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Reversible Ubiquitylation in Plant Biology

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889194414 Year: Pages: 115 DOI: 10.3389/978-2-88919-441-4 Language: English
Publisher: Frontiers Media SA
Subject: Botany --- Science (General)
Added to DOAB on : 2016-02-05 17:24:33
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Reversible ubiquitylation plays an important regulatory role in almost all aspects of cellular and organismal processes in plants. Its pervasive regulatory role in plant biology is primarily due to the involvement of a large set of ubiquitin system constituents (encoded by approximately 6% Arabidopsis genome), the huge number of important cellular proteins targeted as substrates, and various drastic effects on the modified proteins. The major components of the ubiquitin system include a large set of enzymes and proteins involved in ubiquitin conjugation (E1s, E2s, and E3s) and deconjugation (deubiquitinases of different classes) and post ubiquitin conjugation components such as ubiquitin receptors, endocytic machineries, and 26S proteasome. The established substrates include transcriptional activators and repressors, signaling components, key metabolic enzymes, and critical mechanistic components of major cellular processes and regulatory mechanisms. Post-translational modification of proteins by reversible ubiquitylation could drastically affects the modified proteins by proteolytic processing and turnover, altering catalytic activity, subcellular targeting, and protein-protein interaction. Continued efforts are being carried out to identify novel substrates critical for various cellular and organismal processes, to determine effects of reversible ubiquitylation on the modified substrates, to determine signaling determinants triggering reversible ubiquitylation of specific substrates, to illustrate individual components of the ubiquitin system for their in vivo functions and involved mechanistic roles, and to determine mechanistic roles of modification acting on critical components of major cellular processes and regulatory mechanisms. The aim of this special topic is to serve as a platform to report most recent advances on those above listed current research endeavors. We welcome article types including original research, review, mini review, method, and perspective/opinion/hypothesis.

Ubiquitin and Ubiquitin-Relative SUMO in DNA Damage Response

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889454419 Year: Pages: 183 DOI: 10.3389/978-2-88945-441-9 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Genetics
Added to DOAB on : 2018-11-16 17:17:57
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DNA damage response (DDR) is a term that includes a variety of highly sophisticated mechanisms that cells have evolved in safeguarding the genome from the deleterious consequences of DNA damage. It is estimated that every single cell receives tens of thousands of DNA lesions per day. Failure of DDR to properly respond to DNA damage leads to stem cell dysfunction, accelerated ageing, various degenerative diseases or cancer. The sole function of DDR is to recognize diverse DNA lesions, signal their presence, activate cell cycle arrest and finally recruit specific DNA repair proteins to fix the DNA damage and thus prevent genomic instability. DDR is composed of hundreds of spatiotemporally regulated and interconnected proteins, which are able to promptly respond to various DNA lesions. So it is not surprising that mutations in genes encoding various DDR proteins cause embryonic lethality, malignancies, neurodegenerative diseases and premature ageing. The importance of DDR for cell survival and genome stability is unquestionable, but how the sophisticated network of hundreds of different DDR proteins is spatiotemporally coordinated is far from being understood. In the last ten years ubiquitin (ubiquitination) and the ubiquitin-relative SUMO (sumoylation) have emerged as essential posttranslational modifications that regulate DDR. Beside a plethora of ubiqutin and sumo E1-activating enzymes, E2-conjugating enzymes, E3-ligases and ubiquitin/sumo proteases involved in ubiquitination and sumoylation, the complexity of ubiqutin and sumo systems is additionally increased by the fact that both ubiquitin and sumo can form a variety of different chains on substrates which govern the substrate fate, such as its interaction with other proteins, changing its enzymatic activity or promoting substrate degradation. The importance of ubiquitin/SUMO systems in the orchestration of DDR is best illustrated in patients with mutations in E3-ubiquitin ligases BRCA1 or RNF168. BRCA1 is essential for proper function of DDR and its mutations lead to triple-negative breast and ovarian cancers. RNF168 is an E3 ubiquitin ligase, which creates the ubiquitin docking platform for recruitment of different DNA damage signalling and repair proteins at sites of DNA lesion, and its mutations cause RIDDLE syndrome characterized by radiosensitivity, immunodeficiency and learning disability. In addition, recently discovered the ubiquitin receptor protein SPRTN is part of the DNA replication machinery and its mutations cause early-onset hepatocellular carcinoma and premature ageing in humans. Despite more than 700 different enzymes directly involved in ubiquitination and sumoylation processes only few of them are known to play a role in DDR. Therefore, we feel that the role of ubiquitin and the ubiquitin-related SUMO in DDR is far from being understood, and that this is the emerging field that will hugely expand in the next decade due to the rapid development of a new generation of technologies, which will allow us a more robust and precise analyses of human genome, transcriptome and proteome. In this Research Topic we provide a comprehensive overview of our current understanding of ubiquitin and SUMO pathways in all aspects of DDR, from DNA replication to different DNA repair pathways, and demonstrate how alterations in these pathways cause genomic instability that is linked to degenerative diseases, cancer and pathological ageing.

Cancer-associated defects in the DNA damage response: drivers for malignant transformation and potential therapeutic targets

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199495 Year: Pages: 107 DOI: 10.3389/978-2-88919-949-5 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Genetics
Added to DOAB on : 2016-01-19 14:05:46
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For this eBook, and the associated Research Topic in Frontiers in Genetics, entitled: ‘Cancer-associated defects in the DNA damage response: drivers for malignant transformation and potential therapeutic targets’ we have selected 10 papers that each discusses important, yet distinct aspects of the response to DNA damage in normal cells and cancer cells. Using an evolutionary conserved signaling network called the ‘DNA damage response (DDR)’ cells maintain the integrity of their genome, and thus safeguard cellular functioning and the ability to create viably progeny. Initially, the DDR appeared to consist of few linear kinase-driven pathways. However, research over the past decades in model organisms, as well as in the human system has revealed that the DDR is a complex signaling network, wired by multiple parallel pathways and displaying extensive crosstalk. Besides phosphorylation, multiple other post-translational modifications, including ubiquitination and sumoylation, are involved to achieve chromatin remodeling and initiation of DNA repair. Also, rather than being a cell-intrinsic phenomenon, we increasingly appreciate that cell-cell communication is involved. The recognition and repair of DNA damage is essential to maintain normal physiology. Multiple pathological conditions have been attributed to defective DNA repair, most notably accelerated aging, neurodegeneration and cancer. In the context of cancer, through repair of DNA damage or elimination of irreparably damaged cells, the DDR clearly has a tumor-suppressive role. Indeed, many tumor cells show partially inactivated DDR signaling, which allows proliferation in the context of DNA damage-inducing oncogenes. Simultaneously, loss of specific DDR signaling nodes creates a specific dependence of tumor cells on their remaining DDR components, and thus creates therapeutic opportunities. Especially in the context of cancer treatment, numerous targeted agents are under investigation, either to potentiate the cytotoxic effects of chemo-radiotherapy, or to induce synthetic lethality with cancer-specific alterations, with the treatment of BRCA1/2 mutant cancers with PARP1 inhibitors as a prototype example. We have selected four review articles that provide insight into the key components and the wiring of the DDR and DNA repair. Torgovnick and Schumacher review the involvement of DNA repair in the initiation and treatment of cancer, Brinkmann et al., describe the involvement of ubiquitination in DNA damage signaling and Jaiswal and Lindqvist discuss how cell-extrinsic signaling participates in communication of DNA damage to neighboring cells. In addition, Shatneyeva and colleagues review the connection between the cellular response to DNA damage and escape from immune surveillance. Concerning the therapeutic application of targeting the DDR and DNA repair, three articles were included. Krajewska and van Vugt review the wiring of homologous recombination and how this offers therapeutic opportunities. Additionally, Knittel and colleagues describe how genetic loss of the central DDR component ATM in chronic lymphocytic leukemia can be exploited therapeutically by targeting certain parallel DNA repair pathways. Syljuasen and colleagues report on how targeting of the DDR can be used as a therapeutic strategy in lung cancer. Finally, three chapters describe newly identified regulators of the cellular response to DNA damage. Von Morgen et al. describe the R2TP complex, Lezzi and Fanciluuli review the involvement of Che-1/AATF in the DDR, and Ohms and co-authors describe how retrotransposons are at the basis of increased genomic instability. Altogether, these articles describe how defective responses to DNA damage underlie disease - and especially in the context of cancer -can be exploited to better treat disease.

Emotional Modulation of the Synapse

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889196067 Year: Pages: 135 DOI: 10.3389/978-2-88919-606-7 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Neurology
Added to DOAB on : 2016-08-16 10:34:25
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Highly emotional events tend to be well remembered. The adaptive value in this is clear – those events that have a bearing on survival should be stored for future use as long-term memories whereas memories of inconsequential events would not as likely contribute to future survival. Enduring changes in the structure and function of synapses, neural circuitry, and ultimately behavior, can be modulated by highly aversive or rewarding experiences. In the last decade, the convergence of cellular, molecular, and systems neuroscience has produced new insights into the biological mechanisms that determine whether a memory will be stored for the long-term or lost forever. This Research Topic brings together leading experts, who work at multiple levels of analysis, to reveal recent discoveries and concepts regarding the synaptic mechanisms of consolidation and extinction of emotionally arousing memories.

Roles of NF-κB in Cancer and Their Therapeutic Approaches

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ISBN: 9783038971177 9783038971184 Year: Pages: X, 330 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Oncology --- Biology
Added to DOAB on : 2018-08-15 10:52:09
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Although mortality rates have declined in recent years, the majority of cancers are still difficult to treat and the medical need for better cancer treatment is evident. The current anticancer armamentarium includes many active agents that are applied across tumor types. However, most of these broadly-active anticancer drugs have a small therapeutic index and barely discriminate between malignant and normal cells. In recent years the focus has shifted to the development of rationally designed, molecularly-targeted therapy for the treatment of a specific cancer, therefore offering the promise of greater specificity coupled with reduced systemic toxicity. NF-kB transcription factor family as emerged as such a promising target for cancer therapy. This Special Issue will explore the routes from NF-kB basic research, cancer research and oncogenomics into the development of NF-kB-based cancer therapeutics and biomarkers.We invite research and review papers in any area of the NF-kB field that are related, but not limited to, fundamental understanding of NF-kB signaling pathways, gene expression profiling, epigenetic regulation, diagnostic, prognostic and pharmacogenomic biomarkers, molecular targets driving the progression of human cancers, cancer drug development on these targets, clinical trial with new agents, and validation in animal models.We hope that this Special Issue reflects the exciting era that we are living in with respect to the field of NF-kB and its applications in cancer research.

Molecular Mechanism of Alzheimer's Disease

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ISBN: 9783039214075 / 9783039214082 Year: Pages: 228 DOI: 10.3390/books978-3-03921-408-2 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology
Added to DOAB on : 2019-12-09 11:49:16
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Alzheimer’s disease (AD) is an age-related neurological disease that affects tens of millions of people, in addition to their carers. Hallmark features of AD include plaques composed of amyloid beta, as well as neurofibrillary tangles of tau protein. However, despite more than a century of study, the cause of Alzheimer’s disease remains unresolved. The roles of amyloid beta and tau are being questioned and other causes of AD are now under consideration. The contributions of researchers, model organisms, and various hypotheses will be examined in this Special Issue.

Keywords

?-secretase --- amyloid beta --- calcium signaling --- drug target discovery --- endoplasmic reticulum --- inositol 1,4,5-trisphosphate receptor --- ion channel --- oxidative stress --- ryanodine receptor --- therapy --- amyloid-? oligomer --- protein aggregation --- A?O receptors --- Alzheimer’s disease --- neurodegeneration --- amyloid ? --- Alzheimer’s disease --- cognitive function --- dairy products --- dementia --- inflammation --- microglia --- Alzheimer’s disease --- yeast --- Tau --- amyloid ? --- ubiquitin --- aggregation --- oligomerization --- prion --- CDK5R1 --- lncRNAs --- Alzheimer’s disease --- miR-15/107 --- NEAT1 --- HOTAIR --- MALAT1 --- heat shock response --- heat shock protein --- Alzheimer’s disease --- beta amyloid --- yeast --- Alzheimer’s disease --- complement receptor 1 --- CR1 length polymorphism --- CR1 density --- complement C3b/C4b receptor --- complement --- dementia --- molecular biology --- neurosciences --- genetic risk --- Alzheimer’s disease --- brain glucose metabolism --- neuronal differentiation --- neuronal degeneration --- Prolyl isomerases --- Pin1 --- type 2 diabetes --- type 3 diabetes --- miR-34c --- dendritic spine --- Alzheimer’s disease --- Alzheimer’s disease --- positron emission tomography (PET) --- magnetic resonance imaging (MRI) --- Alzheimer’s disease --- cystathionine-?-lyase CTH gene --- DNA methylation --- epigenetics --- epigenome-wide association study --- methylome --- methylenetetrahydrofolate reductase MTHFR gene --- nutrition --- S-adenosylmethionine --- vitamin B complex --- Alzheimer’s disease --- sleep disturbance --- sleep fragmentation --- slow-wave sleep --- amyloid beta --- tau --- proteostasis --- default-mode network --- cognitive behavioral therapy for insomnia --- APOE gene --- apolipoprotein E --- DNA methylation --- mild cognitive impairment --- Hispanics

DNA Replication Stress

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ISBN: 9783039213894 / 9783039213900 Year: Pages: 368 DOI: 10.3390/books978-3-03921-390-0 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology
Added to DOAB on : 2019-12-09 16:10:12
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This Special Issue of International Journal of Molecular Sciences (IJMS) is dedicated to the mechanisms mediated at the molecular and cellular levels in response to adverse genomic perturbations and DNA replication stress. The relevant proteins and processes play paramount roles in nucleic acid transactions to maintain genomic stability and cellular homeostasis. A total of 18 articles are presented which encompass a broad range of highly relevant topics in genome biology. These include replication fork dynamics, DNA repair processes, DNA damage signaling and cell cycle control, cancer biology, epigenetics, cellular senescence, neurodegeneration, and aging. As Guest Editor for this IJMS Special Issue, I am very pleased to offer this collection of riveting articles centered on the theme of DNA replication stress. The blend of articles builds upon a theme that DNA damage has profound consequences for genomic stability and cellular homeostasis that affect tissue function, disease, cancer, and aging at multiple levels and through unique mechanisms. I thank the authors for their excellent contributions, which provide new insight into this fascinating and highly relevant area of genome biology.

Keywords

barley --- chromosome --- DNA replication pattern --- EdU --- mutagens --- DNA replication --- DNA damage --- DNA repair --- genome integrity --- A549 cells --- H1299 cells --- heterogeneity --- DNA damage response --- 8-chloro-adenosine --- DNA replication --- S phase --- origin firing --- TopBP1 --- ATR --- DNA fiber assay --- APE2 --- ATR-Chk1 DDR pathway --- Genome integrity --- SSB end resection --- SSB repair --- SSB signaling --- DNA replication stress --- genome stability --- ubiquitin --- replication fork restart --- translesion synthesis --- template-switching --- homologous recombination --- Fanconi Anemia --- G protein-coupled receptor (GPCR) --- aging --- DNA damage --- ?-arrestin --- G protein-coupled receptor kinase (GRK) --- interactome --- G protein-coupled receptor kinase interacting protein 2 (GIT2) --- ataxia telangiectasia mutated (ATM) --- clock proteins --- energy metabolism --- neurodegeneration --- cellular senescence --- ageing --- Alzheimer’s disease --- multiple sclerosis --- Parkinson’s disease --- lipofuscin --- SenTraGorTM (GL13) --- senolytics --- DNA replication --- DNA repair --- DNA damage response --- DNA translocation --- DNA helicase --- superfamily 2 ATPase --- replication restart --- fork reversal --- fork regression --- chromatin remodeler --- C9orf72 --- ALS --- motor neuron disease --- R loops, nucleolar stress --- neurodegeneration --- Difficult-to-Replicate Sequences --- replication stress --- non-B DNA --- Polymerase eta --- Polymerase kappa --- genome instability --- common fragile sites --- Microsatellites --- cancer --- DNA double-strand repair --- premature aging --- post-translational modification --- protein stability --- replication stress --- Werner Syndrome --- Werner Syndrome Protein --- dormant origins --- replicative stress --- replication timing --- DNA damage --- genome instability --- cancer --- Thermococcus eurythermalis --- endonuclease IV --- AP site analogue --- spacer --- DNA repair --- DNA repair --- double strand break repair --- exonuclease 1 --- EXO1 --- mismatch repair --- MMR --- NER --- nucleotide excision repair --- strand displacements --- TLS --- translesion DNA synthesis --- POL? --- mutation frequency --- mutations spectra --- SupF --- mutagenicity --- oxidative stress --- DNA damage --- DNA repair --- replication --- 8-oxoG --- epigenetic --- gene expression --- helicase --- cell cycle checkpoints --- genomic instability --- G2-arrest --- cell death --- repair of DNA damage --- adaptation --- n/a

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