scholarly journals X-linked intellectual disability mutations alter the conformational state of a histone demethylase's sensing of chromatin

2022 ◽  
Author(s):  
Fatima S. Ugur ◽  
Mark J. S. Kelly ◽  
Danica Galonic Fujimori
Keyword(s):  
Intellectual Disability ◽  
Neural Development ◽  
Catalytic Domain ◽  
Dna Recognition ◽  
Chromatin Modification ◽  
Conformational State ◽  
Histone Demethylases ◽  
Unique Role ◽  
Conformational Rearrangement ◽  
Model Recognition

The H3K4me3 chromatin modification, a hallmark of promoters of actively transcribed genes, is dynamically removed by the KDM5 family of histone demethylases. The KDM5 demethylases have a number of accessory domains, two of which, ARID and PHD1, lie within the catalytic domain. KDM5C, which has a unique role in neural development, harbors a number of mutations adjacent to its accessory domains that cause X-linked intellectual disability (XLID). The roles of these accessory domains remain unknown, limiting an understanding of how XLID mutations affect KDM5C activity. We find that while the ARID and PHD1 domains are required for efficient nucleosome demethylation, the PHD1 domain alone has an inhibitory role in KDM5C catalysis. We further find that binding of the H3 tail to PHD1 is coupled to the recognition of linker DNA by KDM5C. Our data suggests a model in which the PHD1 domain regulates DNA recognition by the ARID domain based on available substrate cues. In this model, recognition of distinct chromatin features is coupled to a conformational rearrangement of the ARID and PHD1 domains, which in turn modulates the positioning of the catalytic domain for efficient nucleosome demethylation. Importantly, we find that XLID mutations adjacent to the ARID and PHD1 domains alter the conformational state of these domains to enhance DNA binding. This results in the loss of specificity in chromatin recognition by KDM5C and renders catalytic activity sensitive to inhibition by linker DNA. Our findings suggest a unifying model by which XLID mutations alter chromatin recognition and enable euchromatin-specific dysregulation of demethylation by KDM5C.

scholarly journals IQSEC2-Associated Intellectual Disability and Autism

2019 ◽  
Vol 20 (12) ◽  
pp. 3038 ◽  
Author(s):  
Nina S. Levy ◽  
George K. E. Umanah ◽  
Eli J. Rogers ◽  
Reem Jada ◽  
Orit Lache ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Nmda Receptors ◽  
Glutamate Receptors ◽  
Ampa Receptor ◽  
Ampa Receptors ◽  
Neuronal Development ◽  
Catalytic Domain ◽  
Excitatory Synapses ◽  
Ampa Receptor Subunit ◽  
Ion Influx

Mutations in IQSEC2 cause intellectual disability (ID), which is often accompanied by seizures and autism. A number of studies have shown that IQSEC2 is an abundant protein in excitatory synapses and plays an important role in neuronal development as well as synaptic plasticity. Here, we review neuronal IQSEC2 signaling with emphasis on those aspects likely to be involved in autism. IQSEC2 is normally bound to N-methyl-D-aspartate (NMDA)-type glutamate receptors via post synaptic density protein 95 (PSD-95). Activation of NMDA receptors results in calcium ion influx and binding to calmodulin present on the IQSEC2 IQ domain. Calcium/calmodulin induces a conformational change in IQSEC2 leading to activation of the SEC7 catalytic domain. GTP is exchanged for GDP on ADP ribosylation factor 6 (ARF6). Activated ARF6 promotes downregulation of surface α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type glutamate receptors through a c-jun N terminal kinase (JNK)-mediated pathway. NMDA receptors, AMPA receptors, and PSD-95 are all known to be adversely affected in autism. An IQSEC2 transgenic mouse carrying a constitutively active mutation (A350V) shows autistic features and reduced levels of surface AMPA receptor subunit GluA2. Sec7 activity and AMPA receptor recycling are presented as two targets, which may respond to drug treatment in IQSEC2-associated ID and autism.

scholarly journals A missense mutation in the catalytic domain of O ‐GlcNAc transferase links perturbations in protein O ‐GlcNAcylation to X‐linked intellectual disability

FEBS Letters ◽  
2019 ◽  
Vol 594 (4) ◽  
pp. 717-727 ◽  
Author(s):  
Veronica M. Pravata ◽  
Mehmet Gundogdu ◽  
Sergio G. Bartual ◽  
Andrew T. Ferenbach ◽  
Marios Stavridis ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Missense Mutation ◽  
Catalytic Domain ◽  
Glcnac Transferase

scholarly journals Structural basis for two metal-ion catalysis of DNA cleavage by Cas12i2

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Xue Huang ◽  
Wei Sun ◽  
Zhi Cheng ◽  
Minxuan Chen ◽  
Xueyan Li ◽  
...  
Keyword(s):  
Dna Cleavage ◽  
Metal Ion ◽  
Catalytic Domain ◽  
Dna Recognition ◽  
Structural Basis ◽  
Seed Region ◽  
Dna Complexes ◽  
Metal Ion Catalysis ◽  
Type V ◽  
Cas Proteins

Abstract To understand how the RuvC catalytic domain of Class 2 Cas proteins cleaves DNA, it will be necessary to elucidate the structures of RuvC-containing Cas complexes in their catalytically competent states. Cas12i2 is a Class 2 type V-I CRISPR-Cas endonuclease that cleaves target dsDNA by an unknown mechanism. Here, we report structures of Cas12i2–crRNA–DNA complexes and a Cas12i2–crRNA complex. We reveal the mechanism of DNA recognition and cleavage by Cas12i2, and activation of the RuvC catalytic pocket induced by a conformational change of the Helical-II domain. The seed region (nucleotides 1–8) is dispensable for RuvC activation, but the duplex of the central spacer (nucleotides 9–15) is required. We captured the catalytic state of Cas12i2, with both metal ions and the ssDNA substrate bound in the RuvC catalytic pocket. Together, our studies provide significant insights into the DNA cleavage mechanism by RuvC-containing Cas proteins.

scholarly journals Antibody against Microbial Neuraminidases Recognizes Human Sialidase 3 (NEU3): the Neuraminidase/Sialidase Superfamily Revisited

mBio ◽  
2017 ◽  
Vol 8 (3) ◽  
Author(s):  
Chiguang Feng ◽  
Jihong Li ◽  
Greg Snyder ◽  
Wei Huang ◽  
Simeon E. Goldblum ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Clostridium Perfringens ◽  
Neural Development ◽  
Catalytic Domain ◽  
Critical Role ◽  
Microbial Pathogens ◽  
Human Neutrophils ◽  
Sialidase Activity

ABSTRACT Neuraminidases (NAs) are critical virulence factors for several microbial pathogens. With a highly conserved catalytic domain, a microbial NA “superfamily” has been proposed. We previously reported that murine polymorphonuclear leukocyte (PMN) sialidase activity was important in leukocyte trafficking to inflamed sites and that antibodies to Clostridium perfringens NA recognized a cell surface molecule(s), presumed to be a sialidase of eukaryotic origin on interleukin-8-stimulated human and murine PMNs. These antibodies also inhibited cell sialidase activity both in vitro and, in the latter instance, in vivo . We therefore hypothesized that mammalian sialidases share structural homology and epitopes with microbial NAs. We now report that antibodies to one of the isoforms of C. perfringens NA, as well as anti-influenza virus NA serum, recognize human NEU3 but not NEU1 and that antibodies to C. perfringens NA inhibit NEU3 enzymatic activity. We conclude that the previously described microbial NA superfamily extends to human sialidases. Strategies designed to therapeutically inhibit microbial NA may need to consider potential compromising effects on human sialidases, particularly those expressed in cells of the immune system. IMPORTANCE We previously reported that sialidase activity of human neutrophils plays a critical role in the host inflammatory response. Since the catalytic domains of microbial neuraminidases are highly conserved, we hypothesized that antibodies against Clostridium perfringens neuraminidase might inhibit mammalian sialidase activity. Before the recognition of four mammalian sialidase ( Neu ) isoforms, we demonstrated that anti- C. perfringens neuraminidase antibodies inhibited human and murine sialidase activity in vivo and in vitro . We now show that the antibodies to microbial neuraminidase ( C. perfringens and influenza virus) recognize human NEU3, which is important for neural development and cell signaling. Since many microbes that infect mucosal surfaces express neuraminidase, it is possible that the use of sialidase inhibitors (e.g., zanamivir), might also compromise human sialidase activity critical to the human immune response. Alternatively, sialidase inhibitors may prove useful in the treatment of hyperinflammatory conditions.

scholarly journals A Plasmodium falciparum Transcriptional Cyclin-Dependent Kinase-Related Kinase with a Crucial Role in Parasite Proliferation Associates with Histone Deacetylase Activity

2010 ◽  
Vol 9 (6) ◽  
pp. 952-959 ◽  
Author(s):  
Jean Halbert ◽  
Lawrence Ayong ◽  
Leila Equinet ◽  
Karine Le Roch ◽  
Mary Hardy ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plasmodium Falciparum ◽  
Protein Kinases ◽  
Histone Deacetylase ◽  
Crucial Role ◽  
Catalytic Domain ◽  
Regulation Of Gene Expression ◽  
Chromatin Modification ◽  
Site Directed Mutagenesis ◽  
Content Type

ABSTRACT Cyclin-dependent protein kinases (CDKs) are key regulators of the eukaryotic cell cycle and of the eukaryotic transcription machinery. Here we report the characterization of Pfcrk-3 (Plasmodium falciparum CDK-related kinase 3; PlasmoDB identifier PFD0740w), an unusually large CDK-related protein whose kinase domain displays maximal homology to those CDKs which, in other eukaryotes, are involved in the control of transcription. The closest enzyme in Saccharomyces cerevisiae is BUR1 (bypass upstream activating sequence requirement 1), known to control gene expression through interaction with chromatin modification enzymes. Consistent with this, immunofluorescence data show that Pfcrk-3 colocalizes with histones. We show that recombinant Pfcrk-3 associates with histone H1 kinase activity in parasite extracts and that this association is detectable even if the catalytic domain of Pfcrk-3 is rendered inactive by site-directed mutagenesis, indicating that Pfcrk-3 is part of a complex that includes other protein kinases. Immunoprecipitates obtained from extracts of transgenic parasites expressing hemagglutinin (HA)-tagged Pfcrk-3 by using an anti-HA antibody displayed both protein kinase and histone deacetylase activities. Reverse genetics data show that the pfcrk-3 locus can be targeted only if the genetic modification does not cause a loss of function. Taken together, our data strongly suggest that Pfcrk-3 fulfils a crucial role in the intraerythrocytic development of P. falciparum, presumably through chromatin modification-dependent regulation of gene expression.

scholarly journals Disruption of an EHMT1-Associated Chromatin-Modification Module Causes Intellectual Disability

2012 ◽  
Vol 91 (1) ◽  
pp. 73-82 ◽  
Author(s):  
Tjitske Kleefstra ◽  
Jamie M. Kramer ◽  
Kornelia Neveling ◽  
Marjolein H. Willemsen ◽  
Tom S. Koemans ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Chromatin Modification

STEM-07. PRC2 MAINTAINS A CANCER STEM CELL PHENOTYPE IN GLIOBLASTOMA MULTIFORME VIA CHROMATIN MODIFICATION OF H3K27me3

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi22-vi22
Author(s):  
Jack Korleski ◽  
Sweta Shudir ◽  
Christopher Caputo ◽  
Bachchu Lal ◽  
Yuan Rui ◽  
...  
Keyword(s):  
Stem Cell ◽  
Catalytic Domain ◽  
Chromatin Modification ◽  
Therapeutic Benefit ◽  
Cell Phenotype ◽  
Dependent Manner ◽  
Orthotopic Model ◽  
Molecular Approaches ◽  
Therapeutic Development ◽  
Stem Cell Phenotype

Abstract Multi-potent stem-like cells (i.e. cancer stem cells, CSCs) are critical determinants of tumor propagation, therapeutic resistance, and recurrence in glioblastoma (GBM). Modifications in chromatin architecture play a fundamental role in the tumor cell phenotype of GBM. The polycomb repressor complex 2 (PRC2) is a key histone modifier that supports multi-potency and oncogenesis via H3K27 trimethylation (H3K27me3). Understanding how these epigenetic modifications cooperatively drive cancer cell stemness should unveil new targets for therapeutic development in GBM. Using a combination of next-generation sequencing, bioinformatics, and molecular approaches we identified EZH2, the catalytic domain of the PRC2 complex, as a critical mediator of reprograming events in GBM cells. We found that EZH2 is highly induced in response to transgenic Oct4/Sox2 with global increases in H3K27me3. Pharmacological inhibition of EZH2 diminishes self-renewal capacity of GBM neurospheres concurrent with a reduction in gene expression levels of markers and drivers of stemness. Furthermore, we identified and validated a set of 6 putative tumor suppressor genes repressed by Oct4 and Sox2 in a PRC2-dependent manner. We identified miR-217 as an EZH2 regulator in GBM cells and miR-217 reconstitution using advanced nanoparticle formulations re-activates the PRC2-repressed tumor suppressors, inhibited tumor growth and enhanced the effects of ionizing radiation in an orthotopic model of GBM. Taken together, these data show that PRC2-mediated chromatin changes in H3K27me3 help regulate the stem-cell phenotype induced by Oct4 and Sox2 in GBM cells and predict that targeting EZH2 could have therapeutic benefit in GBM.

The reaction mechanism of FokI excludes the possibility of targeting zinc finger nucleases to unique DNA sites

2011 ◽  
Vol 39 (2) ◽  
pp. 584-588 ◽  
Author(s):  
Stephen E. Halford ◽  
Lucy E. Catto ◽  
Christian Pernstich ◽  
David A. Rusling ◽  
Kelly L. Sanders
Keyword(s):  
Zinc Finger ◽  
Dna Sequences ◽  
Catalytic Domain ◽  
Dna Recognition ◽  
Zinc Finger Nucleases ◽  
Target Sequence ◽  
Base Pairs ◽  
Catalytic Domains ◽  
Zinc Finger Domains ◽  
Better Than

The FokI endonuclease is a monomeric protein with discrete DNA-recognition and catalytic domains. The latter has only one active site so, to cut both strands, the catalytic domains from two monomers associate to form a dimer. The dimer involving a monomer at the recognition site and another from free solution is less stable than that from two proteins tethered to the same DNA. FokI thus cleaves DNA with two sites better than one-site DNA. The two sites can be immediately adjacent, but they can alternatively be many hundreds of base pairs apart, in either inverted or repeated orientations. The catalytic domain of FokI is often a component of zinc finger nucleases. Typically, the zinc finger domains of two such nucleases are designed to recognize two neighbouring DNA sequences, with the objective of cutting the DNA exclusively between the target sequences. However, this strategy fails to take account of the fact that the catalytic domains of FokI can dimerize across distant sites or even at a solitary site. Additional copies of either target sequence elsewhere in the chromosome must elicit off-target cleavages.

scholarly journals Histone Demethylases ELF6 and JMJ13 Antagonistically Regulate Self-Fertility in Arabidopsis

2021 ◽  
Vol 12 ◽  
Author(s):  
Charlie Keyzor ◽  
Benoit Mermaz ◽  
Efstathios Trigazis ◽  
SoYoung Jo ◽  
Jie Song
Keyword(s):  
Jasmonic Acid ◽  
Flower Development ◽  
Regulatory Network ◽  
Chromatin Modification ◽  
Epigenetic Silencing ◽  
The Other ◽  
Histone Demethylases ◽  
Dynamic Regulation ◽  
Self Pollination ◽  
And Control

The chromatin modification H3K27me3 is involved in almost every developmental stage in Arabidopsis. Much remains unknown about the dynamic regulation of this histone modification in flower development and control of self-fertility. Here we demonstrate that the H3K27me3-specific demethylases ELF6 and JMJ13 antagonistically regulate carpel and stamen growth and thus modulate self-fertility. Transcriptome and epigenome data are used to identify potential targets of ELF6 and JMJ13 responsible for these physiological functions. We find that ELF6 relieves expansin genes of epigenetic silencing to promote cell elongation in the carpel, enhancing carpel growth and therefore encouraging out-crossing. On the other hand, JMJ13 activates genes of the jasmonic acid regulatory network alongside the auxin responsive SAUR26, to inhibit carpel growth, enhance stamen growth, and overall promote self-pollination. Our evidence provides novel mechanisms of self-fertility regulation in A. thaliana demonstrating how chromatin modifying enzymes govern the equilibrium between flower self-pollination and out-crossing.

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