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Liang J, Cai D. Membrane-less compartments in the nucleus: Separated or connected phases? Curr Opin Cell Biol 2023; 84:102215. [PMID: 37574634 PMCID: PMC10528681 DOI: 10.1016/j.ceb.2023.102215] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023]
Abstract
In recent years, it has become increasingly clear that many nuclear membrane-less compartments have liquid-like properties and may form through the physicochemical process of phase separation. In this review, we will first discuss how various nuclear compartments, such as the genome, transcription compartments, and nuclear bodies are formed through phase separation. Then, we propose that inter-compartmental communications can also be prevalent and may be mediated by inter-compartmental diffusion of macromolecules, fusion among different compartments, and transient or stable contacts among nuclear compartments. Understanding how nuclear compartments communicate with each other represents an exciting new area of research and may reveal important insights about cellular functions and uncover previously under-appreciated disease mechanisms.
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Affiliation(s)
- Jindayi Liang
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Danfeng Cai
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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2
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Chen IT, Chen HC, Lo YH, Lai PY, Hsieh FY, Wu YH, Shih HM, Lai MZ. Promyelocytic leukemia protein targets MK2 to promote cytotoxicity. EMBO Rep 2021; 22:e52254. [PMID: 34633746 PMCID: PMC8647022 DOI: 10.15252/embr.202052254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 09/19/2021] [Accepted: 09/27/2021] [Indexed: 11/09/2022] Open
Abstract
Promyelocytic leukemia protein (PML) is a tumor suppressor possessing multiple modes of action, including induction of apoptosis. We unexpectedly find that PML promotes necroptosis in addition to apoptosis, with Pml-/- macrophages being more resistant to TNF-mediated necroptosis than wild-type counterparts and PML-deficient mice displaying resistance to TNF-induced systemic inflammatory response syndrome. Reduced necroptosis in PML-deficient cells is associated with attenuated receptor-interacting protein kinase 1 (RIPK1) activation, as revealed by reduced RIPK1[S166] phosphorylation, and attenuated RIPK1-RIPK3-MLKL necrosome complex formation. We show that PML deficiency leads to enhanced TNF-induced MAPK-activated kinase 2 (MK2) activation and elevated RIPK1[S321] phosphorylation, which suppresses necrosome formation. MK2 inhibitor treatment or MK2 knockout abrogates resistance to cell death induction in PML-null cells and mice. PML binds MK2 and p38 MAPK, thereby inhibiting p38-MK2 interaction and MK2 activation. Moreover, PML participates in autocrine production of TNF induced by cellular inhibitors of apoptosis 1 (cIAP1)/cIAP2 degradation, since PML-knockout attenuates autocrine TNF. Thus, by targeting MK2 activation and autocrine TNF, PML promotes necroptosis and apoptosis, representing a novel tumor-suppressive activity for PML.
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Affiliation(s)
- I-Ting Chen
- Institute of Molecular Biology, Taipei, Taiwan
| | | | - Yu-Hsun Lo
- Institute of Molecular Biology, Taipei, Taiwan
| | | | - Fu-Yi Hsieh
- Institute of Molecular Biology, Taipei, Taiwan
| | | | - Hsiu-Ming Shih
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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Paulus C, Harwardt T, Walter B, Marxreiter A, Zenger M, Reuschel E, Nevels MM. Revisiting promyelocytic leukemia protein targeting by human cytomegalovirus immediate-early protein 1. PLoS Pathog 2020; 16:e1008537. [PMID: 32365141 PMCID: PMC7224577 DOI: 10.1371/journal.ppat.1008537] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 05/14/2020] [Accepted: 04/13/2020] [Indexed: 12/18/2022] Open
Abstract
Promyelocytic leukemia (PML) bodies are nuclear organelles implicated in intrinsic and innate antiviral defense. The eponymous PML proteins, central to the self-organization of PML bodies, and other restriction factors found in these organelles are common targets of viral antagonism. The 72-kDa immediate-early protein 1 (IE1) is the principal antagonist of PML bodies encoded by the human cytomegalovirus (hCMV). IE1 is believed to disrupt PML bodies by inhibiting PML SUMOylation, while PML was proposed to act as an E3 ligase for IE1 SUMOylation. PML targeting by IE1 is considered to be crucial for hCMV replication at low multiplicities of infection, in part via counteracting antiviral gene induction linked to the cellular interferon (IFN) response. However, current concepts of IE1-PML interaction are largely derived from mutant IE1 proteins known or predicted to be metabolically unstable and globally misfolded. We performed systematic clustered charge-to-alanine scanning mutagenesis and identified a stable IE1 mutant protein (IE1cc172-176) with wild-type characteristics except for neither interacting with PML proteins nor inhibiting PML SUMOylation. Consequently, IE1cc172-176 does not associate with PML bodies and is selectively impaired for disrupting these organelles. Surprisingly, functional analysis of IE1cc172-176 revealed that the protein is hypermodified by mixed SUMO chains and that IE1 SUMOylation depends on nucleosome rather than PML binding. Furthermore, a mutant hCMV expressing IE1cc172-176 was only slightly attenuated compared to an IE1-null virus even at low multiplicities of infection. Finally, hCMV-induced expression of cytokine and IFN-stimulated genes turned out to be reduced rather than increased in the presence of IE1cc172-176 relative to wild-type IE1. Our findings challenge present views on the relationship of IE1 with PML and the role of PML in hCMV replication. This study also provides initial evidence for the idea that disruption of PML bodies upon viral infection is linked to activation rather than inhibition of innate immunity.
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Affiliation(s)
- Christina Paulus
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
| | - Thomas Harwardt
- Institute for Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Bernadette Walter
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
| | - Andrea Marxreiter
- Institute for Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Marion Zenger
- Institute for Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Edith Reuschel
- Department of Obstetrics and Gynecology, Clinic St. Hedwig at Hospital Barmherzige Brüder Regensburg, Regensburg, Germany
| | - Michael M. Nevels
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
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N-terminal sequences in matrin 3 mediate phase separation into droplet-like structures that recruit TDP43 variants lacking RNA binding elements. J Transl Med 2019; 99:1030-1040. [PMID: 31019288 PMCID: PMC6857798 DOI: 10.1038/s41374-019-0260-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 03/29/2019] [Accepted: 04/09/2019] [Indexed: 12/12/2022] Open
Abstract
RNA binding proteins associated with amyotrophic lateral sclerosis (ALS) and muscle myopathy possess sequence elements that are low in complexity, or bear resemblance to yeast prion domains. These sequence elements appear to mediate phase separation into liquid-like membraneless organelles. Using fusion proteins of matrin 3 (MATR3) to yellow fluorescent protein (YFP), we recently observed that deletion of the second RNA recognition motif (RRM2) caused the protein to phase separate and form intranuclear liquid-like droplets. Here, we use fusion constructs of MATR3, TARDBP43 (TDP43) and FUS with YFP or mCherry to examine phase separation and protein colocalization in mouse C2C12 myoblast cells. We observed that the N-terminal 397 amino acids of MATR3 (tagged with a nuclear localization signal and expressed as a fusion protein with YFP) formed droplet-like structures within nuclei. Introduction of the myopathic S85C mutation into NLS-N397 MATR3:YFP, but not ALS mutations F115C or P154S, inhibited droplet formation. Further, we analyzed interactions between variants of MATR3 lacking RRM2 (ΔRRM2) and variants of TDP43 with disabling mutations in its RRM1 domain (deletion or mutation). We observed that MATR3:YFP ΔRRM2 formed droplets that appeared to recruit the TDP43 RRM1 mutants. Further, coexpression of the NLS-397 MATR3:YFP construct with a construct that encodes the prion-like domain of TDBP43 produced intranuclear droplet-like structures containing both proteins. Collectively, our studies show that N-terminal sequences in MATR3 can mediate phase separation into intranuclear droplet-like structures that can recruit TDP43 under conditions of low RNA binding.
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Hoischen C, Monajembashi S, Weisshart K, Hemmerich P. Multimodal Light Microscopy Approaches to Reveal Structural and Functional Properties of Promyelocytic Leukemia Nuclear Bodies. Front Oncol 2018; 8:125. [PMID: 29888200 PMCID: PMC5980967 DOI: 10.3389/fonc.2018.00125] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/05/2018] [Indexed: 12/11/2022] Open
Abstract
The promyelocytic leukemia (pml) gene product PML is a tumor suppressor localized mainly in the nucleus of mammalian cells. In the cell nucleus, PML seeds the formation of macromolecular multiprotein complexes, known as PML nuclear bodies (PML NBs). While PML NBs have been implicated in many cellular functions including cell cycle regulation, survival and apoptosis their role as signaling hubs along major genome maintenance pathways emerged more clearly. However, despite extensive research over the past decades, the precise biochemical function of PML in these pathways is still elusive. It remains a big challenge to unify all the different previously suggested cellular functions of PML NBs into one mechanistic model. With the advent of genetically encoded fluorescent proteins it became possible to trace protein function in living specimens. In parallel, a variety of fluorescence fluctuation microscopy (FFM) approaches have been developed which allow precise determination of the biophysical and interaction properties of cellular factors at the single molecule level in living cells. In this report, we summarize the current knowledge on PML nuclear bodies and describe several fluorescence imaging, manipulation, FFM, and super-resolution techniques suitable to analyze PML body assembly and function. These include fluorescence redistribution after photobleaching, fluorescence resonance energy transfer, fluorescence correlation spectroscopy, raster image correlation spectroscopy, ultraviolet laser microbeam-induced DNA damage, erythrocyte-mediated force application, and super-resolution microscopy approaches. Since most if not all of the microscopic equipment to perform these techniques may be available in an institutional or nearby facility, we hope to encourage more researches to exploit sophisticated imaging tools for their research in cancer biology.
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Characterization of gene regulation and protein interaction networks for Matrin 3 encoding mutations linked to amyotrophic lateral sclerosis and myopathy. Sci Rep 2018; 8:4049. [PMID: 29511296 PMCID: PMC5840295 DOI: 10.1038/s41598-018-21371-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 02/02/2018] [Indexed: 02/08/2023] Open
Abstract
To understand how mutations in Matrin 3 (MATR3) cause amyotrophic lateral sclerosis (ALS) and distal myopathy, we used transcriptome and interactome analysis, coupled with microscopy. Over-expression of wild-type (WT) or F115C mutant MATR3 had little impact on gene expression in neuroglia cells. Only 23 genes, expressed at levels of >100 transcripts showed ≥1.6-fold changes in expression by transfection with WT or mutant MATR3:YFP vectors. We identified ~123 proteins that bound MATR3, with proteins associated with stress granules and RNA processing/splicing being prominent. The interactome of myopathic S85C and ALS-variant F115C MATR3 were virtually identical to WT protein. Deletion of RNA recognition motif (RRM1) or Zn finger motifs (ZnF1 or ZnF2) diminished the binding of a subset of MATR3 interacting proteins. Remarkably, deletion of the RRM2 motif caused enhanced binding of >100 hundred proteins. In live cells, MATR3 lacking RRM2 (ΔRRM2) formed intranuclear spherical structures that fused over time into large structures. Our findings in the cell models used here suggest that MATR3 with disease-causing mutations is not dramatically different from WT protein in modulating gene regulation or in binding to normal interacting partners. The intra-nuclear localization and interaction network of MATR3 is strongly modulated by its RRM2 domain.
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Sawyer IA, Hager GL, Dundr M. Specific genomic cues regulate Cajal body assembly. RNA Biol 2017; 14:791-803. [PMID: 27715441 PMCID: PMC5519236 DOI: 10.1080/15476286.2016.1243648] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/06/2016] [Accepted: 09/27/2016] [Indexed: 02/07/2023] Open
Abstract
The assembly of specialized sub-nuclear microenvironments known as nuclear bodies (NBs) is important for promoting efficient nuclear function. In particular, the Cajal body (CB), a prominent NB that facilitates spliceosomal snRNP biogenesis, assembles in response to genomic cues. Here, we detail the factors that regulate CB assembly and structural maintenance. These include the importance of transcription at nucleating gene loci, the grouping of these genes on human chromosomes 1, 6 and 17, as well as cell cycle and biochemical regulation of CB protein function. We also speculate on the correlation between CB formation and RNA splicing levels in neurons and cancer. The timing and location of these specific molecular events is critical to CB assembly and its contribution to genome function. However, further work is required to explore the emerging biophysical characteristics of CB assembly and the impact upon subsequent genome reorganization.
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Affiliation(s)
- Iain A. Sawyer
- Department of Cell Biology, Rosalind Franklin University of Medicine & Science, Chicago Medical School, North Chicago, IL, USA
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Miroslav Dundr
- Department of Cell Biology, Rosalind Franklin University of Medicine & Science, Chicago Medical School, North Chicago, IL, USA
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Banani SF, Rice AM, Peeples WB, Lin Y, Jain S, Parker R, Rosen MK. Compositional Control of Phase-Separated Cellular Bodies. Cell 2016; 166:651-663. [PMID: 27374333 DOI: 10.1016/j.cell.2016.06.010] [Citation(s) in RCA: 771] [Impact Index Per Article: 96.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 03/13/2016] [Accepted: 06/01/2016] [Indexed: 12/12/2022]
Abstract
Cellular bodies such as P bodies and PML nuclear bodies (PML NBs) appear to be phase-separated liquids organized by multivalent interactions among proteins and RNA molecules. Although many components of various cellular bodies are known, general principles that define body composition are lacking. We modeled cellular bodies using several engineered multivalent proteins and RNA. In vitro and in cells, these scaffold molecules form phase-separated liquids that concentrate low valency client proteins. Clients partition differently depending on the ratio of scaffolds, with a sharp switch across the phase diagram diagonal. Composition can switch rapidly through changes in scaffold concentration or valency. Natural PML NBs and P bodies show analogous partitioning behavior, suggesting how their compositions could be controlled by levels of PML SUMOylation or cellular mRNA concentration, respectively. The data suggest a conceptual framework for considering the composition and control thereof of cellular bodies assembled through heterotypic multivalent interactions.
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Affiliation(s)
- Salman F Banani
- Department of Biophysics and Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Allyson M Rice
- Department of Biophysics and Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - William B Peeples
- Department of Biophysics and Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yuan Lin
- Department of Biophysics and Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Saumya Jain
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Roy Parker
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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9
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Abstract
A hallmark of Alzheimer's, Huntington's and similar diseases is the assembly of proteins into amyloids rather than folding into their native state. There is an increasing appreciation that amyloids, under specific conditions, may be non-pathogenic. Here we show that amyloids form as a normal part of Xenopus oocyte development. Amyloids are detectable in the cytosol and the nucleus using an amyloid binding dye and antibodies that recognize amyloid structure. In the cytosol, yolk platelets are amyloid reactive, as are a number of yet to be characterized particles. In the nucleus, we find particles associated with transcription by RNA polymerase I, II and III and RNA processing contain amyloids. Nuclear amyloids remain intact for hours following isolation; however, RNase treatment rapidly disrupts nuclear amyloids. Summary: Non-membrane-bound nuclear particles in Xenopus oocytes responsible for RNA transcription, modification and processing contain proteins assembled into amyloids as part of normal development.
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Affiliation(s)
- Michael H Hayes
- Molecular and Cellular Biology Program, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA Medical Scientist Training Program, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Daniel L Weeks
- Molecular and Cellular Biology Program, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA Medical Scientist Training Program, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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10
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Knol JC, de Wit M, Albrethsen J, Piersma SR, Pham TV, Mongera S, Carvalho B, Fijneman RJA, Meijer GA, Jiménez CR. Proteomics of differential extraction fractions enriched for chromatin-binding proteins from colon adenoma and carcinoma tissues. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:1034-43. [PMID: 24361553 DOI: 10.1016/j.bbapap.2013.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 10/28/2013] [Accepted: 12/10/2013] [Indexed: 12/11/2022]
Abstract
BACKGROUND Altered nuclear and genomic structure and function are hallmarks of cancer cells. Research into nuclear proteins in human tissues could uncover novel molecular processes in cancer. Here, we examine biochemical tissue fractions containing chromatin-binding (CB) proteins in the context of colorectal cancer (CRC) progression. METHODS CB protein-containing fractions were biochemically extracted from human colorectal tissues, including carcinomas with chromosomal instability (CIN), carcinomas with microsatellite instability (MIN), and adenomas. The CB proteins were subjected to label-free LC-MS/MS and the data were analyzed by bioinformatics. RESULTS Over 1700 proteins were identified in the CB fraction from colonic tissues, including 938 proteins associated with nuclear annotation. Of the latter, 169 proteins were differential between adenomas and carcinomas. In this adenoma-versus-carcinoma comparison, apart from specific changes in components of the splicing and protein translational machineries, we also identified significant changes in several proteins associated with chromatin-directed functions. Furthermore, several key cell cycle proteins as well as those involved in cellular stress were increased, whereas specific components of chromosome segregation and DNA recombination/repair systems were decreased. CONCLUSIONS Our study identifies proteomic changes at the subnuclear level that are associated with CRC and may be further investigated. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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Affiliation(s)
- Jaco C Knol
- OncoProteomics Laboratory, Dept. of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Meike de Wit
- OncoProteomics Laboratory, Dept. of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Jakob Albrethsen
- OncoProteomics Laboratory, Dept. of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands; Rigshospitalet, Blegdamsvej 9, Copenhagen, Denmark
| | - Sander R Piersma
- OncoProteomics Laboratory, Dept. of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Thang V Pham
- OncoProteomics Laboratory, Dept. of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Sandra Mongera
- Department of Pathology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Beatriz Carvalho
- Department of Pathology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Remond J A Fijneman
- Department of Pathology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Connie R Jiménez
- OncoProteomics Laboratory, Dept. of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands.
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Willadsen K, Mohamad N, Bodén M. NSort/DB: an intranuclear compartment protein database. GENOMICS PROTEOMICS & BIOINFORMATICS 2012; 10:226-9. [PMID: 23084778 PMCID: PMC5054713 DOI: 10.1016/j.gpb.2012.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 04/13/2012] [Indexed: 11/19/2022]
Abstract
Distinct substructures within the nucleus are associated with a wide variety of important nuclear processes. Structures such as chromatin and nuclear pores have specific roles, while others such as Cajal bodies are more functionally varied. Understanding the roles of these membraneless intra-nuclear compartments requires extensive data sets covering nuclear and compartment-associated proteins. NSort/DB is a database providing access to intra- or sub-nuclear compartment associations for the mouse nuclear proteome. Based on resources ranging from large-scale curated data sets to detailed experiments, this data set provides a high-quality set of annotations of non-exclusive association of nuclear proteins with structures such as promyelocytic leukaemia bodies and chromatin. The database is searchable by protein identifier or compartment, and has a documented web service API. The search interface, web service and data download are all freely available online at http://www.nsort.org/db/. Availability of this data set will enable systematic analyses of the protein complements of nuclear compartments, improving our understanding of the diverse functional repertoire of these structures.
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Affiliation(s)
- Kai Willadsen
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Australia.
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12
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Bauer DC, Willadsen K, Buske FA, Lê Cao KA, Bailey TL, Dellaire G, Bodén M. Sorting the nuclear proteome. ACTA ACUST UNITED AC 2011; 27:i7-14. [PMID: 21685104 PMCID: PMC3117375 DOI: 10.1093/bioinformatics/btr217] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Motivation: Quantitative experimental analyses of the nuclear interior reveal a morphologically structured yet dynamic mix of membraneless compartments. Major nuclear events depend on the functional integrity and timely assembly of these intra-nuclear compartments. Yet, unknown drivers of protein mobility ensure that they are in the right place at the time when they are needed. Results: This study investigates determinants of associations between eight intra-nuclear compartments and their proteins in heterogeneous genome-wide data. We develop a model based on a range of candidate determinants, capable of mapping the intra-nuclear organization of proteins. The model integrates protein interactions, protein domains, post-translational modification sites and protein sequence data. The predictions of our model are accurate with a mean AUC (over all compartments) of 0.71. We present a complete map of the association of 3567 mouse nuclear proteins with intra-nuclear compartments. Each decision is explained in terms of essential interactions and domains, and qualified with a false discovery assessment. Using this resource, we uncover the collective role of transcription factors in each of the compartments. We create diagrams illustrating the outcomes of a Gene Ontology enrichment analysis. Associated with an extensive range of transcription factors, the analysis suggests that PML bodies coordinate regulatory immune responses. Contact:m.boden@uq.edu.au Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Denis C Bauer
- Queensland Brain Institute, School of Chemistry and Molecular Biosciences, Queensland Facility for Advanced Bioinformatics, The University of Queensland, St Lucia, Australia
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13
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Németh A, Längst G. Genome organization in and around the nucleolus. Trends Genet 2011; 27:149-56. [DOI: 10.1016/j.tig.2011.01.002] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 01/03/2011] [Accepted: 01/04/2011] [Indexed: 10/18/2022]
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Scott MS, Boisvert FM, Lamond AI, Barton GJ. PNAC: a protein nucleolar association classifier. BMC Genomics 2011; 12:74. [PMID: 21272300 PMCID: PMC3038921 DOI: 10.1186/1471-2164-12-74] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 01/27/2011] [Indexed: 01/11/2023] Open
Abstract
Background Although primarily known as the site of ribosome subunit production, the nucleolus is involved in numerous and diverse cellular processes. Recent large-scale proteomics projects have identified thousands of human proteins that associate with the nucleolus. However, in most cases, we know neither the fraction of each protein pool that is nucleolus-associated nor whether their association is permanent or conditional. Results To describe the dynamic localisation of proteins in the nucleolus, we investigated the extent of nucleolar association of proteins by first collating an extensively curated literature-derived dataset. This dataset then served to train a probabilistic predictor which integrates gene and protein characteristics. Unlike most previous experimental and computational studies of the nucleolar proteome that produce large static lists of nucleolar proteins regardless of their extent of nucleolar association, our predictor models the fluidity of the nucleolus by considering different classes of nucleolar-associated proteins. The new method predicts all human proteins as either nucleolar-enriched, nucleolar-nucleoplasmic, nucleolar-cytoplasmic or non-nucleolar. Leave-one-out cross validation tests reveal sensitivity values for these four classes ranging from 0.72 to 0.90 and positive predictive values ranging from 0.63 to 0.94. The overall accuracy of the classifier was measured to be 0.85 on an independent literature-based test set and 0.74 using a large independent quantitative proteomics dataset. While the three nucleolar-association groups display vastly different Gene Ontology biological process signatures and evolutionary characteristics, they collectively represent the most well characterised nucleolar functions. Conclusions Our proteome-wide classification of nucleolar association provides a novel representation of the dynamic content of the nucleolus. This model of nucleolar localisation thus increases the coverage while providing accurate and specific annotations of the nucleolar proteome. It will be instrumental in better understanding the central role of the nucleolus in the cell and its interaction with other subcellular compartments.
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Affiliation(s)
- Michelle S Scott
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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