1
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Osman A, Lindén M, Österlund T, Vannas C, Andersson L, Escobar M, Ståhlberg A, Åman P. Identification of genomic binding sites and direct target genes for the transcription factor DDIT3/CHOP. Exp Cell Res 2023; 422:113418. [PMID: 36402425 DOI: 10.1016/j.yexcr.2022.113418] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 11/03/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022]
Abstract
DDIT3 is a tightly regulated basic leucine zipper (bZIP) transcription factor and key regulator in cellular stress responses. It is involved in a variety of pathological conditions and may cause cell cycle block and apoptosis. It is also implicated in differentiation of some specialized cell types and as an oncogene in several types of cancer. DDIT3 was originally believed to act as a dominant-negative inhibitor by forming heterodimers with other bZIP transcription factors, preventing their DNA binding and transactivating functions. DDIT3 has, however, been reported to bind DNA and regulate target genes. Here, we employed ChIP sequencing combined with microarray-based expression analysis to identify direct binding motifs and target genes of DDIT3. The results reveal DDIT3 binding to motifs similar to other bZIP transcription factors, known to form heterodimers with DDIT3. Binding to a class III satellite DNA repeat sequence was also detected. DDIT3 acted as a DNA-binding transcription factor and bound mainly to the promotor region of regulated genes. ChIP sequencing analysis of histone H3K27 methylation and acetylation showed a strong overlap between H3K27-acetylated marks and DDIT3 binding. These results support a role for DDIT3 as a transcriptional regulator of H3K27ac-marked genes in transcriptionally active chromatin.
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Affiliation(s)
- Ayman Osman
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Malin Lindén
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tobias Österlund
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Christoffer Vannas
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lisa Andersson
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Mandy Escobar
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Pierre Åman
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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2
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Short Linear Motifs in Colorectal Cancer Interactome and Tumorigenesis. Cells 2022; 11:cells11233739. [PMID: 36496998 PMCID: PMC9737320 DOI: 10.3390/cells11233739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/16/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Colorectal tumorigenesis is driven by alterations in genes and proteins responsible for cancer initiation, progression, and invasion. This multistage process is based on a dense network of protein-protein interactions (PPIs) that become dysregulated as a result of changes in various cell signaling effectors. PPIs in signaling and regulatory networks are known to be mediated by short linear motifs (SLiMs), which are conserved contiguous regions of 3-10 amino acids within interacting protein domains. SLiMs are the minimum sequences required for modulating cellular PPI networks. Thus, several in silico approaches have been developed to predict and analyze SLiM-mediated PPIs. In this review, we focus on emerging evidence supporting a crucial role for SLiMs in driver pathways that are disrupted in colorectal cancer (CRC) tumorigenesis and related PPI network alterations. As a result, SLiMs, along with short peptides, are attracting the interest of researchers to devise small molecules amenable to be used as novel anti-CRC targeted therapies. Overall, the characterization of SLiMs mediating crucial PPIs in CRC may foster the development of more specific combined pharmacological approaches.
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3
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Alves de Souza SM, de Araújo TS, Ferretti GDDS, Kalume DE, Cordeiro Y, Almeida MDS, de Souza TLF. Novel Method for the Production, Purification, and Characterization of Recombinant Lunasin: Identification of Disulfide Cross-Linked Dimers. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10466-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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4
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Davis RB, Kaur T, Moosa MM, Banerjee PR. FUS oncofusion protein condensates recruit mSWI/SNF chromatin remodeler via heterotypic interactions between prion-like domains. Protein Sci 2021; 30:1454-1466. [PMID: 34018649 PMCID: PMC8197437 DOI: 10.1002/pro.4127] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 12/19/2022]
Abstract
Fusion transcription factors generated by genomic translocations are common drivers of several types of cancers including sarcomas and leukemias. Oncofusions of the FET (FUS, EWSR1, and TAF15) family proteins result from the fusion of the prion-like domain (PLD) of FET proteins to the DNA-binding domain (DBD) of certain transcription regulators and are implicated in aberrant transcriptional programs through interactions with chromatin remodelers. Here, we show that FUS-DDIT3, a FET oncofusion protein, undergoes PLD-mediated phase separation into liquid-like condensates. Nuclear FUS-DDIT3 condensates can recruit essential components of the global transcriptional machinery such as the chromatin remodeler SWI/SNF. The recruitment of mammalian SWI/SNF (mSWI/SNF) is driven by heterotypic PLD-PLD interactions between FUS-DDIT3 and core subunits of SWI/SNF, such as the catalytic component BRG1. Further experiments with single-molecule correlative force-fluorescence microscopy support a model wherein the fusion protein forms condensates on DNA surface and enrich BRG1 to activate transcription by ectopic chromatin remodeling. Similar PLD-driven co-condensation of mSWI/SNF with transcription factors can be employed by other oncogenic fusion proteins with a generic PLD-DBD domain architecture for global transcriptional reprogramming.
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Affiliation(s)
- Richoo B. Davis
- Department of PhysicsUniversity at BuffaloBuffaloNew YorkUSA
| | - Taranpreet Kaur
- Department of PhysicsUniversity at BuffaloBuffaloNew YorkUSA
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5
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Canales Á, Rösinger M, Sastre J, Felli IC, Jiménez-Barbero J, Giménez-Gallego G, Fernández-Tornero C. Hidden α-helical propensity segments within disordered regions of the transcriptional activator CHOP. PLoS One 2017; 12:e0189171. [PMID: 29211802 PMCID: PMC5718554 DOI: 10.1371/journal.pone.0189171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/20/2017] [Indexed: 11/18/2022] Open
Abstract
C/EBP-homologous protein (CHOP) is a key determinant of the apoptotic response to endoplasmic reticulum stress or DNA damage. As a member of the C/EBP family, CHOP contains a low complexity N-terminal region involved in transcriptional activation, followed by a bZIP that binds DNA after dimerization. However, in contrast to other C/EBPs, CHOP directs binding to non-canonical C/EBP sites due to unique substitutions in its DNA-binding domain. Herein, we show that the N-terminal region of CHOP is intrinsically unstructured but contains two segments presenting α-helical propensity. One of these segments is conserved in other C/EBPs and mediates essential roles of CHOP, including regulation through phosphorylation. The second segment is placed within a proteolytic-resistant portion of the protein and exhibits reduced flexibility. Moreover, the DNA-binding region of CHOP also contains a segment with α-helical character towards its most N-terminal part. Our results suggest that structure-prone segments scattered within disordered regions may be critical for macromolecular recognition during CHOP-mediated transcriptional activation.
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Affiliation(s)
- Ángeles Canales
- Departamento de Química Orgánica I, Universidad Complutense de Madrid, Madrid, Spain
- * E-mail: (CFT); (AC)
| | | | - Javier Sastre
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Isabella C. Felli
- Magnetic Resonance Center & Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
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Na I, Meng F, Kurgan L, Uversky VN. Autophagy-related intrinsically disordered proteins in intra-nuclear compartments. MOLECULAR BIOSYSTEMS 2017; 12:2798-817. [PMID: 27377881 DOI: 10.1039/c6mb00069j] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Recent analyses indicated that autophagy can be regulated via some nuclear transcriptional networks and many important players in the autophagy and other forms of programmed cell death are known to be intrinsically disordered. To this end, we analyzed similarities and differences in the intrinsic disorder distribution of nuclear and non-nuclear proteins related to autophagy. We also looked at the peculiarities of the distribution of the intrinsically disordered autophagy-related proteins in various intra-nuclear organelles, such as the nucleolus, chromatin, Cajal bodies, nuclear speckles, promyelocytic leukemia (PML) nuclear bodies, nuclear lamina, nuclear pores, and perinucleolar compartment. This analysis revealed that the autophagy-related proteins constitute about 2.5% of the non-nuclear proteins and 3.3% of the nuclear proteins, which corresponds to a substantial enrichment by about 32% in the nucleus. Curiously, although, in general, the autophagy-related proteins share similar characteristics of disorder with a generic set of all non-nuclear proteins, chromatin and nuclear speckles are enriched in the intrinsically disordered autophagy proteins (29 and 37% of these proteins are disordered, respectively) and have high disorder content at 0.24 and 0.27, respectively. Therefore, our data suggest that some of the nuclear disordered proteins may play important roles in autophagy.
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Affiliation(s)
- Insung Na
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Fanchi Meng
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23219, USA.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA. and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA and Biology Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia and Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
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7
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Killoran RC, Sowole MA, Halim MA, Konermann L, Choy WY. Conformational characterization of the intrinsically disordered protein Chibby: Interplay between structural elements in target recognition. Protein Sci 2016; 25:1420-9. [PMID: 27082063 DOI: 10.1002/pro.2936] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 04/09/2016] [Accepted: 04/11/2016] [Indexed: 11/12/2022]
Abstract
The protein Chibby (Cby) is an antagonist of the Wnt signaling pathway, where it inhibits the binding between the transcriptional coactivator β-catenin and the Tcf/Lef transcription factors. The 126 residue Cby is partially disordered; its N-terminal half is unstructured while its C-terminal half comprises a coiled-coil domain. Previous structural analyses of Cby using NMR spectroscopy suffered from severe line broadening for residues within the protein's C-terminal half, hindering detailed characterization of the coiled-coil domain. Here, we use hydrogen/deuterium exchange-mass spectrometry (HDX-MS) to examine Cby's C-terminal half. Results reveal that Cby is divided into three structural elements: a disordered N-terminal half, a coiled-coil domain, and a C-terminal unstructured extension consisting of the last ∼ 25 residues (which we term C-terminal extension). A series of truncation constructs were designed to assess the roles of individual structural elements in protein stability and Cby binding to TC-1, a positive regulator of the Wnt signaling pathway. CD and NMR data show that Cby maintains coiled-coil structure upon deletion of either disordered region. NMR and ITC binding experiments between Cby and TC-1 illustrate that the interaction is retained upon deletion of either Cby's N-terminal half or its C-terminal extension. Intriguingly, Cby's C-terminal half alone binds to TC-1 with significantly greater affinity compared to full-length Cby, implying that target binding of the coiled-coil domain is affected by the flanking disordered regions.
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Affiliation(s)
- Ryan C Killoran
- Department of Biochemistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Modupeola A Sowole
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Mohammad A Halim
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Lars Konermann
- Department of Biochemistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada.,Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada.,Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
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8
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Structural biology of intrinsically disordered proteins: Revisiting unsolved mysteries. Biochimie 2016; 125:112-8. [PMID: 27004461 DOI: 10.1016/j.biochi.2016.03.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/17/2016] [Indexed: 01/30/2023]
Abstract
The emergence of intrinsically disordered proteins (IDPs) has challenged the classical protein structure-function paradigm by introducing a new paradigm of "coupled binding and folding". This paradigm suggests that IDPs fold upon binding to their partners. Further studies, however, revealed a novel and previously unrecognized phenomenon of "uncoupled binding and folding" suggesting that IDPs do not necessarily fold upon interaction with their lipid and protein partners. The complex and often unusual biophysics of IDPs makes structural characterization of these proteins and their complexes not only challenging but often resulting in opposite conclusions. For this reason, some crucial questions in this field remain unsolved for well over a decade. Considering an important role of IDPs in cellular regulation, signaling and control in health and disease, more efforts are needed to solve these mysteries. Here, I focus on two long-standing contradictions in the literature concerning dimerization and membrane-binding activities of IDPs. Molecular explanation of these discrepancies is provided. I also demonstrate how resolution of these critical issues in the field of IDPs results in our expanded understanding of cell function and has multiple applications in biology and medicine.
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9
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Sigalov AB. Unusual biophysics of immune signaling-related intrinsically disordered proteins. SELF NONSELF 2014; 1:271-281. [PMID: 21487502 DOI: 10.4161/self.1.4.13641] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 09/15/2010] [Accepted: 09/15/2010] [Indexed: 11/19/2022]
Abstract
Intrinsically disordered (ID) regions, the regions that lack a well-defined three-dimensional structure under physiological conditions, are preferentially located in the cytoplasmic segments of plasma membrane proteins, many of which are known to be involved in cell signaling. This is in line with our studies that demonstrated that cytoplasmic domains of signaling subunits of immune receptors, including those of ζ, CD3ε, CD3δ and CD3γ chains of T cell receptor, Igα and Igβ chains of B cell receptor as well as the Fc receptor γ chain represent a novel class of ID proteins (IDPs). The domains all have one or more copies of an immunoreceptor tyrosine-based activation motif, tyrosine residues of which are phosphorylated upon receptor engagement in an early and obligatory event in the signaling cascade. Our studies of these IDPs revealed several unusual biophysical phenomena, including (1) the specific dimerization of disordered protein molecules, (2) the fast and slow dimerization equilibrium, depending on the protein, (3) no disorder-to-order transition and the lack of significant chemical shift and peak intensity changes upon dimerization or interaction with a well-folded partner protein and (4) the dual mode of binding to model membranes (with and without folding), depending on the lipid bilayer stability. Here, I highlight several of these studies that not only facilitate a rethinking process of the fundamental paradigms in protein biophysics but also open new perspectives on the molecular mechanisms involved in receptor signaling.
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10
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Homodimerization propensity of the intrinsically disordered N-terminal domain of Ultraspiracle from Aedes aegypti. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1153-66. [PMID: 24704038 DOI: 10.1016/j.bbapap.2014.03.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 03/21/2014] [Accepted: 03/25/2014] [Indexed: 11/20/2022]
Abstract
The mosquito Aedes aegypti is the principal vector of dengue, one of the most devastating arthropod-borne viral infections in humans. The isoform specific A/B region, called the N-terminal domain (NTD), is hypervariable in sequence and length and is poorly conserved within the Ultraspiracle (Usp) family. The Usp protein together with ecdysteroid receptor (EcR) forms a heterodimeric complex. Up until now, there has been little data on the molecular properties of the isolated Usp-NTD. Here, we describe the biochemical and biophysical properties of the recombinant NTD of the Usp isoform B (aaUsp-NTD) from A. aegypti. These results, in combination with in silico bioinformatics approaches, indicate that aaUsp-NTD exhibits properties of an intrinsically disordered protein (IDP). We also present the first experimental evidence describing the dimerization propensity of the isolated NTD of Usp. These characteristics also appear for other members of the Usp family in different species, for example, in the Usp-NTD from Drosophila melanogaster and Bombyx mori. However, aaUsp-NTD exhibits the strongest homodimerization potential. We postulate that the unique dimerization of the NTD might be important for Usp function by providing an additional platform for interactions, in addition to the nuclear receptor superfamily dimerization via DNA binding domains and ligand binding domains that has already been extensively documented. Furthermore, the unique NTD-NTD interaction that was observed might contribute new insight into the dimerization propensities of nuclear receptors.
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11
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Rydberg J, Baltzer L, Sarojini V. Intrinsically unstructured proteins by design-electrostatic interactions can control binding, folding, and function of a helix-loop-helix heterodimer. J Pept Sci 2013; 19:461-9. [PMID: 23813758 DOI: 10.1002/psc.2520] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 04/16/2013] [Accepted: 04/19/2013] [Indexed: 11/10/2022]
Abstract
Intrinsically disordered proteins that exist as unordered monomeric structures in aqueous solution at pH 7 but fold into four-helix bundles upon binding to recognized polypeptide targets have been designed. NMR and CD spectra of the monomeric polypeptides show the hallmarks of unordered structures, whereas in the bound state they are highly helical. Analytical ultracentrifugation data shows that the polypeptides bind to their targets to form exclusively heterodimers at neutral pH. To demonstrate the relationship between binding, folding, and function, a catalytic site for ester hydrolysis was introduced into an unordered and largely inactive monomer, but that was structured and catalytically active in the presence of a specific polypeptide target. Electrostatic interactions between surface-exposed residues inhibited the binding and folding of the monomers at pH 7. Charge-charge repulsion between ionizable amino acids was thus found to be sufficient to disrupt binding between polypeptide chains despite their inherent propensities for structure formation and may be involved in the folding and function of inherently disordered proteins in biology.
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Affiliation(s)
- Johan Rydberg
- Department of Chemistry-IFM, Linköping University, 581 83, Linköping, Sweden
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12
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Jauhiainen A, Thomsen C, Strömbom L, Grundevik P, Andersson C, Danielsson A, Andersson MK, Nerman O, Rörkvist L, Ståhlberg A, Åman P. Distinct cytoplasmic and nuclear functions of the stress induced protein DDIT3/CHOP/GADD153. PLoS One 2012; 7:e33208. [PMID: 22496745 PMCID: PMC3322118 DOI: 10.1371/journal.pone.0033208] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 02/10/2012] [Indexed: 11/29/2022] Open
Abstract
DDIT3, also known as GADD153 or CHOP, encodes a basic leucine zipper transcription factor of the dimer forming C/EBP family. DDIT3 is known as a key regulator of cellular stress response, but its target genes and functions are not well characterized. Here, we applied a genome wide microarray based expression analysis to identify DDIT3 target genes and functions. By analyzing cells carrying tamoxifen inducible DDIT3 expression constructs we show distinct gene expression profiles for cells with cytoplasmic and nuclear localized DDIT3. Of 175 target genes identified only 3 were regulated by DDIT3 in both cellular localizations. More than two thirds of the genes were downregulated, supporting a role for DDIT3 as a dominant negative factor that could act by either cytoplasmic or nuclear sequestration of dimer forming transcription factor partners. Functional annotation of target genes showed cell migration, proliferation and apoptosis/survival as the most affected categories. Cytoplasmic DDIT3 affected more migration associated genes, while nuclear DDIT3 regulated more cell cycle controlling genes. Cell culture experiments confirmed that cytoplasmic DDIT3 inhibited migration, while nuclear DDIT3 caused a G1 cell cycle arrest. Promoters of target genes showed no common sequence motifs, reflecting that DDIT3 forms heterodimers with several alternative transcription factors that bind to different motifs. We conclude that expression of cytoplasmic DDIT3 regulated 94 genes. Nuclear translocation of DDIT3 regulated 81 additional genes linked to functions already affected by cytoplasmic DDIT3. Characterization of DDIT3 regulated functions helps understanding its role in stress response and involvement in cancer and degenerative disorders.
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Affiliation(s)
- Alexandra Jauhiainen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Christer Thomsen
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Linda Strömbom
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Pernilla Grundevik
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Carola Andersson
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Anna Danielsson
- Department of Oncology, Institute of Clinical Sciences, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Mattias K. Andersson
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Olle Nerman
- Department of Mathematical Statistics, Chalmers University of Technology, Gothenburg, Sweden
- Department of Mathematical Statistics, University of Gothenburg, Gothenburg, Sweden
| | - Linda Rörkvist
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Pierre Åman
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
- * E-mail:
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13
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Singh VK, Rahman MN, Munro K, Uversky VN, Smith SP, Jia Z. Free cysteine modulates the conformation of human C/EBP homologous protein. PLoS One 2012; 7:e34680. [PMID: 22496840 PMCID: PMC3319616 DOI: 10.1371/journal.pone.0034680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 03/08/2012] [Indexed: 01/01/2023] Open
Abstract
The C/EBP Homologous Protein (CHOP) is a nuclear protein that is integral to the unfolded protein response culminating from endoplasmic reticulum stress. Previously, CHOP was shown to comprise extensive disordered regions and to self-associate in solution. In the current study, the intrinsically disordered nature of this protein was characterized further by comprehensive in silico analyses. Using circular dichroism, differential scanning calorimetry and nuclear magnetic resonance, we investigated the global conformation and secondary structure of CHOP and demonstrated, for the first time, that conformational changes in this protein can be induced by the free amino acid L-cysteine. Addition of L-cysteine caused a significant dose-dependent decrease in the protein helicity--dropping from 69.1% to 23.8% in the presence of 1 mM of L-cysteine--and a sequential transition to a more disordered state, unlike that caused by thermal denaturation. Furthermore, the presence of small amounts of free amino acid (80 µM, an 8:1 cysteine∶CHOP ratio) during CHOP thermal denaturation altered the molecular mechanism of its melting process, leading to a complex, multi-step transition. On the other hand, high levels (4 mM) of free L-cysteine seemed to cause a complete loss of rigid cooperatively melting structure. These results suggested a potential regulatory function of L-cysteine which may lead to changes in global conformation of CHOP in response to the cellular redox state and/or endoplasmic reticulum stress.
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Affiliation(s)
- Vinay K. Singh
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Mona N. Rahman
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Kim Munro
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Vladimir N. Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, Florida, United States of America
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Steven P. Smith
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
- * E-mail:
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14
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Aguado-Llera D, Bacarizo J, Gregorio-Teruel L, Taberner FJ, Cámara-Artigas A, Neira JL. Biophysical characterization of the isolated C-terminal region of the transient receptor potential vanilloid 1. FEBS Lett 2012; 586:1154-9. [DOI: 10.1016/j.febslet.2012.03.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 03/14/2012] [Accepted: 03/14/2012] [Indexed: 11/28/2022]
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15
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Sandri-Goldin RM. The many roles of the highly interactive HSV protein ICP27, a key regulator of infection. Future Microbiol 2012; 6:1261-77. [PMID: 22082288 DOI: 10.2217/fmb.11.119] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Human herpes viruses cause an array of illnesses ranging from cancers for Epstein?Barr virus and Kaposi?s sarcoma-associated herpes virus, to painful skin lesions, and more rarely, keratitis and encephalitis for HSV. All herpes viruses encode a multifunctional protein, typified by HSV ICP27, which plays essential roles in viral infection. ICP27 functions in all stages of mRNA biogenesis from transcription, RNA processing and export through to translation. ICP27 has also been implicated in nuclear protein quality control, cell cycle control, activation of stress signaling pathways and prevention of apoptosis. ICP27 interacts with many proteins and it binds RNA. This article focuses on how ICP27 performs its many roles and highlights similarities with its homologs, which could be targets for antiviral intervention.
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Affiliation(s)
- Rozanne M Sandri-Goldin
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA 92697, USA.
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Sigalov AB. Interplay Between Protein Order, Disorder and Oligomericity in Receptor Signaling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 725:50-73. [DOI: 10.1007/978-1-4614-0659-4_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Sigalov AB. Uncoupled binding and folding of immune signaling-related intrinsically disordered proteins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2011; 106:525-36. [DOI: 10.1016/j.pbiomolbio.2011.08.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 08/10/2011] [Indexed: 10/17/2022]
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Mokhtarzada S, Yu C, Brickenden A, Choy WY. Structural characterization of partially disordered human Chibby: insights into its function in the Wnt-signaling pathway. Biochemistry 2011; 50:715-26. [PMID: 21182262 PMCID: PMC3031990 DOI: 10.1021/bi101236z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
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The Wnt/β-catenin signaling pathway is critical to embryonic development as well as adult tissue regeneration. Dysregulation of this pathway can lead to a variety of human diseases, in particular cancers. Chibby (Cby), a small and highly conserved protein, plays an antagonistic role in Wnt signaling by inhibiting the binding of β-catenin to Tcf/Lef family proteins, a protein interaction that is essential for the transcriptional activation of Wnt target genes. Cby is also involved in regulating intracellular distribution of β-catenin. Phosphorylated Cby forms a ternary complex with 14-3-3 protein and β-catenin, facilitating the export of β-catenin from the nucleus. On the other hand, the antagonistic function of Cby is inhibited upon binding to thyroid cancer-1 (TC-1). To dissect the structure−function relationship of Cby, we have used NMR spectroscopy, ESI-MS, CD, and DLS to extensively characterize the structure of human Cby. Our results show that the 126-residue Cby is partially disordered under nondenaturing conditions. While the N-terminal portion of the protein is predominantly unstructured in solution, the C-terminal half of Cby adopts a coiled-coil structure through self-association. Initial data for the binding studies of Cby to 14-3-3ζ (one of the isoforms in the 14-3-3 family) and TC-1 via these two distinct structural modules have also been obtained. It is noteworthy that in a recent large-scale analysis of the intrinsically disordered proteome of mouse, a substantial number of disordered proteins are predicted to have coiled-coil motif presence in their sequences. The combination of these two molecular recognition features could facilitate disordered Cby in assembling protein complexes via different modes of interaction.
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Affiliation(s)
- Sulayman Mokhtarzada
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada N6A 5C1
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Sigalov AB. The SCHOOL of nature: II. Protein order, disorder and oligomericity in transmembrane signaling. SELF/NONSELF 2010; 1:89-102. [PMID: 21487511 PMCID: PMC3065667 DOI: 10.4161/self.1.2.11590] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 02/20/2010] [Accepted: 02/22/2010] [Indexed: 11/19/2022]
Abstract
Recent reports have revealed that many proteins that do not adopt globular structures under native conditions, thus termed intrinsically disordered proteins (IDPs), are involved in cell signaling. Intriguingly, physiologically relevant oligomerization of IDPs has been recently observed and shown to exhibit unique biophysical characteristics, including the lack of significant changes in chemical shift and peak intensity upon binding. In this work, I summarize several distinct features of protein disorder that are especially important as related to receptor-mediated transmembrane signal transduction. I also hypothesize that interactions of IDPs with their protein or lipid partners represent a general biphasic process with the "no disorder-to-order" fast interaction which, depending on the interacting partner, may or may not be accompanied by the slow formation of a secondary structure. Further, I suggest signaling-related functional connections between protein order, disorder, and oligomericity and hypothesize that receptor oligomerization induced or tuned upon ligand binding outside the cell is translated across the membrane into protein oligomerization inside the cell, thus providing a general platform, the Signaling Chain HOmoOLigomerization (SCHOOL) platform, for receptor-mediated signaling. This structures our current multidisciplinary knowledge and views of the mechanisms governing the coupling of recognition to signal transduction and cell response. Importantly, this approach not only reveals previously unrecognized striking similarities in the basic mechanistic principles of function of numerous functionally diverse and unrelated surface membrane receptors, but also suggests the similarity between therapeutic targets, thus opening new horizons for both fundamental and clinically relevant studies.
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Sigalov AB. Protein intrinsic disorder and oligomericity in cell signaling. ACTA ACUST UNITED AC 2010; 6:451-61. [DOI: 10.1039/b916030m] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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