scholarly journals A proteomics study identifying interactors of the FSHD2 gene product SMCHD1 reveals RUVBL1-dependent DUX4 repression

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Remko Goossens ◽  
Mara S. Tihaya ◽  
Anita van den Heuvel ◽  
Klorane Tabot-Ndip ◽  
Iris M. Willemsen ◽  
...  
Keyword(s):  
Potential Function ◽  
Gene Clusters ◽  
Autosomal Gene ◽  
Interacting Proteins ◽  
Inhibitory Protein ◽  
Inactive X Chromosome ◽  
Proteomics Approach ◽  
Epigenetic Repression ◽  
Structural Maintenance Of Chromosomes

AbstractStructural Maintenance of Chromosomes Hinge Domain Containing 1 (SMCHD1) is a chromatin repressor, which is mutated in > 95% of Facioscapulohumeral dystrophy (FSHD) type 2 cases. In FSHD2, SMCHD1 mutations ultimately result in the presence of the cleavage stage transcription factor DUX4 in muscle cells due to a failure in epigenetic repression of the D4Z4 macrosatellite repeat on chromosome 4q, which contains the DUX4 locus. While binding of SMCHD1 to D4Z4 and its necessity to maintain a repressive D4Z4 chromatin structure in somatic cells are well documented, it is unclear how SMCHD1 is recruited to D4Z4, and how it exerts its repressive properties on chromatin. Here, we employ a quantitative proteomics approach to identify and characterize novel SMCHD1 interacting proteins, and assess their functionality in D4Z4 repression. We identify 28 robust SMCHD1 nuclear interactors, of which 12 are present in D4Z4 chromatin of myocytes. We demonstrate that loss of one of these SMCHD1 interacting proteins, RuvB-like 1 (RUVBL1), further derepresses DUX4 in FSHD myocytes. We also confirm the interaction of SMCHD1 with EZH inhibitory protein (EZHIP), a protein which prevents global H3K27me3 deposition by the Polycomb repressive complex PRC2, providing novel insights into the potential function of SMCHD1 in the repression of DUX4 in the early stages of embryogenesis. The SMCHD1 interactome outlined herein can thus provide further direction into research on the potential function of SMCHD1 at genomic loci where SMCHD1 is known to act, such as D4Z4 repeats, the inactive X chromosome, autosomal gene clusters, imprinted loci and telomeres.

scholarly journals Sortase-Catalyzed Assembly of Distinct Heteromeric Fimbriae in Actinomyces naeslundii

2007 ◽  
Vol 189 (8) ◽  
pp. 3156-3165 ◽  
Author(s):  
Arunima Mishra ◽  
Asis Das ◽  
John O. Cisar ◽  
Hung Ton-That
Keyword(s):  
Gene Cluster ◽  
Biochemical Analysis ◽  
Gene Clusters ◽  
Oral Diseases ◽  
Actinomyces Naeslundii ◽  
Molecular Investigation ◽  
A Minor ◽  
Assembly Pathways

ABSTRACT Two types of adhesive fimbriae are expressed by Actinomyces; however, the architecture and the mechanism of assembly of these structures remain poorly understood. In this study we characterized two fimbrial gene clusters present in the genome of Actinomyces naeslundii strain MG-1. By using immunoelectron microscopy and biochemical analysis, we showed that the fimQ-fimP-srtC1-fimR gene cluster encodes a fimbrial structure (designated type 1) that contains a major subunit, FimP, forming the shaft and a minor subunit, FimQ, located primarily at the tip. Similarly, the fimB-fimA-srtC2 gene cluster encodes a distinct fimbrial structure (designated type 2) composed of a shaft protein, FimA, and a tip protein, FimB. By using allelic exchange, we constructed an in-frame deletion mutant that lacks the SrtC2 sortase. This mutant produces abundant type 1 fimbriae and expresses the monomeric FimA and FimB proteins, but it does not assemble type 2 fimbriae. Thus, SrtC2 is a fimbria-specific sortase that is essential for assembly of the type 2 fimbriae. Together, our experiments pave the way for several lines of molecular investigation that are necessary to elucidate the fimbrial assembly pathways in Actinomyces and their function in the pathogenesis of different biofilm-related oral diseases.

scholarly journals Epigenetic regulation of epithelial dectin-1 through an IL-33-STAT3 axis in allergic disease

2020 ◽  
Author(s):  
Hwan Mee Yong ◽  
Naina Gour ◽  
Deepika Sharma ◽  
Syed Muaz Khalil ◽  
Andrew P. Lane ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Allergic Disease ◽  
Epigenetic Regulation ◽  
Allergic Diseases ◽  
Respiratory Epithelium ◽  
Fine Tuning ◽  
Proximal Promoter ◽  
Epigenetic Repression ◽  
Inflammatory Molecules

AbstractAllergic diseases arise in susceptible individuals in part because of decrements in protective pathways. The mechanism by which these anti-inflammatory molecules become repressed remains unclear. We have previously reported that epithelial dectin-1 prevents aberrant type 2 responses and is downregulated in the epithelium of allergic patients. Here we report that dectin-1 is constitutively expressed by the respiratory epithelium in humans, and that IL-33 specifically acts as a repressor of dectin-1. Mechanistically, this occurs via IL-33-dependent STAT3 activation and the subsequent repression of the dectin-1 gene, CLEC7A. We have identified a novel enhancer region upstream of the proximal promoter of CLEC7A that is only accessible in epithelial cells, but not in hematopoietic cells. Epigenetic repression of CLEC7A through this newly identified locus, downstream of an aberrant IL-33-STAT3 axis, occurs in the epithelium of allergic individuals. Collectively, our data identify a mechanism of epigenetic fine-tuning of dectin-1 expression in epithelial cells that may participate in allergenicity.

scholarly journals Gene Expression Dynamics during Diabetic Periodontitis

2012 ◽  
Vol 91 (12) ◽  
pp. 1160-1165 ◽  
Author(s):  
O.M. Andriankaja ◽  
J. Galicia ◽  
G. Dong ◽  
W. Xiao ◽  
F. Alawi ◽  
...  
Keyword(s):  
Cell Signaling ◽  
Cell Activity ◽  
Gene Clusters ◽  
Mrna Levels ◽  
Tnf Inhibitor ◽  
Periodontal Inflammation ◽  
Gene Expression Dynamics ◽  
Tnf Inhibition ◽  
Type 2 Diabetic

Diabetes impairs the resolution of periodontal inflammation. We explored pathways altered by inflammation in the diabetic periodontium by using ligatures to induce periodontitis in type-2 diabetic Goto-Kakizaki rats. Ligatures were removed after 7 days, and rats were then treated with TNF inhibitor (pegsunercept) or vehicle alone and euthanized 4 days later. RNA was extracted from periodontal tissue, examined by mRNA profiling, and further analyzed by functional criteria. We found that 1,754 genes were significantly up-regulated and 1,243 were down-regulated by pegsunercept (p < 0.05). Functional analysis revealed up-regulation of neuron-associated and retina-associated gene clusters as well as those related to cell activity and signaling. Others were down-regulated by TNF inhibition and included genes associated with host defense, apoptosis, cell signaling and activity, and coagulation/hemostasis/complement. For selected genes, findings with microarray and rt-PCR agreed. PPAR-α was investigated further by immunohistochemistry due to its anti-inflammatory function and was found to be up-regulated in the gingiva during the resolution of periodontal inflammation and suppressed by diabetes. The results indicate that diabetes-enhanced inflammation both up- and down-regulates genes involved in cellular activity and cell signaling, while it predominantly up-regulates genes involved in the host response, apoptosis, and coagulation/homeostasis/complement and down-regulates mRNA levels of neuron, retina, and energy/metabolism-associated genes.

Proteins interact with the cytosolic mineralocorticoid receptor depending on the ligand

2008 ◽  
Vol 295 (1) ◽  
pp. H361-H365 ◽  
Author(s):  
Miriam Weber ◽  
Martin Wehling ◽  
Ralf Lösel
Keyword(s):  
Mineralocorticoid Receptor ◽  
Steroid Receptors ◽  
Interacting Proteins ◽  
Receptor Ligands ◽  
Affinity Isolation ◽  
Proteomics Approach ◽  
Native Electrophoresis ◽  
Monomeric Proteins ◽  
Shock Proteins ◽  
Blue Native

Steroid receptors belonging to the superfamily of nuclear receptors do not exist as single monomeric proteins but mediate their effects by the interaction with numerous other proteins, e.g., cofactors for transcription, but also other proteins involved in cellular signaling. This interaction may be ligand dependent, which explains the differential effects of receptor ligands. Whereas some receptors, e.g., the estrogen receptor, have been studied in great detail, much less is known about proteins interacting with the mineralocorticoid receptor (MR). In this study, we aimed to identify interacting proteins using a proteomics approach involving tagged receptor constructs. After affinity isolation of MR complexes, blue native electrophoresis revealed the presence of several populations of MR complexes differing in size and composition. During the identification of interacting proteins, various heat shock proteins but also several previously undescribed potential interactors were found, including 14-3-3-ε. We also demonstrate here that the cytosolic MR in the presence of detergent interacts in a ligand-selective manner with glucose-regulated protein 78 and propionyl-CoA carboxylase-β precursor, which are found in the unliganded or aldosterone-containing complex but not with spironolactone.

scholarly journals Interactomic analysis reveals a new homeostatic role for the HIV restriction factor TRIM5α in mitophagy

2021 ◽  
Author(s):  
Bhaskar Saha ◽  
Michelle R Salemi ◽  
Geneva L Williams ◽  
Michael L Paffett ◽  
Brett Phinney ◽  
...  
Keyword(s):  
Mitochondrial Damage ◽  
Multiple Roles ◽  
Interacting Proteins ◽  
Wild Type ◽  
Cellular Functions ◽  
Mitochondrial Quality Control ◽  
Data Set ◽  
Antiviral Signaling ◽  
Contact Sites ◽  
Proteomics Approach

The protein TRIM5α has multiple roles in anti-retroviral defense, but the mechanisms underlying TRIM5α action are unclear. Here, we used an APEX2-based proteomics approach to identify TRIM5α-interacting proteins. Analysis of the TRIM5α interactome found proteins participating in a wide variety of cellular functions including regulating antiviral signaling pathways. We used this data set to uncover a novel role for TRIM5α in mitophagy, an autophagy-based mode of mitochondrial quality control that is compromised in multiple human diseases. Mitochondrial damage triggered the relocalization of TRIM5α to ER-mitochondria contact sites where TRIM5α colocalized with markers of autophagy initiation and autophagosome biogenesis. Furthermore, we found that TRIM5α knockout attenuated both Parkin-dependent and Parkin-independent mitophagy by preventing the recruitment of autophagy regulators FIP200 and ATG13 to unhealthy mitochondria. Finally, TRIM5α knockout cells showed reduced mitochondrial function under basal conditions and were more susceptible to uncontrolled immune activation and cell death in response to mitochondrial damage than were wild type cells. Taken together, our studies have identified a homeostatic role for a protein previously recognized exclusively for its antiviral actions.

An analysis of splicing, actin-binding properties, heterodimerization and molecular interactions of the non-muscle α-actinins

2013 ◽  
Vol 452 (3) ◽  
pp. 477-488 ◽  
Author(s):  
Kate S. Foley ◽  
Paul W. Young
Keyword(s):  
Molecular Interactions ◽  
Molecular Basis ◽  
Sequence Similarity ◽  
Actin Binding ◽  
Interacting Proteins ◽  
Binding Properties ◽  
High Sequence Similarity ◽  
Glomerular Function ◽  
Proteomics Approach ◽  
First Time

The non-muscle α-actinin isoforms (actinin-1 and -4) are closely related dimeric actin filament cross-linking proteins. Despite high sequence similarity, unique properties have been ascribed to actinin-4 in particular. For example, actinin-4, but not actinin-1, is essential for normal glomerular function in the kidney, is overexpressed in several cancers and can translocate to the nucleus to regulate transcription. To understand the molecular basis for such isoform-specific functions we have, for the first time, comprehensively compared these proteins in terms of alternative splicing, actin-binding properties, heterodimer formation and molecular interactions. We find that the Ca2+-insensitive variant of actinin-4 is expressed only in the nervous system and thus cannot be regarded as a smooth muscle isoform, as is the case for the Ca2+-insensitive variant of actinin-1. The actin-binding properties of actinin-1 and -4 are similar and are unlikely to explain isoform-specific functions. Surprisingly, we reveal that actinin-1/-4 heterodimers, rather than homodimers, are the most abundant form of actinin in many cell lines. Finally, we use a proteomics approach to identify potential isoform-specific interactions. The results of the present study indicate that actinin-1 and -4 can readily form heterodimers composed of monomers that may have different properties and interacting proteins. This significantly alters our view of non-muscle actinin function.

scholarly journals Identification of FBXO25-interacting proteins using an integrated proteomics approach

PROTEOMICS ◽  
2010 ◽  
Vol 10 (15) ◽  
pp. 2746-2757 ◽  
Author(s):  
Felipe R. Teixeira ◽  
Sami Yokoo ◽  
Carlos A. Gartner ◽  
Adriana O. Manfiolli ◽  
Munira M. A. Baqui ◽  
...  
Keyword(s):  
Interacting Proteins ◽  
Proteomics Approach

Novel clathrin activity: developments in health and disease

2014 ◽  
Vol 5 (2) ◽  
pp. 175-182 ◽  
Author(s):  
Joel A. Ybe
Keyword(s):  
Chromosome Segregation ◽  
Interacting Proteins ◽  
Mitotic Spindles ◽  
Tumor Suppressor P53 ◽  
Anti Cancer ◽  
Recent Developments ◽  
Infection Pathways ◽  
Health And Disease ◽  
Cancer Activity

AbstractClathrin self-assembles into a coat around vesicles filled with cargo such as nutrients, hormones, and proteins destined for degradation. Recent developments indicate clathrin is not a specialist, but is involved in different processes relevant to health and disease. Clathrin is used to strengthen centrosomes and mitotic spindles essential for chromosome segregation in cell division. In Wnt signaling, clathrin is a component of signalosomes on the plasma membrane needed to produce functional Wnt receptors. In glucose metabolism, a muscle-specific isoform, CHC22 clathrin, is key to the formation of storage compartments for GLUT4 receptor, and CHC22 dysfunction has been tied to type 2 diabetes. The activity of clathrin to self-assemble and to work with huntingtin-interacting proteins to organize actin is exploited by Listeria and enteropathic Escherichia coli in their infection pathways. Finally, there is an important connection between clathrin and human malignancies. Clathrin is argued to help transactivate tumor suppressor p53 that controls specific genes in DNA repair and apoptosis. However, this is debatable because trimeric clathrin must be made monomeric. To get insight on how the clathrin structure could be converted, the crystal structure of the trimerization domain is used in the development of the detrimerization switch hypothesis. This novel hypothesis will be relevant if connections continue to be found between CHC17 and p53 anti-cancer activity in the nucleus.

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