1
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Howe J, Weeks A, Reardon P, Barbar E. Multivalent binding of the hub protein LC8 at a newly discovered site in 53BP1. Biophys J 2022; 121:4433-4442. [PMID: 36335430 PMCID: PMC9748353 DOI: 10.1016/j.bpj.2022.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/28/2022] [Accepted: 11/03/2022] [Indexed: 11/06/2022] Open
Abstract
Tumor suppressor p53 binding protein 1 (53BP1) is a scaffolding protein involved in poly-ADP ribose polymerase inhibitor hypersensitivity in BRCA1-negative cancers. 53BP1 plays a critical role in the DNA damage response and relies on its oligomerization to create foci that promote repair of DNA double-strand breaks. Previous work shows that mutation of either the oligomerization domain or the dynein light chain 8 (LC8)-binding sites of 53BP1 results in reduced accumulation of 53BP1 at double-strand breaks. Mutation of both abolishes focus formation almost completely. Here, we show that, contrary to current literature, 53BP1 contains three LC8-binding sites, all of which are conserved in mammals. Isothermal titration calorimetry measuring binding affinity of 53BP1 variants with LC8 shows that the third LC8-binding site has a high affinity and can bind LC8 in the absence of other sites. NMR titrations confirm that the third site binds LC8 even in variants that lack the other LC8-binding sites. The third site is the closest to the oligomerization domain of 53BP1, and its discovery would challenge our current understanding of the role of LC8 in 53BP1 function.
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Affiliation(s)
- Jesse Howe
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon
| | - Austin Weeks
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon
| | - Patrick Reardon
- Oregon State University NMR Facility, Oregon State University, Corvallis, Oregon
| | - Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon.
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2
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The interaction between LC8 and LCA5 reveals a novel oligomerization function of LC8 in the ciliary-centrosome system. Sci Rep 2022; 12:15623. [PMID: 36114230 PMCID: PMC9481538 DOI: 10.1038/s41598-022-19454-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
Dynein light chain LC8 is a small dimeric hub protein that recognizes its partners through short linear motifs and is commonly assumed to drive their dimerization. It has more than 100 known binding partners involved in a wide range of cellular processes. Recent large-scale interaction studies suggested that LC8 could also play a role in the ciliary/centrosome system. However, the cellular function of LC8 in this system remains elusive. In this work, we characterized the interaction of LC8 with the centrosomal protein lebercilin (LCA5), which is associated with a specific form of ciliopathy. We showed that LCA5 binds LC8 through two linear motifs. In contrast to the commonly accepted model, LCA5 forms dimers through extensive coiled coil formation in a LC8-independent manner. However, LC8 enhances the oligomerization ability of LCA5 that requires a finely balanced interplay of coiled coil segments and both binding motifs. Based on our results, we propose that LC8 acts as an oligomerization engine that is responsible for the higher order oligomer formation of LCA5. As LCA5 shares several common features with other centrosomal proteins, the presented LC8 driven oligomerization could be widespread among centrosomal proteins, highlighting an important novel cellular function of LC8.
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3
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The role of dancing duplexes in biology and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021. [PMID: 34656330 DOI: 10.1016/bs.pmbts.2021.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Across species, a common protein assembly arises: proteins containing structured domains separated by long intrinsically disordered regions, and dimerized through a self-association domain or through strong protein interactions. These systems are termed "IDP duplexes." These flexible dimers have roles in diverse pathologies including development of cancer, viral infections, and neurodegenerative disease. Here we discuss the role of disorder in IDP duplexes with similar domain architectures that bind hub protein, LC8. LC8-binding IDP duplexes are categorized into three groups: IDP duplexes that contain a self-association domain that is extended by LC8 binding, IDP duplexes that have no self-association domain and are dimerized through binding several copies of LC8, and multivalent LC8-binders that also have a self-association domain. Additionally, we discuss non-LC8-binding IDP duplexes with similar domain organizations, including the Nucleocapsid protein of SARS-CoV-2. We propose that IDP duplexes have structural features that are essential in many biological processes and that improved understanding of their structure function relationship will provide new therapeutic opportunities.
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4
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Loening NM, Barbar E. Structural characterization of the self-association domain of swallow. Protein Sci 2021; 30:1056-1063. [PMID: 33641207 DOI: 10.1002/pro.4055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 01/29/2023]
Abstract
Swallow, a 62 kDa multidomain protein, is required for the proper localization of several mRNAs involved in the development of Drosophila oocytes. The dimerization of Swallow depends on a 71-residue self-association domain in the center of the protein sequence, and is significantly stabilized by a binding interaction with dynein light chain (LC8). Here, we detail the use of solution-state nuclear magnetic resonance spectroscopy to characterize the structure of this self-association domain, thereby establishing that this domain forms a parallel coiled-coil and providing insight into how the stability of the dimerization interaction is regulated.
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Affiliation(s)
| | - Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
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5
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Schnabl J, Wang J, Hohmann U, Gehre M, Batki J, Andreev VI, Purkhauser K, Fasching N, Duchek P, Novatchkova M, Mechtler K, Plaschka C, Patel DJ, Brennecke J. Molecular principles of Piwi-mediated cotranscriptional silencing through the dimeric SFiNX complex. Genes Dev 2021; 35:392-409. [PMID: 33574069 PMCID: PMC7919418 DOI: 10.1101/gad.347989.120] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
Nuclear Argonaute proteins, guided by their bound small RNAs to nascent target transcripts, mediate cotranscriptional silencing of transposons and repetitive genomic loci through heterochromatin formation. The molecular mechanisms involved in this process are incompletely understood. Here, we show that the SFiNX complex, a silencing mediator downstream from nuclear Piwi-piRNA complexes in Drosophila, facilitates cotranscriptional silencing as a homodimer. The dynein light chain protein Cut up/LC8 mediates SFiNX dimerization, and its function can be bypassed by a heterologous dimerization domain, arguing for a constitutive SFiNX dimer. Dimeric, but not monomeric SFiNX, is capable of forming molecular condensates in a nucleic acid-stimulated manner. Mutations that prevent SFiNX dimerization result in loss of condensate formation in vitro and the inability of Piwi to initiate heterochromatin formation and silence transposons in vivo. We propose that multivalent SFiNX-nucleic acid interactions are critical for heterochromatin establishment at piRNA target loci in a cotranscriptional manner.
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Affiliation(s)
- Jakob Schnabl
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School at the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Juncheng Wang
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ulrich Hohmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Maja Gehre
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Julia Batki
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Veselin I Andreev
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School at the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Kim Purkhauser
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Nina Fasching
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Peter Duchek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Clemens Plaschka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
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6
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Loening NM, Saravanan S, Jespersen NE, Jara K, Barbar E. Interplay of Disorder and Sequence Specificity in the Formation of Stable Dynein-Dynactin Complexes. Biophys J 2020; 119:950-965. [PMID: 32814057 DOI: 10.1016/j.bpj.2020.07.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/21/2020] [Accepted: 07/27/2020] [Indexed: 01/22/2023] Open
Abstract
Cytoplasmic dynein is a eukaryotic motor protein complex that, along with its regulatory protein dynactin, is essential to the transport of organelles within cells. The interaction of dynein with dynactin is regulated by binding between the intermediate chain (IC) subunit of dynein and the p150Glued subunit of dynactin. Even though in the rat versions of these proteins this interaction primarily involves the single α-helix region at the N-terminus of the IC, in Drosophila and yeast ICs the removal of a nascent helix (H2) downstream of the single α-helix considerably diminishes IC-p150Glued complex stability. We find that for ICs from various species, there is a correlation between disorder in H2 and its contribution to binding affinity, and that sequence variations in H2 that do not change the level of disorder show similar binding behavior. Analysis of the structure and interactions of the IC from Chaetomium thermophilum demonstrates that the H2 region of C. thermophilum IC has a low helical propensity and establishes that H2 binds directly to the coiled-coil 1B (CC1B) domain of p150Glued, thus explaining why H2 is necessary for tight binding. Isothermal titration calorimetry, circular dichroism, and NMR studies of smaller CC1B constructs localize the region of CC1B most essential for a tight interaction with IC. These results suggest that it is the level of disorder in H2 of IC along with its charge, rather than sequence specificity, that underlie its importance in initiating tight IC-p150Glued complex formation. We speculate that the nascent H2 helix may provide conformational flexibility to initiate binding, whereas those species that have a fully folded H2 have co-opted an alternative mechanism for promoting p150Glued binding.
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Affiliation(s)
| | - Sanjana Saravanan
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon
| | - Nathan E Jespersen
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon
| | - Kayla Jara
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon
| | - Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon.
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7
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Jespersen N, Barbar E. Emerging Features of Linear Motif-Binding Hub Proteins. Trends Biochem Sci 2020; 45:375-384. [DOI: 10.1016/j.tibs.2020.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/05/2020] [Accepted: 01/21/2020] [Indexed: 01/15/2023]
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8
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Jespersen NE, Leyrat C, Gérard FC, Bourhis JM, Blondel D, Jamin M, Barbar E. The LC8-RavP ensemble Structure Evinces A Role for LC8 in Regulating Lyssavirus Polymerase Functionality. J Mol Biol 2019; 431:4959-4977. [PMID: 31634467 PMCID: PMC7060403 DOI: 10.1016/j.jmb.2019.10.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/11/2019] [Accepted: 10/11/2019] [Indexed: 12/25/2022]
Abstract
The rabies and Ebola viruses recruit the highly conserved host protein LC8 for their own reproductive success. In vivo knockouts of the LC8 recognition motif within the rabies virus phosphoprotein (RavP) result in completely nonlethal viral infections. In this work, we examine the molecular role LC8 plays in viral lethality. We show that RavP and LC8 colocalize in rabies infected cells, and that LC8 interactions are essential for efficient viral polymerase functionality. NMR, SAXS, and molecular modeling demonstrate that LC8 binding to a disordered linker adjacent to an endogenous dimerization domain results in restrictions in RavP domain orientations. The resulting ensemble structure of RavP-LC8 tetrameric complex is similar to that of a related virus phosphoprotein that does not bind LC8, suggesting that with RavP, LC8 binding acts as a switch to induce a more active conformation. The high conservation of the LC8 motif in Lyssavirus phosphoproteins and its presence in other analogous proteins such as the Ebola virus VP35 evinces a broader purpose for LC8 in regulating downstream phosphoprotein functions vital for viral replication.
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Affiliation(s)
- Nathan E Jespersen
- From the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Cedric Leyrat
- Institut de Génomique Fonctionnelle, CNRS UMR-5203 INSERM U1191, University of Montpellier, Montpellier, France
| | - Francine C Gérard
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 38000, Grenoble, France
| | - Jean-Marie Bourhis
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 38000, Grenoble, France
| | - Danielle Blondel
- Institut de Biologie Intégrative de La Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Marc Jamin
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 38000, Grenoble, France
| | - Elisar Barbar
- From the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA.
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9
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Clark S, Myers JB, King A, Fiala R, Novacek J, Pearce G, Heierhorst J, Reichow SL, Barbar EJ. Multivalency regulates activity in an intrinsically disordered transcription factor. eLife 2018; 7:36258. [PMID: 29714690 PMCID: PMC5963919 DOI: 10.7554/elife.36258] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/23/2018] [Indexed: 12/19/2022] Open
Abstract
The transcription factor ASCIZ (ATMIN, ZNF822) has an unusually high number of recognition motifs for the product of its main target gene, the hub protein LC8 (DYNLL1). Using a combination of biophysical methods, structural analysis by NMR and electron microscopy, and cellular transcription assays, we developed a model that proposes a concerted role of intrinsic disorder and multiple LC8 binding events in regulating LC8 transcription. We demonstrate that the long intrinsically disordered C-terminal domain of ASCIZ binds LC8 to form a dynamic ensemble of complexes with a gradient of transcriptional activity that is inversely proportional to LC8 occupancy. The preference for low occupancy complexes at saturating LC8 concentrations with both human and Drosophila ASCIZ indicates that negative cooperativity is an important feature of ASCIZ-LC8 interactions. The prevalence of intrinsic disorder and multivalency among transcription factors suggests that formation of heterogeneous, dynamic complexes is a widespread mechanism for tuning transcriptional regulation.
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Affiliation(s)
- Sarah Clark
- Department of Biochemistry and Biophysics, Oregon State University, Oregon, United States
| | - Janette B Myers
- Department of Chemistry, Portland State University, Oregon, United States
| | - Ashleigh King
- St. Vincent's Institute of Medical Research, The University of Melbourne, Victoria, Australia.,Department of Medicine, St. Vincent's Health, The University of Melbourne, Victoria, Australia
| | - Radovan Fiala
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jiri Novacek
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Grant Pearce
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jörg Heierhorst
- St. Vincent's Institute of Medical Research, The University of Melbourne, Victoria, Australia.,Department of Medicine, St. Vincent's Health, The University of Melbourne, Victoria, Australia
| | - Steve L Reichow
- Department of Chemistry, Portland State University, Oregon, United States
| | - Elisar J Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Oregon, United States
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10
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Erdős G, Szaniszló T, Pajkos M, Hajdu-Soltész B, Kiss B, Pál G, Nyitray L, Dosztányi Z. Novel linear motif filtering protocol reveals the role of the LC8 dynein light chain in the Hippo pathway. PLoS Comput Biol 2017; 13:e1005885. [PMID: 29240760 PMCID: PMC5746249 DOI: 10.1371/journal.pcbi.1005885] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 12/28/2017] [Accepted: 11/20/2017] [Indexed: 01/12/2023] Open
Abstract
Protein-protein interactions (PPIs) formed between short linear motifs and globular domains play important roles in many regulatory and signaling processes but are highly underrepresented in current protein-protein interaction databases. These types of interactions are usually characterized by a specific binding motif that captures the key amino acids shared among the interaction partners. However, the computational proteome-level identification of interaction partners based on the known motif is hindered by the huge number of randomly occurring matches from which biologically relevant motif hits need to be extracted. In this work, we established a novel bioinformatic filtering protocol to efficiently explore interaction network of a hub protein. We introduced a novel measure that enabled the optimization of the elements and parameter settings of the pipeline which was built from multiple sequence-based prediction methods. In addition, data collected from PPI databases and evolutionary analyses were also incorporated to further increase the biological relevance of the identified motif hits. The approach was applied to the dynein light chain LC8, a ubiquitous eukaryotic hub protein that has been suggested to be involved in motor-related functions as well as promoting the dimerization of various proteins by recognizing linear motifs in its partners. From the list of putative binding motifs collected by our protocol, several novel peptides were experimentally verified to bind LC8. Altogether 71 potential new motif instances were identified. The expanded list of LC8 binding partners revealed the evolutionary plasticity of binding partners despite the highly conserved binding interface. In addition, it also highlighted a novel, conserved function of LC8 in the upstream regulation of the Hippo signaling pathway. Beyond the LC8 system, our work also provides general guidelines that can be applied to explore the interaction network of other linear motif binding proteins or protein domains. Fine-tuning of many cellular processes relies on weak, transient protein-protein interactions. Such interactions often involve compact functional modules, called short linear motifs (SLiMs) that can bind to specific globular domains. SLiM-mediated interactions can carry out diverse molecular functions by targeting proteins to specific cellular locations, regulating the activity and binding preferences of proteins, or aiding the assembly of macromolecular complexes. The key to the function of SLiMs is their small size and highly flexible nature. At the same time, these properties make their experimental identification challenging. Consequently, only a small portion of SLiM-mediated interactions is currently known. This underlies the importance of novel computational methods that can reliably identify candidate sites involved in binding to linear motif binding domains. Here we present a novel bioinformatic approach that efficiently predicts new binding partners for SLiM-binding domains. We applied this method to the dynein light chain LC8, a protein that was already known to bind many partners in a wide range of organisms. With this method, we not only significantly expanded the interaction network of LC8, but also identified a novel function of LC8 in a highly important pathway controlling organ size in animals.
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Affiliation(s)
- Gábor Erdős
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Tamás Szaniszló
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Mátyás Pajkos
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Borbála Hajdu-Soltész
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Bence Kiss
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Gábor Pál
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Zsuzsanna Dosztányi
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
- * E-mail:
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11
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Dynein Light Chain LC8 Is Required for RNA Polymerase I-Mediated Transcription in Trypanosoma brucei, Facilitating Assembly and Promoter Binding of Class I Transcription Factor A. Mol Cell Biol 2015; 36:95-107. [PMID: 26459761 DOI: 10.1128/mcb.00705-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/05/2015] [Indexed: 12/22/2022] Open
Abstract
Dynein light chain LC8 is highly conserved among eukaryotes and has both dynein-dependent and dynein-independent functions. Interestingly, LC8 was identified as a subunit of the class I transcription factor A (CITFA), which is essential for transcription by RNA polymerase I (Pol I) in the parasite Trypanosoma brucei. Given that LC8 has never been identified with a basal transcription factor and that T. brucei relies on RNA Pol I for expressing the variant surface glycoprotein (VSG), the key protein in antigenic variation, we investigated the CITFA-specific role of LC8. Depletion of LC8 from mammalian-infective bloodstream trypanosomes affected cell cycle progression, reduced the abundances of rRNA and VSG mRNA, and resulted in rapid cell death. Sedimentation analysis, coimmunoprecipitation of recombinant proteins, and bioinformatic analysis revealed an LC8 binding site near the N terminus of the subunit CITFA2. Mutation of this site prevented the formation of a CITFA2-LC8 heterotetramer and, in vivo, was lethal, affecting assembly of a functional CITFA complex. Gel shift assays and UV cross-linking experiments identified CITFA2 as a promoter-binding CITFA subunit. Accordingly, silencing of LC8 or CITFA2 resulted in a loss of CITFA from RNA Pol I promoters. Hence, we discovered an LC8 interaction that, unprecedentedly, has a basal function in transcription.
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12
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Jie J, Löhr F, Barbar E. Interactions of Yeast Dynein with Dynein Light Chain and Dynactin: GENERAL IMPLICATIONS FOR INTRINSICALLY DISORDERED DUPLEX SCAFFOLDS IN MULTIPROTEIN ASSEMBLIES. J Biol Chem 2015; 290:23863-74. [PMID: 26253171 DOI: 10.1074/jbc.m115.649715] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Indexed: 11/06/2022] Open
Abstract
Intrinsically disordered protein (IDP) duplexes composed of two IDP chains cross-linked by bivalent partner proteins form scaffolds for assembly of multiprotein complexes. The N-terminal domain of dynein intermediate chain (N-IC) is one such IDP that forms a bivalent scaffold with multiple dynein light chains including LC8, a hub protein that promotes duplex formation of diverse IDP partners. N-IC also binds a subunit of the dynein regulator, dynactin. Here we characterize interactions of a yeast ortholog of N-IC (N-Pac11) with yeast LC8 (Dyn2) or with the intermediate chain-binding subunit of yeast dynactin (Nip100). Residue level changes in Pac11 structure are monitored by NMR spectroscopy, and binding energetics are monitored by isothermal titration calorimetry (ITC). N-Pac11 is monomeric and primarily disordered except for a single α-helix (SAH) at the N terminus and a short nascent helix, LH, flanked by the two Dyn2 recognition motifs. Upon binding Dyn2, the only Pac11 residues making direct protein-protein interactions are in and immediately flanking the recognition motifs. Dyn2 binding also orders LH residues of Pac11. Upon binding Nip100, only Pac11 SAH residues make direct protein-protein interactions, but LH residues at a distant sequence position and L1 residues in an adjacent linker are also ordered. The long distance, ligand-dependent ordering of residues reveals new elements of dynamic structure within IDP linker regions.
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Affiliation(s)
- Jing Jie
- From the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331 and
| | - Frank Löhr
- the Institute of Biophysical Chemistry, Goethe-University, D-60438 Frankfurt, Germany
| | - Elisar Barbar
- From the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331 and
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13
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Clark SA, Jespersen N, Woodward C, Barbar E. Multivalent IDP assemblies: Unique properties of LC8-associated, IDP duplex scaffolds. FEBS Lett 2015; 589:2543-51. [PMID: 26226419 DOI: 10.1016/j.febslet.2015.07.032] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 07/17/2015] [Accepted: 07/17/2015] [Indexed: 01/17/2023]
Abstract
A wide variety of subcellular complexes are composed of one or more intrinsically disordered proteins (IDPs) that are multivalent, flexible, and characterized by dynamic binding of diverse partner proteins. These multivalent IDP assemblies, of broad functional diversity, are classified here into five categories distinguished by the number of IDP chains and the arrangement of partner proteins in the functional complex. Examples of each category are summarized in the context of the exceptional molecular and biological properties of IDPs. One type - IDP duplex scaffolds - is considered in detail. Its unique features include parallel alignment of two IDP chains, formation of new self-associated domains, enhanced affinity for additional bivalent ligands, and ubiquitous binding of the hub protein LC8. For two IDP duplex scaffolds, dynein intermediate chain IC and nucleoporin Nup159, these duplex features, together with the inherent flexibility of IDPs, are central to their assembly and function. A new type of IDP-LC8 interaction, distributed binding of LC8 among multiple IDP recognition sites, is described for Nup159 assembly.
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Affiliation(s)
- Sarah A Clark
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, United States
| | - Nathan Jespersen
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, United States
| | - Clare Woodward
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, St. Paul, MN 55108, United States
| | - Elisar Barbar
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, United States.
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Barbar E, Nyarko A. Polybivalency and disordered proteins in ordering macromolecular assemblies. Semin Cell Dev Biol 2014; 37:20-5. [PMID: 25263009 DOI: 10.1016/j.semcdb.2014.09.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 09/10/2014] [Accepted: 09/13/2014] [Indexed: 12/20/2022]
Abstract
Intrinsically disordered proteins (IDPs) are prevalent in macromolecular assemblies and are thought to mediate protein recognition in complex regulatory processes and signaling pathways. The formation of a polybivalent scaffold is a key process by which IDPs drive early steps in macromolecular assemblies. Three intrinsically disordered proteins, IC, Swallow and Nup159, are core components, respectively, of cytoplasmic dynein, bicoid mRNA localization apparatus, and nuclear pore complexes. In all three systems, the hub protein LC8 recognizes on the IDP, short linear motifs that are fully disordered in the apo form, but adopt a β-strand when bound to LC8. The IDP/LC8 complex forms a bivalent scaffold primed to bind additional bivalent ligands. Scaffold formation also promotes self-association and/or higher order organization of the IDP components at a site distant from LC8 binding. Rigorous thermodynamic analyses imply that association of additional bivalent ligands is driven by entropic effects where the first binding event is weak but subsequent binding of additional ligands occurs with higher affinity. Here, we review specific examples of macromolecular assemblies in which polybivalency of aligned IDP duplexes not only enhances binding affinity and results in formation of a stable complex but also compensates unfavorable steric and enthalpic interactions. We propose that polybivalent scaffold assembly involving IDPs and LC8-like proteins is a general process in the cell biology of a class of multi-protein structures that are stable yet fine-tuned for diverse cellular requirements.
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Affiliation(s)
- Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, United States.
| | - Afua Nyarko
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, United States
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Barbar E, Nyarko A. NMR Characterization of Self-Association Domains Promoted by Interactions with LC8 Hub Protein. Comput Struct Biotechnol J 2014; 9:e201402003. [PMID: 24757501 PMCID: PMC3995210 DOI: 10.5936/csbj.201402003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/04/2014] [Accepted: 02/08/2014] [Indexed: 01/04/2023] Open
Abstract
Most proteins in interaction networks have a small number of partners, while a few, called hubs, participate in a large number of interactions and play a central role in cell homeostasis. One highly conserved hub is a protein called LC8 that was originally identified as an essential component of the multi-subunit complex dynein but later shown to be also critical in multiple protein complexes in diverse systems. What is intriguing about this hub protein is that it does not passively bind its various partners but emerging evidence suggests that LC8 acts as a dimerization engine that promotes self-association and/or higher order organization of its primarily disordered monomeric partners. This structural organization process does not require ATP but is triggered by long-range allosteric regulation initiated by LC8 binding a pair of disordered chains forming a bivalent or polybivalent scaffold. This review focuses on the role of LC8 in promoting self-association of two of its binding partners, a dynein intermediate chain and a non dynein protein called Swallow.
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Affiliation(s)
- Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Afua Nyarko
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
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