Search Results

You searched for all publications:

with publication states 'Published (Approved)'

Search Again...

These results only include publications that have been reviewed and processed by Diamond Light Source. To also view papers that have not yet been processed click here.

You can use the folder icon under Actions to collate papers as required. You can then click on View Folder in the left-hand navigation to review and/or download your folder.

Exact matches
Related results

11 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2 [Next/Last]

Instruments / Technical Area	Publication Details	Published
I04-1-Macromolecular Crystallography (fixed wavelength)	Structure and methyl-lysine binding selectivity of the HUSH complex subunit MPP8 Nikos Nikolopoulos , Shun-Ichiro Oda , Daniil M. Prigozhin , Yorgo Modis Journal Of Molecular Biology 7 DOI: 10.1016/j.jmb.2024.168890 Diamond Proposal Number(s): [21426] Open Access Show Abstract ▼ Abstract: The Human Silencing Hub (HUSH) guards the genome from the pathogenic effects of retroelement expression. Composed of MPP8, TASOR, and Periphilin-1, HUSH recognizes actively transcribed retrotransposed sequences by the presence of long (>1.5-kb) nascent transcripts without introns. HUSH recruits effectors that alter chromatin structure, degrade transcripts, and deposit transcriptionally repressive epigenetic marks. Here, we report the crystal structure of the C-terminal domain (CTD) of MPP8 necessary for HUSH activity. The MPP8 CTD consists of five ankyrin repeats followed by a domain with structural homology to the PINIT domains of Siz/PIAS-family SUMO E3 ligases. AlphaFold3 modeling of the MPP8-TASOR complex predicts that a SPOC domain and a domain with a novel fold in TASOR form extended interaction interfaces with the MPP8 CTD. Point mutations at these interfaces resulted in loss of HUSH-dependent transcriptional repression in a cell-based reporter assay, validating the AlphaFold3 model. The MPP8 chromodomain, known to bind the repressive mark H3K9me3, bound with similar or higher affinity to sequences in the H3K9 methyltransferase subunits SETDB1, ATF7IP, G9a, and GLP. Hence, MPP8 promotes heterochromatinization by recruiting H3K9 methyltransferases. Our work identifies novel structural elements in MPP8 required for HUSH complex assembly and silencing, thereby fulfilling vital functions in controlling retrotransposons.	Dec 2024
I03-Macromolecular Crystallography I04-Macromolecular Crystallography	Crystal structure and biochemical activity of the macrodomain from rubella virus p150 Guido A. Stoll , Nikos Nikolopoulos , Haoming Zhai , Liao Zhang , Christopher H. Douse , Yorgo Modis Journal Of Virology DOI: 10.1128/jvi.01777-23 Diamond Proposal Number(s): [21426] Show Abstract ▼ Abstract: Rubella virus encodes a nonstructural polyprotein with RNA polymerase, methyltransferase, and papain-like cysteine protease activities, along with a putative macrodomain of unknown function. Macrodomains bind ADP–ribose adducts, a post-translational modification that plays a key role in host–virus conflicts. Some macrodomains can also remove the mono-ADP–ribose adduct or degrade poly-ADP–ribose chains. Here, we report high-resolution crystal structures of the macrodomain from rubella virus nonstructural protein p150, with and without ADP–ribose binding. The overall fold is most similar to macroD-type macrodomains from various nonviral species. The specific composition and structure of the residues that coordinate ADP–ribose in the rubella virus macrodomain are most similar to those of macrodomains from alphaviruses. Isothermal calorimetry shows that the rubella virus macrodomain binds ADP–ribose in solution. Enzyme assays show that the rubella virus macrodomain can hydrolyze both mono- and poly-ADP–ribose adducts. Site-directed mutagenesis identifies Asn39 and Cys49 required for mono-ADP-ribosylhydrolase (de-MARylation) activity.	Jan 2024
I04-Macromolecular Crystallography	Structure and functional mapping of the KRAB‐KAP1 repressor complex Guido A. Stoll , Ninoslav Pandiloski , Christopher H. Douse , Yorgo Modis The Embo Journal 55 DOI: 10.15252/embj.2022111179 Diamond Proposal Number(s): [21426] Open Access Show Abstract ▼ Abstract: Transposable elements are a genetic reservoir from which new genes and regulatory elements can emerge. However, expression of transposable elements can be pathogenic and is therefore tightly controlled. KRAB domain-containing zinc finger proteins (KRAB-ZFPs) recruit the co-repressor KRAB-associated protein 1 (KAP1/TRIM28) to regulate many transposable elements, but how KRAB-ZFPs and KAP1 interact remains unclear. Here, we report the crystal structure of the KAP1 tripartite motif (TRIM) in complex with the KRAB domain from a human KRAB-ZFP, ZNF93. Structure-guided mutations in the KAP1-KRAB binding interface abolished repressive activity in an epigenetic transcriptional silencing assay. Deposition of H3K9me3 over thousands of loci is lost genome-wide in cells expressing a KAP1 variant with mutations that abolish KRAB binding. Our work identifies and functionally validates the KRAB-KAP1 molecular interface, which is critical for a central transcriptional control axis in vertebrates. In addition, the structure-based prediction of KAP1 recruitment efficiency will enable optimization of KRABs used in CRISPRi.	Nov 2022
Krios I-Titan Krios I at Diamond	A bioactive phlebovirus-like envelope protein in a hookworm endogenous virus Monique Merchant , Carlos P. Mata , Yangci Liu , Haoming Zhai , Anna V. Protasio , Yorgo Modis Science Advances 8 DOI: 10.1126/sciadv.abj6894 Diamond Proposal Number(s): [17434, 20121] Open Access Show Abstract ▼ Abstract: Endogenous viral elements (EVEs), accounting for 15% of our genome, serve as a genetic reservoir from which new genes can emerge. Nematode EVEs are particularly diverse and informative of virus evolution. We identify Atlas virus—an intact retrovirus-like EVE in the human hookworm Ancylostoma ceylanicum, with an envelope protein genetically related to GN-GC glycoproteins from the family Phenuiviridae. A cryo-EM structure of Atlas GC reveals a class II viral membrane fusion protein fold not previously seen in retroviruses. Atlas GC has the structural hallmarks of an active fusogen. Atlas GC trimers insert into membranes with endosomal lipid compositions and low pH. When expressed on the plasma membrane, Atlas GC has cell-cell fusion activity. With its preserved biological activities, Atlas GC has the potential to acquire a cellular function. Our work reveals structural plasticity in reverse-transcribing RNA viruses.	May 2022
Krios I-Titan Krios I at Diamond	MDA5 disease variant M854K prevents ATP-dependent structural discrimination of viral and cellular RNA Qin Yu , Alba Herrero Del Valle , Rahul Singh , Yorgo Modis Nature Communications 12 DOI: 10.1038/s41467-021-27062-5 Diamond Proposal Number(s): [17434] Open Access Show Abstract ▼ Abstract: Our innate immune responses to viral RNA are vital defenses. Long cytosolic double-stranded RNA (dsRNA) is recognized by MDA5. The ATPase activity of MDA5 contributes to its dsRNA binding selectivity. Mutations that reduce RNA selectivity can cause autoinflammatory disease. Here, we show how the disease-associated MDA5 variant M854K perturbs MDA5-dsRNA recognition. M854K MDA5 constitutively activates interferon signaling in the absence of exogenous RNA. M854K MDA5 lacks ATPase activity and binds more stably to synthetic Alu:Alu dsRNA. CryoEM structures of MDA5-dsRNA filaments at different stages of ATP hydrolysis show that the K854 sidechain forms polar bonds that constrain the conformation of MDA5 subdomains, disrupting key steps in the ATPase cycle- RNA footprint expansion and helical twist modulation. The M854K mutation inhibits ATP-dependent RNA proofreading via an allosteric mechanism, allowing MDA5 to form signaling complexes on endogenous RNAs. This work provides insights on how MDA5 recognizes dsRNA in health and disease.	Nov 2021
I02-Macromolecular Crystallography I03-Macromolecular Crystallography	TASOR is a pseudo-PARP that directs HUSH complex assembly and epigenetic transposon control Christopher Douse , Iva A. Tchasovnikarova , Richard T. Timms , Anna V. Protasio , Marta Seczynska , Daniil M. Prigozhin , Anna Albecka , James Wagstaff , James C. Williamson , Stefan M. V. Freund , Paul J. Lehner , Yorgo Modis Nature Communications 11 DOI: 10.1038/s41467-020-18761-6 Diamond Proposal Number(s): [11235] Open Access Show Abstract ▼ Abstract: The HUSH complex represses retroviruses, transposons and genes to maintain the integrity of vertebrate genomes. HUSH regulates deposition of the epigenetic mark H3K9me3, but how its three core subunits — TASOR, MPP8 and Periphilin — contribute to assembly and targeting of the complex remains unknown. Here, we define the biochemical basis of HUSH assembly and find that its modular architecture resembles the yeast RNA-induced transcriptional silencing complex. TASOR, the central HUSH subunit, associates with RNA processing components. TASOR is required for H3K9me3 deposition over LINE-1 repeats and repetitive exons in transcribed genes. In the context of previous studies, this suggests that an RNA intermediate is important for HUSH activity. We dissect the TASOR and MPP8 domains necessary for transgene repression. Structure-function analyses reveal TASOR bears a catalytically-inactive PARP domain necessary for targeted H3K9me3 deposition. We conclude that TASOR is a multifunctional pseudo-PARP that directs HUSH assembly and epigenetic regulation of repetitive genomic targets.	Oct 2020
I04-1-Macromolecular Crystallography (fixed wavelength)	Periphilin self-association underpins epigenetic silencing by the HUSH complex Daniil M. Prigozhin , Christopher H. Douse , Laura E Farleigh , Anna Albecka , Iva a. Tchasovnikarova , Richard T Timms , Shun-Ichiro Oda , Frank Adolf , Stefan M. V. Freund , Sarah Maslen , Paul J Lehner , Yorgo Modis Nucleic Acids Research 48, 10313 - 10328 DOI: 10.1093/nar/gkaa785 Diamond Proposal Number(s): [15916] Open Access Show Abstract ▼ Abstract: Transcription of integrated DNA from viruses or transposable elements is tightly regulated to prevent pathogenesis. The Human Silencing Hub (HUSH), composed of Periphilin, TASOR and MPP8, silences transcriptionally active viral and endogenous transgenes. HUSH recruits effectors that alter the epigenetic landscape and chromatin structure, but how HUSH recognizes target loci and represses their expression remains unclear. We identify the physicochemical properties of Periphilin necessary for HUSH assembly and silencing. A disordered N-terminal domain (NTD) and structured C-terminal domain are essential for silencing. A crystal structure of the Periphilin-TASOR minimal core complex shows Periphilin forms an α-helical homodimer, bound by a single TASOR molecule. The NTD forms insoluble aggregates through an arginine/tyrosine-rich sequence reminiscent of low-complexity regions from self-associating RNA-binding proteins. Residues required for TASOR binding and aggregation were required for HUSH-dependent silencing and genome-wide deposition of repressive mark H3K9me3. The NTD was functionally complemented by low-complexity regions from certain RNA-binding proteins and proteins that form condensates or fibrils. Our work suggests the associative properties of Periphilin promote HUSH aggregation at target loci.	Oct 2020
I03-Macromolecular Crystallography I04-Macromolecular Crystallography	FAMIN is a multifunctional purine enzyme enabling the purine nucleotide cycle M. Zaeem Cader , Rodrigo Pereira De Almeida Rodrigues , James A. West , Gavin W. Sewell , Muhammad N. Md-Ibrahim , Stephanie Reikine , Giuseppe Sirago , Lukas W. Unger , Ana Belén Iglesias-Romero , Katharina Ramshorn , Lea-Maxie Haag , Svetlana Saveljeva , Jana-Fabienne Ebel , Philip Rosenstiel , Nicole C. Kaneider , James C. Lee , Trevor D. Lawley , Allan Bradley , Gordon Dougan , Yorgo Modis , Julian L. Griffin , Arthur Kaser Cell 180, 278 - 295.e23 DOI: 10.1016/j.cell.2019.12.017 Diamond Proposal Number(s): [15916] Open Access Show Abstract ▼ Abstract: Mutations in FAMIN cause arthritis and inflammatory bowel disease in early childhood, and a common genetic variant increases the risk for Crohn's disease and leprosy. We developed an unbiased liquid chromatography-mass spectrometry screen for enzymatic activity of this orphan protein. We report that FAMIN phosphorolytically cleaves adenosine into adenine and ribose-1-phosphate. Such activity was considered absent from eukaryotic metabolism. FAMIN and its prokaryotic orthologs additionally have adenosine deaminase, purine nucleoside phosphorylase, and S-methyl-5′-thioadenosine phosphorylase activity, hence, combine activities of the namesake enzymes of central purine metabolism. FAMIN enables in macrophages a purine nucleotide cycle (PNC) between adenosine and inosine monophosphate and adenylosuccinate, which consumes aspartate and releases fumarate in a manner involving fatty acid oxidation and ATP-citrate lyase activity. This macrophage PNC synchronizes mitochondrial activity with glycolysis by balancing electron transfer to mitochondria, thereby supporting glycolytic activity and promoting oxidative phosphorylation and mitochondrial H+ and phosphate recycling.	Jan 2020
I03-Macromolecular Crystallography	Structure of KAP1 tripartite motif identifies molecular interfaces required for retroelement silencing Guido A. Stoll , Shun-Ichiro Oda , Zheng-Shan Chong , Minmin Yu , Stephen H. Mclaughlin , Yorgo Modis Proceedings Of The National Academy Of Sciences 60 DOI: 10.1073/pnas.1901318116 Diamond Proposal Number(s): [15916] Open Access Show Abstract ▼ Abstract: Retroviruses can integrate their DNA into the host-cell genome. Inherited retroviral DNA and other transposable elements account for more than half of the human genome. Transposable elements must be tightly regulated to restrict their proliferation and prevent toxic gene expression. KAP1/TRIM28 is an essential regulator of transposable element transcription. We determined the crystal structure of the KAP1 TRIM. The structure identifies a protein–protein interaction site required for recruitment of KAP1 to transposable elements. An epigenetic gene silencing assay confirms the importance of this site for KAP1-dependent silencing. We also show that KAP1 self-assembles in solution, but this self-assembly is not required for silencing. Our work provides insights into KAP1-dependent silencing and tools for expanding our mechanistic understanding of this process.	Jul 2019
Krios I-Titan Krios I at Diamond Krios II-Titan Krios II at Diamond	Cryo-EM structures of MDA5-dsRNA filaments at different stages of ATP hydrolysis Qin Yu , Kun Qu , Yorgo Modis Molecular Cell DOI: 10.1016/j.molcel.2018.10.012 Diamond Proposal Number(s): [17434, 21021] Open Access Show Abstract ▼ Abstract: Double-stranded RNA (dsRNA) is a potent proinflammatory signature of viral infection. Long cytosolic dsRNA is recognized by MDA5. The cooperative assembly of MDA5 into helical filaments on dsRNA nucleates the assembly of a multiprotein type I interferon signaling platform. Here, we determined cryoelectron microscopy (cryo-EM) structures of MDA5-dsRNA filaments with different helical twists and bound nucleotide analogs at resolutions sufficient to build and refine atomic models. The structures identify the filament-forming interfaces, which encode the dsRNA binding cooperativity and length specificity of MDA5. The predominantly hydrophobic interface contacts confer flexibility, reflected in the variable helical twist within filaments. Mutation of filament-forming residues can result in loss or gain of signaling activity. Each MDA5 molecule spans 14 or 15 RNA base pairs, depending on the twist. Variations in twist also correlate with variations in the occupancy and type of nucleotide in the active site, providing insights on how ATP hydrolysis contributes to MDA5-dsRNA recognition.	Nov 2018

Publications Database

Search Results

You searched for all publications:

Search Again...

Subject Areas (check all that apply) select all

Instruments used to collect data (check all that apply) select all

Collaborations involved (check all that apply) select all

Diamond Offline Facilities used

Relevant Technical Areas (check all that apply) select all

Menu for Anonymous User