platform. This approach has the potential to accelerate the unbiased target identification for immunotherapy of AML.

10.
Sci Rep ; 11(1): 7256, 2021 03 31.
Artículo en Inglés | MEDLINE | ID: mdl-33790358

RESUMEN

Alteration of epigenetic modifications plays an important role in human cancer. Notably, the dysregulation of histone post-translational modifications (PTMs) has been associated with several cancers including colorectal cancer (CRC). However, the signature of histone PTMs on circulating nucleosomes is still not well described. We have developed a fast and robust enrichment method to isolate circulating nucleosomes from plasma for further downstream proteomic analysis. This method enabled us to quantify the global alterations of histone PTMs from 9 CRC patients and 9 healthy donors. Among 54 histone proteoforms identified and quantified in plasma samples, 13 histone PTMs were distinctive in CRC. Notably, methylation of histone H3K9 and H3K27, acetylation of histone H3 and citrullination of histone H2A1R3 were upregulated in plasma of CRC patients. A comparative analysis of paired samples identified 3 common histone PTMs in plasma and tumor tissue including the methylation and acetylation state of lysine 27 of histone H3. Moreover, we highlight for the first time that histone H2A1R3 citrulline is a modification upregulated in CRC patients. This new method presented herein allows the detection and quantification of histone variants and histone PTMs from circulating nucleosomes in plasma samples and could be used for biomarker discovery of cancer.


Asunto(s)
Neoplasias Colorrectales/sangre , Epigenómica , Regulación Neoplásica de la Expresión Génica , Histonas/sangre , Proteínas de Neoplasias/sangre , Nucleosomas/metabolismo , Proteómica , Regulación hacia Arriba , Acetilación , Citrulinación , Femenino , Humanos , Masculino , Metilación
11.
Cell Rep ; 32(13): 108190, 2020 09 29.
Artículo en Inglés | MEDLINE | ID: mdl-32997987

RESUMEN

Kinetochores are macromolecular protein assemblies at centromeres that mediate accurate chromosome segregation during cell division. The outer kinetochore KNL1SPC105, MIS12MTW1, and NDC80NDC80 complexes assemble the KMN network, which harbors the sites of microtubule binding and spindle assembly checkpoint signaling. The buildup of the KMN network that transmits microtubule pulling forces to budding yeast point centromeres is poorly understood. Here, we identify 225 inter-protein crosslinks by mass spectrometry on KMN complexes isolated from Saccharomyces cerevisiae that delineate the KMN subunit connectivity for outer kinetochore assembly. C-Terminal motifs of Nsl1 and Mtw1 recruit the SPC105 complex through Kre28, and both motifs aid tethering of the NDC80 complex by the previously reported Dsn1 C terminus. We show that a hub of three C-terminal MTW1 subunit motifs mediates the cooperative stabilization of the KMN network, which is augmented by a direct NDC80-SPC105 association.


Asunto(s)
Cinetocoros/metabolismo , Espectrometría de Masas/métodos , Proteínas Asociadas a Microtúbulos/metabolismo , Saccharomyces cerevisiae/metabolismo , Saccharomycetales/patogenicidad , Secuencia de Aminoácidos
12.
Elife ; 82019 05 21.
Artículo en Inglés | MEDLINE | ID: mdl-31112132

RESUMEN

Kinetochores are macromolecular protein complexes at centromeres that ensure accurate chromosome segregation by attaching chromosomes to spindle microtubules and integrating safeguard mechanisms. The inner kinetochore is assembled on CENP-A nucleosomes and has been implicated in establishing a kinetochore-associated pool of Aurora B kinase, a chromosomal passenger complex (CPC) subunit, which is essential for chromosome biorientation. By performing crosslink-guided in vitro reconstitution of budding yeast kinetochore complexes we showed that the Ame1/Okp1CENP-U/Q heterodimer, which forms the COMA complex with Ctf19/Mcm21CENP-P/O, selectively bound Cse4CENP-A nucleosomes through the Cse4 N-terminus. The Sli15/Ipl1INCENP/Aurora-B core-CPC interacted with COMA in vitro through the Ctf19 C-terminus whose deletion affected chromosome segregation fidelity in Sli15 wild-type cells. Tethering Sli15 to Ame1/Okp1 rescued synthetic lethality upon Ctf19 depletion in a Sli15 centromere-targeting deficient mutant. This study shows molecular characteristics of the point-centromere kinetochore architecture and suggests a role for the Ctf19 C-terminus in mediating CPC-binding and accurate chromosome segregation.


Asunto(s)
Cinetocoros/química , Mapas de Interacción de Proteínas , Proteínas de Saccharomyces cerevisiae/análisis , Saccharomycetales/química , Unión Proteica
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