The LIM-Only Factor LMO4 Regulates Expression of the BMP7 Gene Through an HDAC2-Dependent Mechanism, and Controls Cell Prolifera
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Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins
International Journal of Molecular Sciences Article Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins M. Quadir Siddiqui 1,† , Maulik D. Badmalia 1,† and Trushar R. Patel 1,2,3,* 1 Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; [email protected] (M.Q.S.); [email protected] (M.D.B.) 2 Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive, Calgary, AB T2N 4N1, Canada 3 Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada * Correspondence: [email protected] † These authors contributed equally to the work. Abstract: Members of the human Zyxin family are LIM domain-containing proteins that perform critical cellular functions and are indispensable for cellular integrity. Despite their importance, not much is known about their structure, functions, interactions and dynamics. To provide insights into these, we used a set of in-silico tools and databases and analyzed their amino acid sequence, phylogeny, post-translational modifications, structure-dynamics, molecular interactions, and func- tions. Our analysis revealed that zyxin members are ohnologs. Presence of a conserved nuclear export signal composed of LxxLxL/LxxxLxL consensus sequence, as well as a possible nuclear localization signal, suggesting that Zyxin family members may have nuclear and cytoplasmic roles. The molecular modeling and structural analysis indicated that Zyxin family LIM domains share Citation: Siddiqui, M.Q.; Badmalia, similarities with transcriptional regulators and have positively charged electrostatic patches, which M.D.; Patel, T.R. -
Signaling Pathway Activities Improve Prognosis for Breast Cancer Yunlong Jiao1,2,3,4, Marta R
bioRxiv preprint doi: https://doi.org/10.1101/132357; this version posted April 29, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Signaling Pathway Activities Improve Prognosis for Breast Cancer Yunlong Jiao1,2,3,4, Marta R. Hidalgo5, Cankut Çubuk6, Alicia Amadoz5, José Carbonell- Caballero5, Jean-Philippe Vert1,2,3,4, and Joaquín Dopazo6,7,8,* 1MINES ParisTech, PSL Research University, Centre for Computational Biology, 77300 Fontainebleau, France; 2Institut Curie, 75248 Paris Cedex, Franc; 3INSERM, U900, 75248 Paris Cedex, France; 4Ecole Normale Supérieure, Department of Mathematics and their Applications, 75005 Paris, France; 5 Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), 46012 Valencia, Spain; 6Clinical Bioinformatics Research Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, 41013, Sevilla, Spain; 7Functional Genomics Node (INB), FPS, Hospital Virgen del Rocío, 41013 Sevilla, Spain; 8 Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, 41013, Sevilla, Spain *To whom correspondence should be addressed. Abstract With the advent of high-throughput technologies for genome-wide expression profiling, a large number of methods have been proposed to discover gene-based signatures as biomarkers to guide cancer prognosis. However, it is often difficult to interpret the list of genes in a prognostic signature regarding the underlying biological processes responsible for disease progression or therapeutic response. A particularly interesting alternative to gene-based biomarkers is mechanistic biomarkers, derived from signaling pathway activities, which are known to play a key role in cancer progression and thus provide more informative insights into cellular functions involved in cancer mechanism. -
Lipid Droplets Protect Human Β Cells from Lipotoxic-Induced Stress and Cell
bioRxiv preprint doi: https://doi.org/10.1101/2021.06.19.449124; this version posted June 20, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Lipid droplets protect human β cells from lipotoxic-induced stress and cell identity changes Xin Tong1 and Roland Stein1,2 1Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 2Corresponding author: [email protected]; Tel: 615-322-7026 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.06.19.449124; this version posted June 20, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract (200 words) Free fatty acids (FFAs) are often stored in lipid droplet (LD) depots for eventual metabolic and/or synthetic use in many cell types, such a muscle, liver, and fat. In pancreatic islets, overt LD accumulation was detected in humans but not mice. LD buildup in islets was principally observed after roughly 11 years of age, increasing throughout adulthood under physiologic conditions, and also enriched in type 2 diabetes. To obtain insight into the role of LDs in human islet β cell function, the levels of a key LD structural protein, perilipin2 (PLIN2), were manipulated by lentiviral-mediated knock-down (KD) or over-expression (OE) in EndoCβH2-Cre cells, a human cell line with adult islet β-like properties. -
Supplementary Table 1
Supplementary Table 1. Large-scale quantitative phosphoproteomic profiling was performed on paired vehicle- and hormone-treated mTAL-enriched suspensions (n=3). A total of 654 unique phosphopeptides corresponding to 374 unique phosphoproteins were identified. The peptide sequence, phosphorylation site(s), and the corresponding protein name, gene symbol, and RefSeq Accession number are reported for each phosphopeptide identified in any one of three experimental pairs. For those 414 phosphopeptides that could be quantified in all three experimental pairs, the mean Hormone:Vehicle abundance ratio and corresponding standard error are also reported. Peptide Sequence column: * = phosphorylated residue Site(s) column: ^ = ambiguously assigned phosphorylation site Log2(H/V) Mean and SE columns: H = hormone-treated, V = vehicle-treated, n/a = peptide not observable in all 3 experimental pairs Sig. column: * = significantly changed Log 2(H/V), p<0.05 Log (H/V) Log (H/V) # Gene Symbol Protein Name Refseq Accession Peptide Sequence Site(s) 2 2 Sig. Mean SE 1 Aak1 AP2-associated protein kinase 1 NP_001166921 VGSLT*PPSS*PK T622^, S626^ 0.24 0.95 PREDICTED: ATP-binding cassette, sub-family A 2 Abca12 (ABC1), member 12 XP_237242 GLVQVLS*FFSQVQQQR S251^ 1.24 2.13 3 Abcc10 multidrug resistance-associated protein 7 NP_001101671 LMT*ELLS*GIRVLK T464, S468 -2.68 2.48 4 Abcf1 ATP-binding cassette sub-family F member 1 NP_001103353 QLSVPAS*DEEDEVPVPVPR S109 n/a n/a 5 Ablim1 actin-binding LIM protein 1 NP_001037859 PGSSIPGS*PGHTIYAK S51 -3.55 1.81 6 Ablim1 actin-binding -
Disparate Binding Kinetics by an Intrinsically Disordered Domain Enables Temporal Regulation of Transcriptional Complex Formation
Disparate binding kinetics by an intrinsically disordered domain enables temporal regulation of transcriptional complex formation Neil O. Robertsona, Ngaio C. Smitha, Athina Manakasa, Mahiar Mahjouba, Gordon McDonaldb, Ann H. Kwana, and Jacqueline M. Matthewsa,1 aSchool of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia; and bCentre for Translational Data Science, University of Sydney, Sydney, NSW 2006 Edited by G. Marius Clore, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, and approved March 26, 2018 (received for review August 18, 2017) Intrinsically disordered regions are highly represented among C-terminal domain (Fig. 1A). LIM domain binding protein 1 mammalian transcription factors, where they often contribute to (LDB1) interacts with all LIM-HD/LMO proteins through a the formation of multiprotein complexes that regulate gene expres- disordered LIM interaction domain (LID) (Fig. 1A), which folds sion. An example of this occurs with LIM-homeodomain (LIM-HD) on binding to LIM1+2 domains to form extended modular com- proteins in the developing spinal cord. The LIM-HD protein LHX3 and plexes (9–11). Competition for LDB1 by LIM-HD/LMO proteins the LIM-HD cofactor LDB1 form a binary complex that gives rise to contributes to a so-called transcriptional “LIM code” that helps interneurons, whereas in adjacent cell populations, LHX3 and LDB1 determine cell fate in the developing spinal cord (12). A binary form a rearranged ternary complex with the LIM-HD protein ISL1, complex comprising LDB1 bound to the LIM-HD protein resulting in motor neurons. The protein–protein interactions within LHX3 triggers differentiation of V2-interneurons (V2-INs) these complexes are mediated by ordered LIM domains in the LIM- (Fig. -
An Evolutionarily Acquired Microrna Shapes Development of Mammalian Cortical Projections
An evolutionarily acquired microRNA shapes development of mammalian cortical projections Jessica L. Diaza,1, Verl B. Siththanandana,1, Victoria Lua,1, Nicole Gonzalez-Navaa, Lincoln Pasquinab,c, Jessica L. MacDonaldb,c,2, Mollie B. Woodworthb,c,d, Abdulkadir Ozkanb,c, Ramesh Naire, Zihuai Hea, Vibhu Sahnib,c,3, Peter Sarnowf, Theo D. Palmera, Jeffrey D. Macklisb,c,4,5, and Suzanne Tharina,g,4,5 aDepartment of Neurosurgery, Stanford University, Stanford, CA 94305; bDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138; cCenter for Brain Science, Harvard University, Cambridge, MA 02138; dDepartment of Ophthalmology, Stanford University, Stanford, CA 94305; eDepartment of Genetics, Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305; fDepartment of Microbiology and Immunology, Stanford University, Stanford, CA 94305; and gDivision of Neurosurgery, Palo Alto Veterans Affairs Health Care System, Palo Alto, CA 94304 Edited by Carla J. Shatz, Stanford University, Stanford, CA, and approved September 29, 2020 (received for review April 8, 2020) The corticospinal tract is unique to mammals and the corpus layers (13). In the mouse, CSMN and a subset of CPN are gen- callosum is unique to placental mammals (eutherians). The emer- erated around embryonic day 13.5 (e13.5), and both reside in the gence of these structures is thought to underpin the evolutionary deep cortical layer V (Fig. 1A). A larger subset of CPN is gener- acquisition of complex motor and cognitive skills. Corticospinal ated around e15.5, and it populates the superficial cortical layer(s) motor neurons (CSMN) and callosal projection neurons (CPN) are II/III (Fig. -
Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in -
81428 LMO4 (D6V4Z) Rabbit Mab
Revision 1 C 0 2 - t LMO4 (D6V4Z) Rabbit mAb a e r o t S Orders: 877-616-CELL (2355) [email protected] 8 Support: 877-678-TECH (8324) 2 4 Web: [email protected] 1 www.cellsignal.com 8 # 3 Trask Lane Danvers Massachusetts 01923 USA For Research Use Only. Not For Use In Diagnostic Procedures. Applications: Reactivity: Sensitivity: MW (kDa): Source/Isotype: UniProt ID: Entrez-Gene Id: WB H M Endogenous 16 Rabbit IgG P61968 8543 Product Usage Information Application Dilution Western Blotting 1:1000 Storage Supplied in 10 mM sodium HEPES (pH 7.5), 150 mM NaCl, 100 µg/ml BSA, 50% glycerol and less than 0.02% sodium azide. Store at –20°C. Do not aliquot the antibody. Specificity / Sensitivity LMO4 (D6V4Z) Rabbit mAb recognizes endogenous levels of total LMO4 protein. Species Reactivity: Human, Mouse Species predicted to react based on 100% sequence homology: Rat Source / Purification Monoclonal antibody is produced by immunizing animals with a synthetic peptide corresponding to residues near the carboxy terminus of human LMO4 protein. Background LMO4 is a LIM zinc-binding domain-containing protein. LMO4 cDNA was first isolated from a breast tumor cDNA library (1). This transcriptional modulator is overexpressed in several epithelial cancers such as prostate, pancreas, and breast (2-4). LMO4 exhibits pro-oncogenic activities by inducing centrosome amplification and mitotic spindle abnormalities (5). LMO4 is also expressed in the brain, in regions involved in learning and the regulation of motivated behavior. In the basolateral amygdala, LMO4 functions to negatively regulate fear learning (6). Furthermore, in the nucleus accumbens, LMO4 was found to regulate the behavioral effects of cocaine (7). -
Spatial and Temporal Aspects of Signalling 6 1
r r r Cell Signalling Biology Michael J. Berridge Module 6 Spatial and Temporal Aspects of Signalling 6 1 Module 6 Spatial and Temporal Aspects of Signalling Synopsis The function and efficiency of cell signalling pathways are very dependent on their organization both in space and time. With regard to spatial organization, signalling components are highly organized with respect to their cellular location and how they transmit information from one region of the cell to another. This spatial organization of signalling pathways depends on the molecular interactions that occur between signalling components that use signal transduction domains to construct signalling pathways. Very often, the components responsible for information transfer mechanisms are held in place by being attached to scaffolding proteins to form macromolecular signalling complexes. Sometimes these macromolecular complexes can be organized further by being localized to specific regions of the cell, as found in lipid rafts and caveolae or in the T-tubule regions of skeletal and cardiac cells. Another feature of the spatial aspects concerns the local Another important temporal aspect is timing and signal and global aspects of signalling. The spatial organization of integration, which relates to the way in which functional signalling molecules mentioned above can lead to highly interactions between signalling pathways are determined localized signalling events, but when the signalling mo- by both the order and the timing of their presentations. lecules are more evenly distributed, signals can spread The organization of signalling systems in both time and more globally throughout the cell. In addition, signals space greatly enhances both their efficiency and versatility. -
University of Birmingham Germline RBBP8 Variants Associated With
University of Birmingham Germline RBBP8 variants associated with early- onset breast cancer compromise replication fork stability The COMPLEXO Network DOI: 10.1172/JCI127521 License: None: All rights reserved Document Version Peer reviewed version Citation for published version (Harvard): The COMPLEXO Network 2020, 'Germline RBBP8 variants associated with early-onset breast cancer compromise replication fork stability', Journal of Clinical Investigation, vol. 130, no. 8, pp. 4069-4080. https://doi.org/10.1172/JCI127521 Link to publication on Research at Birmingham portal Publisher Rights Statement: https://doi.org/10.1172/JCI127521. Copyright © 2020, American Society for Clinical Investigation General rights Unless a licence is specified above, all rights (including copyright and moral rights) in this document are retained by the authors and/or the copyright holders. The express permission of the copyright holder must be obtained for any use of this material other than for purposes permitted by law. •Users may freely distribute the URL that is used to identify this publication. •Users may download and/or print one copy of the publication from the University of Birmingham research portal for the purpose of private study or non-commercial research. •User may use extracts from the document in line with the concept of ‘fair dealing’ under the Copyright, Designs and Patents Act 1988 (?) •Users may not further distribute the material nor use it for the purposes of commercial gain. Where a licence is displayed above, please note the terms and conditions of the licence govern your use of this document. When citing, please reference the published version. Take down policy While the University of Birmingham exercises care and attention in making items available there are rare occasions when an item has been uploaded in error or has been deemed to be commercially or otherwise sensitive. -
Actin Bundling Via LIM Domains
[Plant Signaling & Behavior 3:5, 320-321; May 2008]; ©2008 Landes Bioscience Article Addendum Actin bundling via LIM domains Clément Thomas,* Monika Dieterle, Sabrina Gatti, Céline Hoffmann, Flora Moreau, Jessica Papuga and André Steinmetz Centre de Recherche Public-Santé; Val Fleuri 84; L-1526; Luxembourg Key words: Actin-binding proteins, actin-bundling, cysteine-rich proteins, cytoskeleton, LIM domain. The LIM domain is defined as a protein-protein interaction module involved in the regulation of diverse cellular processes including gene expression and cytoskeleton organization. We distribute. have recently shown that the tobacco WLIM1, a two LIM domain-containing protein, is able to bind to, stabilize and bundle actin filaments, suggesting that it participates to the regulation of actin cytoskeleton structure and dynamics. In the December issue of the Journal of Biological Chemistry we report a domain analysis not that specifically ascribes the actin-related activities of WLIM1 to its two LIM domains. Results suggest that LIM domains func- Figure 1. Domain maps for wild-type WLIM1 (A) and GFP-fused chimeric tion synergistically in the full-length protein to achieve optimal 3xWLIM1 (B). A. WLIM1 basically comprises a short N-terminal domain (Nt), two LIM domains (LIM1Do and LIM2), an interLIM spacer (IL) and a C-terminal activities. Here we briefly summarize relevant data regarding the domain (Ct). B. 3xWLIM1 consists of three tandem WLIM1 copies. This chi- actin-related properties/functions of two LIM domain-containing meric protein has been fused in C-terminus to GFP and transiently expressed proteins in plants and animals. In addition, we provide further in tobacco BY2 cells. -
Early Evolution of the LIM Homeobox Gene Family
Srivastava et al. BMC Biology 2010, 8:4 http://www.biomedcentral.com/1741-7007/8/4 RESEARCH ARTICLE Open Access Early evolution of the LIM homeobox gene family Mansi Srivastava1*, Claire Larroux2, Daniel R Lu1, Kareshma Mohanty1, Jarrod Chapman3, Bernard M Degnan2, Daniel S Rokhsar1,3 Abstract Background: LIM homeobox (Lhx) transcription factors are unique to the animal lineage and have patterning roles during embryonic development in flies, nematodes and vertebrates, with a conserved role in specifying neuronal identity. Though genes of this family have been reported in a sponge and a cnidarian, the expression patterns and functions of the Lhx family during development in non-bilaterian phyla are not known. Results: We identified Lhx genes in two cnidarians and a placozoan and report the expression of Lhx genes during embryonic development in Nematostella and the demosponge Amphimedon. Members of the six major LIM homeobox subfamilies are represented in the genomes of the starlet sea anemone, Nematostella vectensis, and the placozoan Trichoplax adhaerens. The hydrozoan cnidarian, Hydra magnipapillata, has retained four of the six Lhx subfamilies, but apparently lost two others. Only three subfamilies are represented in the haplosclerid demosponge Amphimedon queenslandica. A tandem cluster of three Lhx genes of different subfamilies and a gene containing two LIM domains in the genome of T. adhaerens (an animal without any neurons) indicates that Lhx subfamilies were generated by tandem duplication. This tandem cluster in Trichoplax is likely a remnant of the original chromosomal context in which Lhx subfamilies first appeared. Three of the six Trichoplax Lhx genes are expressed in animals in laboratory culture, as are all Lhx genes in Hydra.