scholarly journals Bridging-induced microphase separation: photobleaching experiments, chromatin domains and the need for active reactions

2020 ◽  
Vol 19 (2) ◽  
pp. 111-118 ◽  
Author(s):  
C A Brackley ◽  
D Marenduzzo
Keyword(s):  
Computer Simulations ◽  
Binding Proteins ◽  
Microphase Separation ◽  
Polymer Physics ◽  
Nuclear Bodies ◽  
Chromosome Organization ◽  
Chromatin Binding ◽  
Post Translational Modification ◽  
Chromatin Domains ◽  
Biophysical Principle

Abstract We review the mechanism and consequences of the ‘bridging-induced attraction’, a generic biophysical principle that underpins some existing models for chromosome organization in 3D. This attraction, which was revealed in polymer physics-inspired computer simulations, is a generic clustering tendency arising in multivalent chromatin-binding proteins, and it provides an explanation for the biogenesis of nuclear bodies and transcription factories via microphase separation. Including post-translational modification reactions involving these multivalent proteins can account for the fast dynamics of the ensuing clusters, as is observed via microscopy and photobleaching experiments. The clusters found in simulations also give rise to chromatin domains that conform well with the observation of A/B compartments in HiC experiments.

scholarly journals Characterization of The Interaction Between RIN13 (RPM1-Interacting13) and Sumo Proteins in Arabidopsis Thaliana

2017 ◽  
Vol 9 (2) ◽  
Author(s):  
Venny Santosa ◽  
Mio Nagabuchi ◽  
Sachiko Okada ◽  
Katsunori Tanaka
Keyword(s):  
Arabidopsis Thaliana ◽  
Fluorescence Microscopy ◽  
Hypersensitive Response ◽  
Stress Responses ◽  
Molecular Interaction ◽  
Nuclear Body ◽  
Chromosome Organization ◽  
Post Translational Modification ◽  
Molecular Studies

<p>Small Ubiquitin-related MOdifier (SUMO) proteins can be found in many organisms, including <em>A. thaliana</em>, which possesses 9 SUMO genes. SUMO binds to various target proteins in a reversible reaction called SUMOylation. SUMOylation participates in transcription, chromosome organization, proteins localizations and stress responses. Our study showed that RIN13 (<span style="text-decoration: underline;">R</span>PM1-<span style="text-decoration: underline;">In</span>teracting<span style="text-decoration: underline;">13</span>/At2g20310) is a target of SUMOylation, which was initially found by interaction between this protein and AtSCE1a (E2). Recent report showed that overexpression of RIN13 enhanced the resistance to pathogen without inducing hypersensitive response. However, the molecular interaction between RIN13 and SUMO proteins and its significance have not been studied yet. Thus, our study aimed to characterize the interaction between RIN13 and SUMO proteins in <em>A. thaliana</em>. The result showed an isoform-specific SUMOylation between RIN13 and SUMO proteins. RIN13 is SUMOylated by SUMO1, 2, 3, and 5. Though expressed ubiquitously in <em>A.thaliana</em>, fluorescence microscopy showed that RIN13 localizes subcellularly in the nuclear body. Moreover, complete abolishment of SUMOylation with inactive E2 suggests the exclusion of RIN13 from nuclear body. These results showed that SUMOylation affected RIN13 localization, and indirectly influenced its interaction to other proteins and putative function. This paper presents evidence of RIN13 SUMOylation. Furthermore, RIN13 function in pathogenic resistance is shown to be supported by SUMOylation. Thus, this study enhanced the understanding of SUMO in plants and served as reference to molecular studies concerning post-translational modification of SUMO.</p>

scholarly journals Chitin-binding proteins in potato (Solanum tuberosum L.) tuber. Characterization, immunolocalization and effects of wounding

1992 ◽  
Vol 283 (3) ◽  
pp. 813-821 ◽  
Author(s):  
D J Millar ◽  
A K Allen ◽  
C G Smith ◽  
C Sidebottom ◽  
A R Slabas ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Binding Proteins ◽  
Solanum Tuberosum L ◽  
Major Protein ◽  
Post Translational Modification ◽  
Terminal Amino Acid ◽  
Terminal Amino ◽  
Terminal Amino Acid Sequence

Tubers of potato (Solanum tuberosum L.) contain a number of chitin-binding proteins which have possible functions in defence against pathogens. A major protein of the tuber is the chitin-binding lectin which has been further characterized with respect to its antigenicity and N-terminal amino acid sequence. By using an antiserum monospecific for tuber lectin in unwounded potato the protein was found in the cytoplasm and vacuole, unusually for a hydroxyproline-rich glycoprotein, but consistent with its soluble nature in subcellular extracts. Little increased synthesis of the lectin precursor or the post-translationally modified form could be demonstrated in excised potato tuber discs. However, after wounding there is increased synthesis of another hydroxyproline-containing glycoprotein of Mr 57,000, which binds to chitin and shares common epitopes with the lectin. In comparison with the tuber lectin, this novel glycoprotein contains less hydroxyproline, but from its overall composition it is clearly not an underhydroxylated form of the tuber lectin. It differed in its N-terminal amino acid sequence and was much less glycosylated, although arabinose was still present. Synthesis of the Mr-57,000 polypeptide began after the initial burst of protein synthesis and increased, reaching a peak at 24 h after wounding. The protein was produced with its enzymes of post-translational modification, prolyl hydroxylase and arabinosyltransferase, concomitantly with the marker enzymes for wounding, phenylalanine ammonia-lyase and membrane-bound phenol oxidase and peroxidase.

scholarly journals A proteomics approach for the identification of nucleophosmin and heterogeneous nuclear ribonucleoprotein C1/C2 as chromatin-binding proteins in response to DNA double-strand breaks

2005 ◽  
Vol 388 (1) ◽  
pp. 7-15 ◽  
Author(s):  
Seung Yun LEE ◽  
Ji-Hye PARK ◽  
Sungsu KIM ◽  
Eun-Jung PARK ◽  
Yungdae YUN ◽  
...  
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Binding Proteins ◽  
Double Strand Breaks ◽  
Nuclear Proteins ◽  
Chromatin Binding ◽  
Strand Breaks ◽  
Heterogeneous Nuclear Ribonucleoprotein ◽  
Proteomics Approach ◽  
Nuclear Ribonucleoprotein

Double-strand breaks (DSBs) of chromosomal DNA trigger the cellular response that activates the pathways for DNA repair and cell-cycle checkpoints, and sometimes the pathways leading to cell death if the damage is too severe to be tolerated. Evidence indicates that, upon generation of DNA DSBs, many nuclear proteins that are involved in DNA repair and checkpoints are recruited to chromatin around the DNA lesions. In the present study we used a proteomics approach to identify DNA-damage-induced chromatin-binding proteins in a systematic way. Two-dimensional gel analysis for protein extracts of chromatin from DNA-damage-induced and control HeLa cells identified four proteins as the candidates for DNA-damage-induced chromatin-binding proteins. MALDI–TOF (matrix-assisted laser-desorption ionization–time-of-flight) MS analysis identified these proteins to be NPM (nucleophosmin), hnRNP (heterogeneous nuclear ribonucleoprotein) C1, hnRNP C2 and 37-kDa laminin-receptor precursor, and the identity of these proteins was further confirmed by immunoblot analysis with specific antibodies. We then demonstrated with chromatin-binding assays that NPM and hnRNP C1/C2, the abundant nuclear proteins with pleiotropic functions, indeed bind to chromatin in a DNA-damage-dependent manner, implicating these proteins in DNA repair and/or damage response. Immunofluorescence experiments showed that NPM, normally present in the nucleoli, is mobilized into the nucleoplasm after DNA damage, and that neither NPM nor hnRNP C1/C2 is actively recruited to the sites of DNA breaks. These results suggest that NPM and hnRNP C1/C2 may function at the levels of the global context of chromatin, rather than by specifically targeting the broken DNA.

The role of chromatin conformations in diffusional transport of chromatin-binding proteins: Cartesian lattice simulations

2008 ◽  
Vol 128 (15) ◽  
pp. 155101 ◽  
Author(s):  
Annika Wedemeier ◽  
Ting Zhang ◽  
Holger Merlitz ◽  
Chen-Xu Wu ◽  
Jörg Langowski
Keyword(s):  
Binding Proteins ◽  
Chromatin Binding

New insights into the activation of sterol regulatory element-binding proteins by proteolytic processing

2013 ◽  
Vol 4 (4) ◽  
pp. 417-423 ◽  
Author(s):  
Jun Inoue ◽  
Ryuichiro Sato
Keyword(s):  
Endoplasmic Reticulum ◽  
Small Molecules ◽  
Recent Progress ◽  
Binding Proteins ◽  
Regulatory Element ◽  
Acid Synthesis ◽  
Proteolytic Processing ◽  
Endoplasmic Reticulum Membrane ◽  
Post Translational Modification ◽  
Sterol Regulatory Element

AbstractSterol regulatory element-binding proteins (SREBPs) are transcription factors that regulate a wide variety of genes involved in cholesterol and fatty acid synthesis. After transcription, SREBPs are controlled at multiple post-transcriptional levels, including proteolytic processing and post-translational modification. Among these, proteolytic processing is a crucial regulatory step that activates SREBPs, which are synthesized as inactive endoplasmic reticulum membrane proteins. In this review, we focus on recent progress with regard to signaling pathways and small molecules that affect activation of SREBPs by proteolytic processing.

scholarly journals Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains

2017 ◽  
Vol 112 (6) ◽  
pp. 1085-1093 ◽  
Author(s):  
Chris A. Brackley ◽  
Benno Liebchen ◽  
Davide Michieletto ◽  
Francois Mouvet ◽  
Peter R. Cook ◽  
...  
Keyword(s):  
Protein Binding ◽  
Nuclear Bodies ◽  
Chromatin Domains

scholarly journals The dynamics of HMG protein–chromatin interactions in living cellsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 87 (1) ◽  
pp. 127-137 ◽  
Author(s):  
Gabi Gerlitz ◽  
Robert Hock ◽  
Tetsuya Ueda ◽  
Michael Bustin
Keyword(s):  
Binding Sites ◽  
Binding Proteins ◽  
Peer Review Process ◽  
High Mobility ◽  
Structural Features ◽  
Chromatin Binding ◽  
Hmg Proteins ◽  
Chromatin Dynamics ◽  
Chromatin Interactions ◽  
Major Factors

The dynamic interaction between nuclear proteins and chromatin leads to the functional plasticity necessary to mount adequate responses to regulatory signals. Here, we review the factors regulating the chromatin interactions of the high mobility group proteins (HMGs), an abundant and ubiquitous superfamily of chromatin-binding proteins in living cells. HMGs are highly mobile and interact with the chromatin fiber in a highly dynamic fashion, as part of a protein network. The major factors that affect the binding of HMGs to chromatin are operative at the level of the single nucleosome. These factors include structural features of the HMGs, competition with other chromatin-binding proteins for nucleosome binding sites, complex formation with protein partners, and post-translational modifications in the protein or in the chromatin-binding sites. The versatile modulation of the interaction between HMG proteins and chromatin plays a role in processes that establish the cellular phenotype.

scholarly journals Pax8 protein stability is controlled by sumoylation

2008 ◽  
Vol 42 (1) ◽  
pp. 35-46 ◽  
Author(s):  
Tiziana de Cristofaro ◽  
Anna Mascia ◽  
Andrea Pappalardo ◽  
Barbara D'Andrea ◽  
Lucio Nitsch ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Critical Role ◽  
Nuclear Bodies ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Signal Transducers ◽  
Protein Protein Interaction ◽  
Sumo Ligase ◽  
Development And Differentiation ◽  
Substitution Mutant

The transcription factor Pax8 is involved in the morphogenesis of the thyroid gland and in the maintenance of the differentiated thyroid phenotype. Despite the critical role played by Pax8 during thyroid development and differentiation, very little is known of its post-translational modifications and how these modifications may regulate its activity. We focused our attention on the study of a specific post-translational modification, i.e., sumoylation. Sumoylation is a dynamic and reversible process regulating gene expression by altering transcription factor stability, protein–protein interaction and subcellular localization of target proteins. The analysis of Pax8 protein sequence revealed the presence of one sumoylation consensus motif (ψKxE), strongly conserved among mammals, amphibians, and fish. We demonstrated that Pax8 is sumoylated by the addition of a single small ubiquitin-like modifier (SUMO) molecule on its lysine residue 309 and that Pax8K309R, a substitution mutant in which the candidate lysine is replaced with an arginine, is no longer modified by SUMO. In addition, we analyzed whether protein inhibitor of activated signal transducers and activators of transcription (PIASy), a member of the PIAS STAT family of proteins, could function as a SUMO ligase and we demonstrated that indeed PIASy is able to increase the fraction of sumoylated Pax8. Interestingly, we show that Pax8 is targeted in the SUMO nuclear bodies, which are structures that regulate the nucleoplasmic concentration of transcription factors by SUMO trapping. Finally, we report here that the steady-state protein level of Pax8 is controlled by sumoylation.

scholarly journals PARprolink: a photoaffinity probe for identifying poly(ADP-ribose)-binding proteins

2020 ◽  
Author(s):  
Morgan Dasovich ◽  
Morgan Q. Beckett ◽  
Scott Bailey ◽  
Shao-En Ong ◽  
Marc M. Greenberg ◽  
...  
Keyword(s):  
Dna Damage ◽  
Dna Damage Response ◽  
Rna Processing ◽  
Binding Proteins ◽  
Post Translational Modification ◽  
Mobility Shift ◽  
Binding Partners ◽  
Damage Response ◽  
Prostate Cancers ◽  
Electrophoretic Mobility Shift Assays

ABSTRACTPost-translational modification of proteins with poly(ADP-ribose) (PAR) is an important component of the DNA damage response. Four PAR synthesis inhibitors have recently been approved for the treatment of breast, ovarian, and prostate cancers. Despite its clinical significance, a molecular understanding of PAR function, including its binding partners, remains incomplete. In this work, we synthesize a PAR photoaffinity probe that captures and isolates endogenous PAR binders. Our method identified dozens of known PAR-binding proteins and hundreds of novel binders involved in DNA repair, RNA processing, and metabolism. PAR binding by eight candidates was confirmed using pull-down and/or electrophoretic mobility shift assays. Using PAR probes of defined lengths, we detected proteins that preferentially bind to 40-mer over 8-mer PAR, indicating that polymer length may regulate the outcome and timing of PAR signaling pathways. This investigation produces the first census of PAR-binding proteins, provides a proteome-wide view of length-selective PAR binding, and associates PAR binding with RNA metabolism and the formation of biomolecular condensates.

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