Altering mammalian transcription networking with ADAADi: An inhibitor of ATP-dependent chromatin remodeling

Active DNA-dependent ATPase A Domain inhibitor (ADAADi) is the only known inhibitor of ATP-dependent chromatin remodeling proteins that targets the ATPase domain of these proteins. The molecule is synthesized by aminoglycoside phosphotransferase enzyme in the presence of aminoglycosides. ADAADi interacts with ATP-dependent chromatin remodeling proteins through motif Ia present in the conserved helicase domain, and thus, can potentially inhibit all members of this family of proteins. We show that mammalian cells are sensitive to ADAADi but with variable responses in different cell lines. ADAADi can be generated from a wide variety of aminoglycosides; however, cells showed differential response to ADAADi generated from various aminoglycosides. Using HeLa and DU145 cells as model system we have explored the effect of ADAADi on cellular functions. We show that the transcriptional network of a cell type is altered when treated with sub-lethal concentration of ADAADi. Although ADAADi has no known effects on DNA chemical and structural integrity, expression of DNA-damage response genes was altered. The transcripts encoding for the pro-apoptotic proteins were found to be upregulated while the anti-apoptotic genes were found to be downregulated. This was accompanied by increased apoptosis leading us to hypothesize that the ADAADi treatment promotes apoptotic-type of cell death by upregulating the transcription of pro-apoptotic genes. ADAADi also inhibited migration of cells as well as their colony forming ability leading us to conclude that the compound has effective anti-tumor properties.

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Sterol and lipid trafficking in mammalian cells

Biochemical Society Transactions ◽

10.1042/bst0340335 ◽

2006 ◽

Vol 34 (3) ◽

pp. 335-339 ◽

Cited By ~ 39

Author(s):

F.R. Maxfield ◽

M. Mondal

Keyword(s):

Membrane Trafficking ◽

Mammalian Cells ◽

Intracellular Transport ◽

Vesicular Transport ◽

Cholesterol Content ◽

Cellular Functions ◽

Lipid Trafficking ◽

Sterol Transport ◽

A Cell ◽

Asymmetrically Distributed

The pathways involved in the intracellular transport and distribution of lipids in general, and sterols in particular, are poorly understood. Cholesterol plays a major role in modulating membrane bilayer structure and important cellular functions, including signal transduction and membrane trafficking. Both the overall cholesterol content of a cell, as well as its distribution in specific organellar membranes are stringently regulated. Several diseases, many of which are incurable at present, have been characterized as results of impaired cholesterol transport and/or storage in the cells. Despite their importance, many fundamental aspects of intracellular sterol transport and distribution are not well understood. For instance, the relative roles of vesicular and non-vesicular transport of cholesterol have not yet been fully determined, nor are the non-vesicular transport mechanisms well characterized. Similarly, whether cholesterol is asymmetrically distributed between the two leaflets of biological membranes, and if so, how this asymmetry is maintained, is poorly understood. In this review, we present a summary of the current understanding of these aspects of intracellular trafficking and distribution of lipids, and more specifically, of sterols.

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MORC2 regulates DNA damage response through a PARP1-dependent pathway

Nucleic Acids Research ◽

10.1093/nar/gkz545 ◽

2019 ◽

Vol 47 (16) ◽

pp. 8502-8520 ◽

Cited By ~ 4

Author(s):

Lin Zhang ◽

Da-Qiang Li

Keyword(s):

Dna Damage ◽

Zinc Finger ◽

Chromatin Remodeling ◽

Dna Damage Response ◽

Mammalian Cells ◽

Cellular Response ◽

Genotoxic Stress ◽

Underlying Mechanism ◽

Dna Lesions ◽

Damage Response

Abstract Microrchidia family CW-type zinc finger 2 (MORC2) is a newly identified chromatin remodeling enzyme with an emerging role in DNA damage response (DDR), but the underlying mechanism remains largely unknown. Here, we show that poly(ADP-ribose) polymerase 1 (PARP1), a key chromatin-associated enzyme responsible for the synthesis of poly(ADP-ribose) (PAR) polymers in mammalian cells, interacts with and PARylates MORC2 at two residues within its conserved CW-type zinc finger domain. Following DNA damage, PARP1 recruits MORC2 to DNA damage sites and catalyzes MORC2 PARylation, which stimulates its ATPase and chromatin remodeling activities. Mutation of PARylation residues in MORC2 results in reduced cell survival after DNA damage. MORC2, in turn, stabilizes PARP1 through enhancing acetyltransferase NAT10-mediated acetylation of PARP1 at lysine 949, which blocks its ubiquitination at the same residue and subsequent degradation by E3 ubiquitin ligase CHFR. Consequently, depletion of MORC2 or expression of an acetylation-defective PARP1 mutant impairs DNA damage-induced PAR production and PAR-dependent recruitment of DNA repair proteins to DNA lesions, leading to enhanced sensitivity to genotoxic stress. Collectively, these findings uncover a previously unrecognized mechanistic link between MORC2 and PARP1 in the regulation of cellular response to DNA damage.

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Regulation of ATM and ATR by Smarcal1 and BRG1

10.1101/261610 ◽

2018 ◽

Cited By ~ 1

Author(s):

Ramesh Sethy ◽

Radhakrishnan Rakesh ◽

Ketki Patne ◽

Vijendra Arya ◽

Tapan Sharma ◽

...

Keyword(s):

Dna Damage ◽

Chromatin Remodeling ◽

Dna Damage Response ◽

Transcriptional Repression ◽

Mammalian Cells ◽

Post Translational Modifications ◽

Osseous Dysplasia ◽

Mitotic Abnormalities ◽

Damage Response ◽

Atr Kinases

ABSTRACTThe G2/M checkpoint is activated on DNA damage by the ATM and ATR kinases that are regulated by post-translational modifications. In this paper, the transcriptional co-regulation of ATM and ATR by SMARCAL1 and BRG1, both members of the ATP-dependent chromatin remodeling protein family, is described. SMARCAL1 and BRG1 co-localize on the promoters of ATM and ATR; downregulation of SMARCAL1/BRG1 results in transcriptional repression of ATM/ATR and therefore, overriding of the G2/M checkpoint leading to mitotic abnormalities. On doxorubicin-induced DNA damage, SMARCAL1 and BRG1 are upregulated and in turn, upregulate the expression of ATM/ATR.Phosphorylation of ATM/ATR is needed for the transcriptional upregulation of SMARCAL1 and BRG1, and therefore, of ATM and ATR on DNA damage. The regulation of ATM/ATR is rendered non-functional if SMARCAL1 and/or BRG1 are absent or if the two proteins are mutated such that they are unable to hydrolyze ATP, as in for example in Schimke Immuno-Osseous Dysplasia and Coffin-Siris Syndrome. Thus, an intricate transcriptional regulation of DNA damage response genes mediated by SMARCAL1 and BRG1 is present in mammalian cells.

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Mutation-Driven Signals of ARID1A and PI3K Pathways in Ovarian Carcinomas: Alteration Is An Opportunity

International Journal of Molecular Sciences ◽

10.3390/ijms20225732 ◽

2019 ◽

Vol 20 (22) ◽

pp. 5732 ◽

Cited By ~ 3

Author(s):

Pradip De ◽

Nandini Dey

Keyword(s):

Chromatin Remodeling ◽

Dynamic Structure ◽

Pi3k Pathway ◽

Genetic Determinants ◽

Cellular Functions ◽

Ovarian Carcinomas ◽

Ovarian Cancers ◽

Damage Repair ◽

Survival Pathway ◽

A Cell

The chromosome is a functionally dynamic structure. The dynamic nature of chromosome functionally connects it to almost every event within a cell, in health and sickness. Chromatin remodeling system acts in unison with the cell survival pathway in mediating a variety of cellular functions, including mitosis, differentiation, DNA damage repair, and apoptosis. In humans, the 16 SWI/SNF complexes are a class of nucleosome remodelers, and ARID1A, an epigenetic tumor suppressor, is a member of mammalian 17 chromatin remodeling complex, SWI/SNF. Alterations of chromatin remodeling system contribute to tumorigenic events in various cancers, including ovarian cancers. Oncogenic changes of genes of the PI3K pathway are one of the potential genetic determinants of ovarian carcinomas. In this review, we present the data demonstrating the co-occurrence of mutations of ARID1A and the PI3K pathway in our cohort of ovarian cancers from the Avera Cancer Institute (SD, USA). Taking into account data from our cohort and the cBioPortal, we interrogate the opportunity provided by this co-occurrence in the context of mutation-driven signals in the life cycle of a tumor cell and its response to the targeted anti-tumor drugs.

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Microtubular and Nuclear Functions of γ-Tubulin: Are They LINCed?

Cells ◽

10.3390/cells8030259 ◽

2019 ◽

Vol 8 (3) ◽

pp. 259 ◽

Cited By ~ 6

Author(s):

Jana Chumová ◽

Hana Kourová ◽

Lucie Trögelová ◽

Petr Halada ◽

Pavla Binarová

Keyword(s):

Chromatin Remodeling ◽

Dna Damage Response ◽

Tumor Suppressors ◽

Molecular Mechanisms ◽

Nuclear Organization ◽

Linc Complex ◽

Cellular Functions ◽

Microtubule Nucleation ◽

Damage Response

γ-Tubulin is a conserved member of the tubulin superfamily with a function in microtubule nucleation. Proteins of γ-tubulin complexes serve as nucleation templates as well as a majority of other proteins contributing to centrosomal and non-centrosomal nucleation, conserved across eukaryotes. There is a growing amount of evidence of γ-tubulin functions besides microtubule nucleation in transcription, DNA damage response, chromatin remodeling, and on its interactions with tumor suppressors. However, the molecular mechanisms are not well understood. Furthermore, interactions with lamin and SUN proteins of the LINC complex suggest the role of γ-tubulin in the coupling of nuclear organization with cytoskeletons. γ-Tubulin that belongs to the clade of eukaryotic tubulins shows characteristics of both prokaryotic and eukaryotic tubulins. Both human and plant γ-tubulins preserve the ability of prokaryotic tubulins to assemble filaments and higher-order fibrillar networks. γ-Tubulin filaments, with bundling and aggregating capacity, are suggested to perform complex scaffolding and sequestration functions. In this review, we discuss a plethora of γ-tubulin molecular interactions and cellular functions, as well as recent advances in understanding the molecular mechanisms behind them.

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Regulation of the cell cycle and centrosome biology by deubiquitylases

Biochemical Society Transactions ◽

10.1042/bst20170087 ◽

2017 ◽

Vol 45 (5) ◽

pp. 1125-1136 ◽

Cited By ~ 6

Author(s):

Sarah Darling ◽

Andrew B. Fielding ◽

Dorota Sabat-Pośpiech ◽

Ian A. Prior ◽

Judy M. Coulson

Keyword(s):

Cell Cycle ◽

Cell Division ◽

Mitotic Spindle ◽

Mammalian Cells ◽

Genetic Material ◽

Post Translational Modification ◽

Cellular Processes ◽

Daughter Cells ◽

Damage Response ◽

A Cell

Post-translational modification of proteins by ubiquitylation is increasingly recognised as a highly complex code that contributes to the regulation of diverse cellular processes. In humans, a family of almost 100 deubiquitylase enzymes (DUBs) are assigned to six subfamilies and many of these DUBs can remove ubiquitin from proteins to reverse signals. Roles for individual DUBs have been delineated within specific cellular processes, including many that are dysregulated in diseases, particularly cancer. As potentially druggable enzymes, disease-associated DUBs are of increasing interest as pharmaceutical targets. The biology, structure and regulation of DUBs have been extensively reviewed elsewhere, so here we focus specifically on roles of DUBs in regulating cell cycle processes in mammalian cells. Over a quarter of all DUBs, representing four different families, have been shown to play roles either in the unidirectional progression of the cell cycle through specific checkpoints, or in the DNA damage response and repair pathways. We catalogue these roles and discuss specific examples. Centrosomes are the major microtubule nucleating centres within a cell and play a key role in forming the bipolar mitotic spindle required to accurately divide genetic material between daughter cells during cell division. To enable this mitotic role, centrosomes undergo a complex replication cycle that is intimately linked to the cell division cycle. Here, we also catalogue and discuss DUBs that have been linked to centrosome replication or function, including centrosome clustering, a mitotic survival strategy unique to cancer cells with supernumerary centrosomes.

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A model for the initial phase of cell/surface interactions based on ligand binding phenomena

Biochemical Journal ◽

10.1042/bj3110917 ◽

1995 ◽

Vol 311 (3) ◽

pp. 917-919 ◽

Cited By ~ 8

Author(s):

J Hubble ◽

R Eisenthal ◽

W J D Whish

Keyword(s):

Mammalian Cells ◽

Clinical Importance ◽

Surface Interactions ◽

Solid Surfaces ◽

Biological Phenomena ◽

Simple Consideration ◽

A Cell ◽

Plausible Mechanism ◽

Cell Surface Interactions ◽

Migration Of Cells

The interaction between mammalian cells and solid surfaces plays an important role in a number of biological phenomena. Of particular clinical importance is the migration of cells suspended in blood to the wall of a blood vessel in the event of tissue damage. While the resultant inflammation often represents a desirable response to an external challenge, responses of this type can also lead to adverse consequences. Although the cell migration phenomenon is well known, a plausible mechanism for controlling the critical ‘rolling’ stages of adhesion has yet to be proposed. In this report we suggest how a simple consideration of ligand/receptor binding interactions can be used to explain a switch between a situation where a cell population is almost entirely in free suspension, to one where a significant fraction is attached to the solid surface.

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Altering Mammalian Transcription Networking with Adaadi: An Inhibitor of Atp-Dependent Chromatin Remodeling

10.1101/723593 ◽

2019 ◽

Cited By ~ 1

Author(s):

Radhakrishnan Rakesh ◽

Saddam Hussain ◽

Kaveri Goel ◽

Soni Sharma ◽

Deepa Bisht ◽

...

Keyword(s):

Transcription Factors ◽

Chromatin Remodeling ◽

Cancer Progression ◽

Mammalian Cells ◽

Transcriptional Control ◽

Cellular Proliferation ◽

Rna Seq ◽

Epigenetic Factors ◽

Aminoglycoside Phosphotransferases ◽

Migration Of Cells

ABSTRACTTranscriptional control has been earnestly pursued for the regulation of cellular proliferation associated with cancer progression. The foundational paradigm of targeting transcription factors has yielded exquisite specificity, but many factors cannot yet be targeted. In contrast, targeting epigenetic factors to control chromatin structure and consequential gene expression generally yields more global effects on transcription. Our working paradigm targets neither specific transcription factors nor global epigenetic factors but ATP-dependent chromatin remodeling factors that regulate expression of a limited set of genes. Active DNA-dependent ATPase A Domain inhibitor (ADAADi) synthesized by aminoglycoside phosphotransferases is the first-in-class inhibitor of ATP-dependent chromatin remodeling proteins that targets the ATPase domain of these proteins. Mammalian cells are sensitive to ADAADi but cell lines are variable in their individual responses to the inhibitor. The ADAADi product can be generated from a variety of aminoglycoside substrates with cells showing differential responses to ADAADi depending on the starting aminoglycoside. RNA seq analysis demonstrated that targeting the chromatin remodeling by treatment with a sub-lethal concentration of ADAADi yields alterations to the transcriptional network of the cell. Predominantly, the tumor-promoting genes were repressed while pro-apoptotic and tumor suppressors genes were upregulated on treatment with ADAADi, leading to apoptotic-type cell death. Treatment with ADAADi reversed the EMT process as well as inhibited migration of cells and their colony forming ability. In conjunction with the previous report that treatment with ADAADi regresses tumors in mouse model, this chromatin remodeling inhibitor shows promising anti-tumor properties by targeting the main hallmarks of cancer.

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Model-guided design of mammalian genetic programs

Science Advances ◽

10.1126/sciadv.abe9375 ◽

2021 ◽

Vol 7 (8) ◽

pp. eabe9375

Author(s):

J. J. Muldoon ◽

V. Kandula ◽

M. Hong ◽

P. S. Donahue ◽

J. D. Boucher ◽

...

Keyword(s):

Mammalian Cells ◽

Computational Models ◽

Biological Complexity ◽

Genetic Circuits ◽

Cellular Functions ◽

High Performing ◽

Design Objective ◽

Complex Functions ◽

Mammalian Genetic ◽

Analog Processing

Genetically engineering cells to perform customizable functions is an emerging frontier with numerous technological and translational applications. However, it remains challenging to systematically engineer mammalian cells to execute complex functions. To address this need, we developed a method enabling accurate genetic program design using high-performing genetic parts and predictive computational models. We built multifunctional proteins integrating both transcriptional and posttranslational control, validated models for describing these mechanisms, implemented digital and analog processing, and effectively linked genetic circuits with sensors for multi-input evaluations. The functional modularity and compositional versatility of these parts enable one to satisfy a given design objective via multiple synonymous programs. Our approach empowers bioengineers to predictively design mammalian cellular functions that perform as expected even at high levels of biological complexity.

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The Role of the Extracellular Matrix Components in Cutaneous Wound Healing

BioMed Research International ◽

10.1155/2014/747584 ◽

2014 ◽

Vol 2014 ◽

pp. 1-8 ◽

Cited By ~ 113

Author(s):

Pawel Olczyk ◽

Łukasz Mencner ◽

Katarzyna Komosinska-Vassev

Keyword(s):

Extracellular Matrix ◽

Wound Healing ◽

Growth Factors ◽

Wound Repair ◽

Structural Integrity ◽

Healing Process ◽

Cellular Functions ◽

Extracellular Matrix Components ◽

Essential Components ◽

Matrix Components

Wound healing is the physiologic response to tissue trauma proceeding as a complex pathway of biochemical reactions and cellular events, secreted growth factors, and cytokines. Extracellular matrix constituents are essential components of the wound repair phenomenon. Firstly, they create a provisional matrix, providing a structural integrity of matrix during each stage of healing process. Secondly, matrix molecules regulate cellular functions, mediate the cell-cell and cell-matrix interactions, and serve as a reservoir and modulator of cytokines and growth factors’ action. Currently known mechanisms, by which extracellular matrix components modulate each stage of the process of soft tissue remodeling after injury, have been discussed.

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