scholarly journals Structural Insights into the Evolutionarily Conserved BAF Chromatin Remodeling Complex

Biology ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 146
Author(s):  
Ryan D. Marcum ◽  
Alexis A. Reyes ◽  
Yuan He
Keyword(s):  
High Frequency ◽  
Human Cancer ◽  
Chromatin Accessibility ◽  
Baf Complex ◽  
Cellular Processes ◽  
Chromatin Remodeling Complex ◽  
Evolutionarily Conserved ◽  
Potential Impact ◽  
Structural Insights

The switch/sucrose nonfermentable (SWI/SNF) family of proteins acts to regulate chromatin accessibility and plays an essential role in multiple cellular processes. A high frequency of mutations has been found in SWI/SNF family subunits by exome sequencing in human cancer, and multiple studies support its role in tumor suppression. Recent structural studies of yeast SWI/SNF and its human homolog, BAF (BRG1/BRM associated factor), have provided a model for their complex assembly and their interaction with nucleosomal substrates, revealing the molecular function of individual subunits as well as the potential impact of cancer-associated mutations on the remodeling function. Here we review the structural conservation between yeast SWI/SNF and BAF and examine the role of highly mutated subunits within the BAF complex.

scholarly journals Structural insights and evaluation of the potential impact of missense variants on the interactions of SLIT2 with ROBO1/4 in cancer progression

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Debmalya Sengupta ◽  
Gairika Bhattacharya ◽  
Sayak Ganguli ◽  
Mainak Sengupta
Keyword(s):  
Lung Cancer ◽  
Cancer Progression ◽  
Structural Parameters ◽  
Homology Modelling ◽  
Missense Variants ◽  
Potential Impact ◽  
The Impact ◽  
Structural Insights ◽  
Rigid Docking

AbstractThe cognate interaction of ROBO1/4 with its ligand SLIT2 is known to be involved in lung cancer progression. However, the precise role of genetic variants, disrupting the molecular interactions is less understood. All cancer-associated missense variants of ROBO1/4 and SLIT2 from COSMIC were screened for their pathogenicity. Homology modelling was done in Modeller 9.17, followed by molecular simulation in GROMACS. Rigid docking was performed for the cognate partners in PatchDock with refinement in HADDOCK server. Post-docking alterations in conformational, stoichiometric, as well as structural parameters, were assessed. The disruptive variants were ranked using a weighted scoring scheme. In silico prioritisation of 825 variants revealed 379 to be potentially pathogenic out of which, about 12% of the variants, i.e. ROBO1 (14), ROBO4 (8), and SLIT2 (23) altered the cognate docking. Six variants of ROBO1 and 5 variants of ROBO4 were identified as "high disruptors" of interactions with SLIT2 wild type. Likewise, 17 and 13 variants of SLIT2 were found to be "high disruptors" of its interaction with ROBO1 and ROBO4, respectively. Our study is the first report on the impact of cancer-associated missense variants on ROBO1/4 and SLIT2 interactions that might be the drivers of lung cancer progression.

scholarly journals The Role of BRG1 in Antioxidant and Redox Signaling

2020 ◽  
Vol 2020 ◽  
pp. 1-12 ◽  
Author(s):  
Shilong You ◽  
Ying Zhang ◽  
Jiaqi Xu ◽  
Hao Qian ◽  
Shaojun Wu ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Chromatin Remodeling ◽  
Redox Homeostasis ◽  
Redox Signaling ◽  
Normal Functioning ◽  
Antioxidant Genes ◽  
Cellular Processes ◽  
Cell Functions ◽  
Chromatin Remodeling Complex

Redox homeostasis is regulated by critical molecules that modulate antioxidant and redox signaling (ARS) within the cell. Imbalances among these molecules can lead to oxidative stress and damage to cell functions, causing a variety of diseases. Brahma-related gene 1 (BRG1), also known as SMARCA4, is the central ATPase catalytic subunit of the switch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex, which plays a core role in DNA replication, repair, recombination, and transcriptional regulation. Numerous recent studies show that BRG1 is involved in the regulation of various cellular processes associated with ARS. BRG1, as a major factor in chromatin remodeling, is essential for the repair of oxidative stress-induced DNA damage and the activation of antioxidant genes under oxidative stress. Consequently, a comprehensive understanding of the roles of BRG1 in redox homeostasis is crucial to understand the normal functioning as well as pathological mechanisms. In this review, we summarized and discussed the role of BRG1 in the regulation of ARS.

scholarly journals Role of the Sin3-Histone Deacetylase Complex in Growth Regulation by the Candidate Tumor Suppressor p33ING1

2002 ◽  
Vol 22 (3) ◽  
pp. 835-848 ◽  
Author(s):  
A. Kuzmichev ◽  
Y. Zhang ◽  
H. Erdjument-Bromage ◽  
P. Tempst ◽  
D. Reinberg
Keyword(s):  
Histone Deacetylases ◽  
Growth Regulation ◽  
Direct Interaction ◽  
Chromatin Remodeling Complex ◽  
Evolutionarily Conserved ◽  
Human Proteins ◽  
Sin3 Complex ◽  
Negative Growth ◽  
Regulated Promoters

ABSTRACT Sin3 is an evolutionarily conserved corepressor that exists in different complexes with the histone deacetylases HDAC1 and HDAC2. Sin3-HDAC complexes are believed to deacetylate nucleosomes in the vicinity of Sin3-regulated promoters, resulting in a repressed chromatin structure. We have previously found that a human Sin3-HDAC complex includes HDAC1 and HDAC2, the histone-binding proteins RbAp46 and RbAp48, and two novel polypeptides SAP30 and SAP18. SAP30 is a specific component of Sin3 complexes since it is absent in other HDAC1/2-containing complexes such as NuRD. SAP30 mediates interactions with different polypeptides providing specificity to Sin3 complexes. We have identified p33ING1b, a negative growth regulator involved in the p53 pathway, as a SAP30-associated protein. Two distinct Sin3-p33ING1b-containing complexes were isolated, one of which associates with the subunits of the Brg1-based Swi/Snf chromatin remodeling complex. The N terminus of p33ING1b, which is divergent among a family of ING1 polypeptides, associates with the Sin3 complex through direct interaction with SAP30. The N-terminal domain of p33 is present in several uncharacterized human proteins. We show that overexpression of p33ING1b suppresses cell growth in a manner dependent on the intact Sin3-HDAC-interacting domain.

scholarly journals Sweetening the hallmarks of cancer: Galectins as multifunctional mediators of tumor progression

2019 ◽  
Vol 217 (2) ◽  
Author(s):  
María Romina Girotti ◽  
Mariana Salatino ◽  
Tomás Dalotto-Moreno ◽  
Gabriel A. Rabinovich
Keyword(s):  
Immune Responses ◽  
Tumor Progression ◽  
Stromal Cells ◽  
Human Cancer ◽  
Invasion And Metastasis ◽  
Hallmarks Of Cancer ◽  
Evolutionarily Conserved ◽  
Proliferative Signaling ◽  
Organizing Principles

Hanahan and Weinberg have proposed 10 organizing principles that enable growth and metastatic dissemination of cancer cells. These distinctive and complementary capabilities, defined as the “hallmarks of cancer,” include the ability of tumor cells and their microenvironment to sustain proliferative signaling, evade growth suppressors, resist cell death, promote replicative immortality, induce angiogenesis, support invasion and metastasis, reprogram energy metabolism, induce genomic instability and inflammation, and trigger evasion of immune responses. These common features are hierarchically regulated through different mechanisms, including those involving glycosylation-dependent programs that influence the biological and clinical impact of each hallmark. Galectins, an evolutionarily conserved family of glycan-binding proteins, have broad influence in tumor progression by rewiring intracellular and extracellular circuits either in cancer or stromal cells, including immune cells, endothelial cells, and fibroblasts. In this review, we dissect the role of galectins in shaping cellular circuitries governing each hallmark of tumors, illustrating relevant examples and highlighting novel opportunities for treating human cancer.

scholarly journals mTOR and Aging: An Old Fashioned Dress

2019 ◽  
Vol 20 (11) ◽  
pp. 2774 ◽  
Author(s):  
Giovanni Stallone ◽  
Barbara Infante ◽  
Concetta Prisciandaro ◽  
Giuseppe Grandaliano
Keyword(s):  
Mammalian Target Of Rapamycin ◽  
Nutrient Sensing ◽  
Protective Effects ◽  
Cellular Functions ◽  
Cellular Processes ◽  
Age Related ◽  
Signalling Network ◽  
Evolutionarily Conserved ◽  
Mtor Signalling

Aging is a physiologic/pathologic process characterized by a progressive impairment of cellular functions, supported by the alterations of several molecular pathways, leading to an increased cell susceptibility to injury. This deterioration is the primary risk factor for several major human pathologies. Numerous cellular processes, including genomic instability, telomere erosion, epigenetic alterations, loss of proteostasis, deregulated nutrient-sensing, mitochondrial dysfunction, stem cell exhaustion, and altered intercellular signal transduction represent common denominators of aging in different organisms. Mammalian target of rapamycin (mTOR) is an evolutionarily conserved nutrient sensing protein kinase that regulates growth and metabolism in all eukaryotic cells. Studies in flies, worms, yeast, and mice support the hypothesis that the mTOR signalling network plays a pivotal role in modulating aging. mTOR is emerging as the most robust mediator of the protective effects of various forms of dietary restriction, which has been shown to extend lifespan and slow the onset of age-related diseases across species. Herein we discuss the role of mTor signalling network in the development of classic age-related diseases, focused on cardiovascular system, immune response, and cancer.

scholarly journals Global Chromatin Changes Resulting from Single-Gene Inactivation—The Role of SMARCB1 in Malignant Rhabdoid Tumor

Cancers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2561
Author(s):  
Colin Kenny ◽  
Elaine O’Meara ◽  
Mevlüt Ulaş ◽  
Karsten Hokamp ◽  
Maureen J. O’Sullivan
Keyword(s):  
Chromatin Remodeling ◽  
Human Cancer ◽  
Single Gene ◽  
Gene Activation ◽  
Suppressor Gene ◽  
Rhabdoid Tumor ◽  
Malignant Rhabdoid Tumor ◽  
Complex Activity ◽  
Baf Complex ◽  
Chromatin Remodeling Complex

Human cancer typically results from the stochastic accumulation of multiple oncogene-activating and tumor-suppressor gene-inactivating mutations. However, this process takes time and especially in the context of certain pediatric cancer, fewer but more ‘impactful’ mutations may in short order produce the full-blown cancer phenotype. This is well exemplified by the highly aggressive malignant rhabdoid tumor (MRT), where the only gene classically showing recurrent inactivation is SMARCB1, a subunit member of the BAF chromatin-remodeling complex. This is true of all three presentations of MRT including MRT of kidney (MRTK), MRT of the central nervous system (atypical teratoid rhabdoid tumor—ATRT) and extracranial, extrarenal rhabdoid tumor (EERT). Our reverse modeling of rhabdoid tumors with isogenic cell lines, either induced or not induced, to express SMARCB1 showed widespread differential chromatin remodeling indicative of altered BAF complex activity with ensuant histone modifications when tested by chromatin immunoprecipitation followed by sequencing (ChIP-seq). The changes due to reintroduction of SMARCB1 were preponderantly at typical enhancers with tandem BAF complex occupancy at these sites and related gene activation, as substantiated also by transcriptomic data. Indeed, for both MRTK and ATRT cells, there is evidence of an overlap between SMARCB1-dependent enhancer activation and tissue-specific lineage-determining genes. These genes are inactive in the tumor state, conceivably arresting the cells in a primitive/undifferentiated state. This epigenetic dysregulation from inactivation of a chromatin-remodeling complex subunit contributes to an improved understanding of the complex pathophysiological basis of MRT, one of the most lethal and aggressive human cancers.

scholarly journals Yeast FIT2 homolog is necessary to maintain cellular proteostasis by regulating lipid homeostasis

2020 ◽  
Author(s):  
Peter Shyu ◽  
Wei Sheng Yap ◽  
Maria L. Gaspar ◽  
Stephen A. Jesch ◽  
Charlie Marvalim ◽  
...  
Keyword(s):  
Stress Response ◽  
Lipid Homeostasis ◽  
Compensatory Mechanism ◽  
Intracellular Lipids ◽  
Cellular Processes ◽  
Unfolded Protein ◽  
Protein Ubiquitination ◽  
Evolutionarily Conserved ◽  
Protein Response

Lipid droplets (LDs) have long been regarded as inert cytoplasmic organelles with the primary function of housing excess intracellular lipids. More recently, LDs have been strongly implicated in conditions of lipid and protein dysregulation. The fat storage inducing transmembrane (FIT) family of proteins comprises of evolutionarily conserved endoplasmic reticulum (ER)-resident proteins that have been reported to induce LD formation. Here, we establish a model system to study the role of S. cerevisiae FIT homologues (ScFIT), SCS3 and YFT2, in proteostasis and stress response pathways. While LD biogenesis and basal ER stress-induced unfolded protein response (UPR) remain unaltered in ScFIT mutants, SCS3 was found to be essential for proper stress-induced UPR activation and for viability in the absence of the sole yeast UPR transducer IRE1. Devoid of a functional UPR, scs3 mutants exhibited accumulation of triacylglycerol within the ER along with aberrant LD morphology, suggesting a UPR-dependent compensatory mechanism for LD maturation. Additionally, SCS3 was necessary to maintain phospholipid homeostasis. Strikingly, the absence of the ScFIT proteins results in the downregulation of the closely-related Heat Shock Response (HSR) pathway. In line with this observation, global protein ubiquitination and the turnover of both ER and cytoplasmic misfolded proteins is impaired in ScFIT cells, while a screen for interacting partners of Scs3 identifies components of the proteostatic machinery as putative targets. Taken together, these suggest that ScFIT proteins may modulate proteostasis and stress response pathways with lipid metabolism at the interface between the two cellular processes.

scholarly journals Membrane and raft association of reggie-1/flotillin-2: role of myristoylation, palmitoylation and oligomerization and induction of filopodia by overexpression

2004 ◽  
Vol 378 (2) ◽  
pp. 509-518 ◽  
Author(s):  
Carolin NEUMANN-GIESEN ◽  
Bianca FALKENBACH ◽  
Peter BEICHT ◽  
Stephanie CLAASEN ◽  
Georg LÜERS ◽  
...  
Keyword(s):  
T Cell Activation ◽  
Cell Activation ◽  
Fluorescent Protein ◽  
Transmembrane Domain ◽  
Insulin Signalling ◽  
Membrane Association ◽  
Cellular Processes ◽  
Evolutionarily Conserved ◽  
Green Fluorescent

The reggie protein family consists of two proteins, reggie-1 and -2, also called flotillins, which are highly ubiquitous and evolutionarily conserved. Both reggies have been shown to be associated with membrane rafts and are involved in various cellular processes such as T-cell activation, phagocytosis and insulin signalling. However, the exact molecular function of these proteins remains to be determined. In addition, the mechanism of membrane association of reggie-1, which does not contain any transmembrane domain, is not known. In this study, we have produced a fusion protein of reggie-1 with enhanced green fluorescent protein and generated targeted substitutions for the inactivation of putative palmitoylation and myristoylation sites. We were able to show that reggie-1 is myristoylated and multiply palmitoylated and that lipid modifications are necessary for membrane association of reggie-1. Overexpression of reggie-1 resulted in the induction of numerous filopodia-like protrusions in various cell lines, suggesting a role for reggie-1 as a signalling protein in actin-dependent processes.

scholarly journals Intrinsic Disorder of the BAF Complex: Roles in Chromatin Remodeling and Disease Development

2019 ◽  
Vol 20 (21) ◽  
pp. 5260 ◽  
Author(s):  
El Hadidy ◽  
Uversky
Keyword(s):  
Chromatin Remodeling ◽  
Regulation Of Gene Expression ◽  
Intrinsic Disorder ◽  
Literature Mining ◽  
Baf Complex ◽  
Chromatin Remodeling Complex ◽  
Significant Barrier ◽  
Polymorphic Structure ◽  
Chromatin Reorganization

The two-meter-long DNA is compressed into chromatin in the nucleus of every cell, which serves as a significant barrier to transcription. Therefore, for processes such as replication and transcription to occur, the highly compacted chromatin must be relaxed, and the processes required for chromatin reorganization for the aim of replication or transcription are controlled by ATP-dependent nucleosome remodelers. One of the most highly studied remodelers of this kind is the BRG1- or BRM-associated factor complex (BAF complex, also known as SWItch/sucrose non-fermentable (SWI/SNF) complex), which is crucial for the regulation of gene expression and differentiation in eukaryotes. Chromatin remodeling complex BAF is characterized by a highly polymorphic structure, containing from four to 17 subunits encoded by 29 genes. The aim of this paper is to provide an overview of the role of BAF complex in chromatin remodeling and also to use literature mining and a set of computational and bioinformatics tools to analyze structural properties, intrinsic disorder predisposition, and functionalities of its subunits, along with the description of the relations of different BAF complex subunits to the pathogenesis of various human diseases.

scholarly journals Involvement of Rac/Cdc42/PAK pathway in cytoskeletal rearrangements.

2009 ◽  
Vol 56 (2) ◽  
Author(s):  
Joanna Szczepanowska
Keyword(s):  
Neurodegenerative Diseases ◽  
Protein Kinases ◽  
Small Gtpases ◽  
Cytoskeletal Reorganization ◽  
Cellular Processes ◽  
Cytoskeletal Structure ◽  
Binding Partners ◽  
Evolutionarily Conserved ◽  
Cytoskeletal Rearrangements

The p21-activated kinases (PAKs) are serine/threonine protein kinases interacting with small GTPases - Rac and Cdc42. PAKs are found in most eukaryotes and play an evolutionarily conserved role in many cellular processes. Six human PAKs have been identified, and based on homology, they can be classified into two groups. This review focuses specifically on the role of Rac/Cdc42 regulated PAKs in maintaining and remodeling cytoskeletal structure in various organisms. A list of PAKs substrates and binding partners implicated directly and indirectly in cytoskeletal reorganization is presented. Also perturbations of the Rac/Cdc42/PAK pathway leading to tumorigenesis and neurodegenerative diseases are reviewed.

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