scholarly journals Cryo-EM structure of SETD2/Set2 methyltransferase bound to a nucleosome containing oncohistone mutations

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Yingying Liu ◽  
Yanjun Zhang ◽  
Han Xue ◽  
Mi Cao ◽  
Guohui Bai ◽  
...  
Keyword(s):  
Histone Modification ◽  
Histone H3 ◽  
Structural Features ◽  
Inhibitory Effect ◽  
Structural Basis ◽  
Activity Regulation ◽  
Wild Type ◽  
Oncogenic Mutation ◽  
Evolutionarily Conserved ◽  
Stable Association

AbstractSubstitution of lysine 36 with methionine in histone H3.3 (H3.3K36M) is an oncogenic mutation that inhibits SETD2-mediated histone H3K36 tri-methylation in tumors. To investigate how the oncohistone mutation affects the function of SETD2 at the nucleosome level, we determined the cryo-EM structure of human SETD2 associated with an H3.3K36M nucleosome and cofactor S-adenosylmethionine (SAM), and revealed that SETD2 is attached to the N-terminal region of histone H3 and the nucleosome DNA at superhelix location 1, accompanied with the partial unwrapping of nucleosome DNA to expose the SETD2-binding site. These structural features were also observed in the previous cryo-EM structure of the fungal Set2–nucleosome complex. By contrast with the stable association of SETD2 with the H3.3K36M nucleosome, the EM densities of SETD2 could not be observed on the wild-type nucleosome surface, suggesting that the association of SETD2 with wild-type nucleosome might be transient. The linker histone H1, which stabilizes the wrapping of nucleosome DNA at the entry/exit sites, exhibits an inhibitory effect on the activities of SETD2 and displays inversely correlated genome distributions with that of the H3K36me3 marks. Cryo-EM analysis of yeast H3K36 methyltransferase Set2 complexed with nucleosomes further revealed evolutionarily conserved structural features for nucleosome recognition in eukaryotes, and provides insights into the mechanism of activity regulation. These findings have advanced our understanding of the structural basis for the tumorigenesis mechanism of the H3.3K36M mutation and highlight the effect of nucleosome conformation on the regulation of histone modification.

scholarly journals Structural basis of the regulation of the normal and oncogenic methylation of nucleosomal histone H3 Lys36 by NSD2

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ko Sato ◽  
Amarjeet Kumar ◽  
Keisuke Hamada ◽  
Chikako Okada ◽  
Asako Oguni ◽  
...  
Keyword(s):  
Histone H3 ◽  
Structural Basis ◽  
Wild Type ◽  
Cryo Electron Microscopy ◽  
Nucleosomal Dna ◽  
Oncogenic Mutations ◽  
Binding Cleft ◽  
Dynamics Simulations ◽  
Nucleosome Binding ◽  
Nucleosomal Histone

AbstractDimethylated histone H3 Lys36 (H3K36me2) regulates gene expression, and aberrant H3K36me2 upregulation, resulting from either the overexpression or point mutation of the dimethyltransferase NSD2, is found in various cancers. Here we report the cryo-electron microscopy structure of NSD2 bound to the nucleosome. Nucleosomal DNA is partially unwrapped, facilitating NSD2 access to H3K36. NSD2 interacts with DNA and H2A along with H3. The NSD2 autoinhibitory loop changes its conformation upon nucleosome binding to accommodate H3 in its substrate-binding cleft. Kinetic analysis revealed that two oncogenic mutations, E1099K and T1150A, increase NSD2 catalytic turnover. Molecular dynamics simulations suggested that in both mutants, the autoinhibitory loop adopts an open state that can accommodate H3 more often than the wild-type. We propose that E1099K and T1150A destabilize the interactions that keep the autoinhibitory loop closed, thereby enhancing catalytic turnover. Our analyses guide the development of specific inhibitors of NSD2.

scholarly journals Structure and Mechanism of Lysine-specific Demethylase Enzymes

2007 ◽  
Vol 282 (49) ◽  
pp. 35425-35429 ◽  
Author(s):  
Ruchi Anand ◽  
Ronen Marmorstein
Keyword(s):  
Substrate Specificity ◽  
Histone Modification ◽  
Crystal Structures ◽  
Histone H3 ◽  
Structural Basis ◽  
Lysine Specific Demethylase ◽  
Histone Modification Mark

The discovery of histone-demethylating enzymes has revealed yet another reversible histone modification mark. In this review, we describe the structural and chemical insights that we have now derived underlying the activity of these enzymes. The recent co-crystal structures of LSD1 bound to a proparylamine-derivatized histone H3 peptide and JHDM structures bound to two different methylated histone H3 peptides illustrate the steric requirements and structural basis for substrate specificity.

scholarly journals Histone H3 Lysine 4 Methylation Marks Postreplicative Human Cytomegalovirus Chromatin

2012 ◽  
Vol 86 (18) ◽  
pp. 9817-9827 ◽  
Author(s):  
Alexandra Nitzsche ◽  
Charlotte Steinhäußer ◽  
Katrin Mücke ◽  
Christina Paulus ◽  
Michael Nevels
Keyword(s):  
Dna Replication ◽  
Dna Synthesis ◽  
Histone Modification ◽  
Dna Polymerase ◽  
Human Cytomegalovirus ◽  
Viral Genome ◽  
Histone H3 ◽  
Viral Dna ◽  
The Impact ◽  
Preferential Incorporation

In the nuclei of permissive cells, human cytomegalovirus genomes form nucleosomal structures initially resembling heterochromatin but gradually switching to a euchromatin-like state. This switch is characterized by a decrease in histone H3 K9 methylation and a marked increase in H3 tail acetylation and H3 K4 methylation across the viral genome. We used ganciclovir and a mutant virus encoding a reversibly destabilized DNA polymerase to examine the impact of DNA replication on histone modification dynamics at the viral chromatin. The changes in H3 tail acetylation and H3 K9 methylation proceeded in a DNA replication-independent fashion. In contrast, the increase in H3 K4 methylation proved to depend widely on viral DNA synthesis. Consistently, labeling of nascent DNA using “click chemistry” revealed preferential incorporation of methylated H3 K4 into viral (but not cellular) chromatin during or following DNA replication. This study demonstrates largely selective epigenetic tagging of postreplicative human cytomegalovirus chromatin.

scholarly journals The GNAQ T96S Mutation Affects Cell Signaling and Enhances the Oncogenic Properties of Hepatocellular Carcinoma

2021 ◽  
Vol 22 (6) ◽  
pp. 3284
Author(s):  
Eugene Choi ◽  
Sung Jean Park ◽  
Gunhee Lee ◽  
Seung Kew Yoon ◽  
Minho Lee ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Expression Vector ◽  
Signal Transduction Pathway ◽  
Inhibitory Effect ◽  
The Cancer Genome Atlas ◽  
Treatment Modalities ◽  
Protein Signaling ◽  
Wild Type ◽  
Anchorage Independent Growth ◽  
Mapk Pathways

Hepatocellular carcinoma (HCC), the most common malignant tumor in the liver, grows and metastasizes rapidly. Despite advances in treatment modalities, the five-year survival rate of HCC remains less than 30%. We sought genetic mutations that may affect the oncogenic properties of HCC, using The Cancer Genome Atlas (TCGA) data analysis. We found that the GNAQ T96S mutation (threonine 96 to serine alteration of the Gαq protein) was present in 12 out of 373 HCC patients (3.2%). To examine the effect of the GNAQ T96S mutation on HCC, we transfected the SK-Hep-1 cell line with the wild-type or the mutant GNAQ T96S expression vector. Transfection with the wild-type GNAQ expression vector enhanced anchorage-independent growth, migration, and the MAPK pathways in the SK-Hep-1 cells compared to control vector transfection. Moreover, cell proliferation, anchorage-independent growth, migration, and the MAPK pathways were further enhanced in the SK-Hep-1 cells transfected with the GNAQ T96S expression vector compared to the wild-type GNAQ-transfected cells. In silico structural analysis shows that the substitution of the GNAQ amino acid threonine 96 with a serine may destabilize the interaction between the regulator of G protein signaling (RGS) protein and GNAQ. This may reduce the inhibitory effect of RGS on GNAQ signaling, enhancing the GNAQ signaling pathway. Single nucleotide polymorphism (SNP) genotyping analysis for Korean HCC patients shows that the GNAQ T96S mutation was found in only one of the 456 patients (0.22%). Our data suggest that the GNAQ T96S hotspot mutation may play an oncogenic role in HCC by potentiating the GNAQ signal transduction pathway.

scholarly journals Structural basis of enzyme activity regulation by the propeptide of l-lysine α-oxidase precursor from Trichoderma viride

2021 ◽  
Vol 5 ◽  
pp. 100044
Author(s):  
Masaki Kitagawa ◽  
Nanako Ito ◽  
Yuya Matsumoto ◽  
Masaya Saito ◽  
Takashi Tamura ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Trichoderma Viride ◽  
Structural Basis ◽  
Activity Regulation

scholarly journals Haploid induction by a maize cenh3 null mutant

2021 ◽  
Vol 7 (4) ◽  
pp. eabe2299 ◽  
Author(s):  
Na Wang ◽  
Jonathan I. Gent ◽  
R. Kelly Dawe
Keyword(s):  
Histone H3 ◽  
Null Mutation ◽  
Null Mutant ◽  
Wild Type ◽  
Haploid Induction ◽  
Cell Divisions ◽  
Gamete Formation ◽  
Simplified Method ◽  
Single Cross ◽  
Subsequent Loss

The production of haploids is an important first step in creating many new plant varieties. One approach used in Arabidopsis involves crossing plants expressing different forms of centromeric histone H3 (CENP-A/CENH3) and subsequent loss of genome with weaker centromeres. However, the method has been ineffective in crop plants. Here, we describe a greatly simplified method based on crossing maize lines that are heterozygous for a cenh3 null mutation. Crossing +/cenh3 to wild-type plants in both directions yielded haploid progeny. Genome elimination was determined by the cenh3 genotype of the gametophyte, suggesting that centromere failure is caused by CENH3 dilution during the postmeiotic cell divisions that precede gamete formation. The cenh3 haploid inducer works as a vigorous hybrid and can be transferred to other lines in a single cross, making it versatile for a variety of applications.

Discovery of natural product ovalicin sensitive type 1 methionine aminopeptidases: molecular and structural basis

2019 ◽  
Vol 476 (6) ◽  
pp. 991-1003 ◽  
Author(s):  
Vijaykumar Pillalamarri ◽  
Tarun Arya ◽  
Neshatul Haque ◽  
Sandeep Chowdary Bala ◽  
Anil Kumar Marapaka ◽  
...  
Keyword(s):  
Natural Product ◽  
Active Site ◽  
Covalent Modification ◽  
Structural Basis ◽  
Wild Type ◽  
Methionine Aminopeptidases ◽  
Synthetic Derivative ◽  
Dynamics Simulations

Abstract Natural product ovalicin and its synthetic derivative TNP-470 have been extensively studied for their antiangiogenic property, and the later reached phase 3 clinical trials. They covalently modify the conserved histidine in Type 2 methionine aminopeptidases (MetAPs) at nanomolar concentrations. Even though a similar mechanism is possible in Type 1 human MetAP, it is inhibited only at millimolar concentration. In this study, we have discovered two Type 1 wild-type MetAPs (Streptococcus pneumoniae and Enterococcus faecalis) that are inhibited at low micromolar to nanomolar concentrations and established the molecular mechanism. F309 in the active site of Type 1 human MetAP (HsMetAP1b) seems to be the key to the resistance, while newly identified ovalicin sensitive Type 1 MetAPs have a methionine or isoleucine at this position. Type 2 human MetAP (HsMetAP2) also has isoleucine (I338) in the analogous position. Ovalicin inhibited F309M and F309I mutants of human MetAP1b at low micromolar concentration. Molecular dynamics simulations suggest that ovalicin is not stably placed in the active site of wild-type MetAP1b before the covalent modification. In the case of F309M mutant and human Type 2 MetAP, molecule spends more time in the active site providing time for covalent modification.

The phosphoenolpyruvate: sugar phosphotransferase system of Streptococcus salivarius. Identification of a IIIman protein

1987 ◽  
Vol 33 (2) ◽  
pp. 118-122 ◽  
Author(s):  
Christian Vadeboncoeur ◽  
Lucie Gauthier
Keyword(s):  
Type Strain ◽  
Wild Type Strain ◽  
Deae Cellulose ◽  
Reaction Medium ◽  
Inhibitory Effect ◽  
Spontaneous Mutant ◽  
Streptococcus Salivarius ◽  
Wild Type ◽  
Phosphotransferase System ◽  
Growth Inhibitory

A double-spontaneous mutant resistant to the growth inhibitory effect of α-methylglucoside and 2-deoxyglucose was isolated from Streptococcus salivarius. This mutant strain, called αS3L11, did not grow on mannose and grew poorly on 5 mM fructose and 5 mM glucose. Isolated membranes of strain αS3L11 were unable to catalyse the phosphoenolpyruvate-dependent phosphorylation of mannose in the presence of purified enzyme I and HPr. Addition of dialysed membrane-free cellular extract of the wild-type strain to the reaction medium restored the activity. The factor that restored the phosphoenolpyruvate–mannose phosphotransferase activity to membranes of strain αS3L11 was called IIIman. This factor was partially purified from the wild-type strain by DEAE-cellulose chromatography, DEAE-TSK chromatography, and molecular seiving on a column of Ultrogel AcA 34. This partially purified preparation also enhanced the phosphoenolpyruvate-dependent phosphorylation of glucose, fructose, and 2-deoxyglucose in strain αS3L11.

scholarly journals Structural Basis of LSD1-CoREST Selectivity in Histone H3 Recognition

2007 ◽  
Vol 282 (28) ◽  
pp. 20070-20074 ◽  
Author(s):  
Federico Forneris ◽  
Claudia Binda ◽  
Antonio Adamo ◽  
Elena Battaglioli ◽  
Andrea Mattevi
Keyword(s):  
Histone H3 ◽  
Structural Basis
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