51
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Rapali P, Radnai L, Süveges D, Harmat V, Tölgyesi F, Wahlgren WY, Katona G, Nyitray L, Pál G. Directed evolution reveals the binding motif preference of the LC8/DYNLL hub protein and predicts large numbers of novel binders in the human proteome. PLoS One 2011; 6:e18818. [PMID: 21533121 PMCID: PMC3078936 DOI: 10.1371/journal.pone.0018818] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 03/10/2011] [Indexed: 11/27/2022] Open
Abstract
LC8 dynein light chain (DYNLL) is a eukaryotic hub protein that is thought to function as a dimerization engine. Its interacting partners are involved in a wide range of cellular functions. In its dozens of hitherto identified binding partners DYNLL binds to a linear peptide segment. The known segments define a loosely characterized binding motif: [D/S]-4K-3X-2[T/V/I]-1Q0[T/V]1[D/E]2. The motifs are localized in disordered segments of the DYNLL-binding proteins and are often flanked by coiled coil or other potential dimerization domains. Based on a directed evolution approach, here we provide the first quantitative characterization of the binding preference of the DYNLL binding site. We displayed on M13 phage a naïve peptide library with seven fully randomized positions around a fixed, naturally conserved glutamine. The peptides were presented in a bivalent manner fused to a leucine zipper mimicking the natural dimer to dimer binding stoichiometry of DYNLL-partner complexes. The phage-selected consensus sequence V-5S-4R-3G-2T-1Q0T1E2 resembles the natural one, but is extended by an additional N-terminal valine, which increases the affinity of the monomeric peptide twentyfold. Leu-zipper dimerization increases the affinity into the subnanomolar range. By comparing crystal structures of an SRGTQTE-DYNLL and a dimeric VSRGTQTE-DYNLL complex we find that the affinity enhancing valine is accommodated in a binding pocket on DYNLL. Based on the in vitro evolved sequence pattern we predict a large number of novel DYNLL binding partners in the human proteome. Among these EML3, a microtubule-binding protein involved in mitosis contains an exact match of the phage-evolved consensus and binds to DYNLL with nanomolar affinity. These results significantly widen the scope of the human interactome around DYNLL and will certainly shed more light on the biological functions and organizing role of DYNLL in the human and other eukaryotic interactomes.
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Affiliation(s)
- Péter Rapali
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - László Radnai
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Dániel Süveges
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Veronika Harmat
- Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
- Protein Modeling Research Group, Hungarian Academy of Sciences, Eötvös Loránd University, Budapest, Hungary
| | - Ferenc Tölgyesi
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | | | - Gergely Katona
- Department of Chemistry, University of Gothenburg, Gothenburg, Sweden
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
- * E-mail: (LN); (GP)
| | - Gábor Pál
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
- * E-mail: (LN); (GP)
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52
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Regué L, Sdelci S, Bertran MT, Caelles C, Reverter D, Roig J. DYNLL/LC8 protein controls signal transduction through the Nek9/Nek6 signaling module by regulating Nek6 binding to Nek9. J Biol Chem 2011; 286:18118-29. [PMID: 21454704 DOI: 10.1074/jbc.m110.209080] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The NIMA family protein kinases Nek9/Nercc1 and the highly similar Nek6 and Nek7 form a signaling module activated in mitosis, when they are involved in the control of spindle organization and function. Here we report that Nek9, the module upstream kinase, binds to DYNLL/LC8, a highly conserved protein originally described as a component of the dynein complex. LC8 is a dimer that interacts with different proteins and has been suggested to act as a dimerization hub promoting the organization and oligomerization of partially disorganized partners. We find that the interaction of LC8 with Nek9 depends on a (K/R)XTQT motif adjacent to the Nek9 C-terminal coiled coil motif, results in Nek9 multimerization, and increases the rate of Nek9 autoactivation. LC8 binding to Nek9 is regulated by Nek9 activity through the autophosphorylation of Ser(944), a residue immediately N-terminal to the (K/R)XTQT motif. Remarkably, LC8 binding interferes with the interaction of Nek9 with its downstream partner Nek6 as well as with Nek6 activation, thus controlling both processes. Our work sheds light into the control of signal transduction through the module formed by Nek9 and Nek6/7 and uncovers a novel manner in which LC8 can regulate partner physiology by interfering with protein complex formation. We suggest that this and other LC8 functions can be specifically regulated by partner phosphorylation.
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Affiliation(s)
- Laura Regué
- Cell Signaling Group, Molecular Medicine Program, Institute for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Spain
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53
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Nyarko A, Barbar E. Light chain-dependent self-association of dynein intermediate chain. J Biol Chem 2011; 286:1556-66. [PMID: 20974845 PMCID: PMC3020764 DOI: 10.1074/jbc.m110.171686] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 10/15/2010] [Indexed: 11/06/2022] Open
Abstract
Dynein light chains are bivalent dimers that bind two copies of dynein intermediate chain IC to form a cargo attachment subcomplex. The interaction of light chain LC8 with the natively disordered N-terminal domain of IC induces helix formation at distant IC sites in or near a region predicted to form a coiled-coil. This fostered the hypothesis that LC8 binding promotes IC self-association to form a coiled-coil or other interchain helical structure. However, recent studies show that the predicted coiled-coil sequence partially overlaps the light chain LC7 recognition sequence on IC, raising questions about the apparently contradictory effects of LC8 and LC7. Here, we use NMR and fluorescence quenching to localize IC self-association to residues within the predicted coiled-coil that also correspond to helix 1 of the LC7 recognition sequence. LC8 binding promotes IC self-association of helix 1 from each of two IC chains, whereas LC7 binding reverses self-association by incorporating the same residues into two symmetrical, but distant, helices of the LC7-IC complex. Isothermal titration experiments confirm the distinction of LC8 enhancement of IC self-association and LC7 binding effects. When all three light chains are bound, IC self-association is shifted to another region. Such flexibility in association modes may function in maintaining a stable and versatile light chain-intermediate chain assembly under changing cellular conditions.
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Affiliation(s)
- Afua Nyarko
- From the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Elisar Barbar
- From the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
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54
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Radnai L, Rapali P, Hódi Z, Süveges D, Molnár T, Kiss B, Bécsi B, Erdödi F, Buday L, Kardos J, Kovács M, Nyitray L. Affinity, avidity, and kinetics of target sequence binding to LC8 dynein light chain isoforms. J Biol Chem 2010; 285:38649-57. [PMID: 20889982 PMCID: PMC2992297 DOI: 10.1074/jbc.m110.165894] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 09/24/2010] [Indexed: 01/22/2023] Open
Abstract
LC8 dynein light chain (DYNLL) is a highly conserved eukaryotic hub protein with dozens of binding partners and various functions beyond being a subunit of dynein and myosin Va motor proteins. Here, we compared the kinetic and thermodynamic parameters of binding of both mammalian isoforms, DYNLL1 and DYNLL2, to two putative consensus binding motifs (KXTQTX and XG(I/V)QVD) and report only subtle differences. Peptides containing either of the above motifs bind to DYNLL2 with micromolar affinity, whereas a myosin Va peptide (lacking the conserved Gln) and the noncanonical Pak1 peptide bind with K(d) values of 9 and 40 μM, respectively. Binding of the KXTQTX motif is enthalpy-driven, although that of all other peptides is both enthalpy- and entropy-driven. Moreover, the KXTQTX motif shows strikingly slower off-rate constant than the other motifs. As most DYNLL partners are homodimeric, we also assessed the binding of bivalent ligands to DYNLL2. Compared with monovalent ligands, a significant avidity effect was found as follows: K(d) values of 37 and 3.5 nM for a dimeric myosin Va fragment and a Leu zipper dimerized KXTQTX motif, respectively. Ligand binding kinetics of DYNLL can best be described by a conformational selection model consisting of a slow isomerization and a rapid binding step. We also studied the binding of the phosphomimetic S88E mutant of DYNLL2 to the dimeric myosin Va fragment, and we found a significantly lower apparent K(d) value (3 μM). We conclude that the thermodynamic and kinetic fine-tuning of binding of various ligands to DYNLL could have physiological relevance in its interaction network.
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Affiliation(s)
- László Radnai
- From the Department of Biochemistry, Eötvös Loránd University, H-1117 Budapest
| | - Péter Rapali
- From the Department of Biochemistry, Eötvös Loránd University, H-1117 Budapest
| | - Zsuzsa Hódi
- From the Department of Biochemistry, Eötvös Loránd University, H-1117 Budapest
| | - Dániel Süveges
- From the Department of Biochemistry, Eötvös Loránd University, H-1117 Budapest
| | - Tamás Molnár
- From the Department of Biochemistry, Eötvös Loránd University, H-1117 Budapest
| | - Bence Kiss
- From the Department of Biochemistry, Eötvös Loránd University, H-1117 Budapest
| | - Bálint Bécsi
- the Department of Medical Chemistry, University of Debrecen, Medical and Health Science Center, H-4032 Debrecen
| | - Ferenc Erdödi
- the Department of Medical Chemistry, University of Debrecen, Medical and Health Science Center, H-4032 Debrecen
| | - László Buday
- the Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1113 Budapest, and
- the Department of Medical Chemistry, Semmelweis University Medical School, H-1094 Budapest, Hungary
| | - József Kardos
- From the Department of Biochemistry, Eötvös Loránd University, H-1117 Budapest
| | - Mihály Kovács
- From the Department of Biochemistry, Eötvös Loránd University, H-1117 Budapest
| | - László Nyitray
- From the Department of Biochemistry, Eötvös Loránd University, H-1117 Budapest
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55
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García-Mayoral MF, Rodríguez-Crespo I, Bruix M. Structural models of DYNLL1 with interacting partners: African swine fever virus protein p54 and postsynaptic scaffolding protein gephyrin. FEBS Lett 2010; 585:53-7. [PMID: 21094642 DOI: 10.1016/j.febslet.2010.11.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 10/18/2010] [Accepted: 11/12/2010] [Indexed: 11/26/2022]
Abstract
DYNLL1, the smallest dynein light chain, interacts with different cargos facilitating their cellular transport. Usually the sequence recognized in the targets is homologous to the GIQVD or the KXTQT motifs with a glutamine that is important for binding. Here we add two new examples of DYNLL1 targets that can be classified into these two groups: ASFV p54 and gephyrin. Using NMR we demonstrate the direct interaction between DYNLL1 and two peptides derived from their interacting sequences. We model the structure of both complexes and show that the overall binding mode is preserved as in other complexes despite differences at the residue-specific interactions.
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Affiliation(s)
- María Flor García-Mayoral
- Departamento de Química Física Biológica, Instituto de Química Física Rocasolano, CSIC, Madrid, Spain.
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56
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Xiao F, Weng J, Fan K, Wang W. Mechanism of Ser88 phosphorylation-induced dimer dissociation in dynein light chain LC8. J Phys Chem B 2010; 114:15663-72. [PMID: 21062069 DOI: 10.1021/jp1048869] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dynein light chain LC8 is a highly conserved, dimeric protein involved in a variety of essential cellular events. Phosphorylation at Ser88 was found to promote mammalian cell survival and regulate the dimer to monomer transition at physiological pH. Combining molecular dynamics (MD) simulation and free energy calculation methods, we explored the atomistic mechanism of the phosphorylation-induced dimer dissociation. The MD simulation revealed that phosphorylation/phosphomimetic mutation at Ser88 opens an entrance into the dimer interface for water molecules, which disturb the hydrogen bond network around His55 and is expected to raise the pK(a) value and protonation ratio of His55 as well. The free energy calculations showed that the S88E mutation destabilized the dimer by 6.6 kcal/mol, in good agreement with the experimental value of 8.1 kcal/mol. The calculated destabilization upon phosphorylation is 50.8 kcal/mol, showing that phosphorylation definitely prevents dimer formation under physiological conditions. Further analysis of the calculated free energy changes demonstrated that the electrostatic contribution dominates the impact of phosphorylation on dimer dissociation.
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Affiliation(s)
- Fei Xiao
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, People's Republic of China
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57
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Kuta A, Deng W, Morsi El-Kadi A, Banks GT, Hafezparast M, Pfister KK, Fisher EMC. Mouse cytoplasmic dynein intermediate chains: identification of new isoforms, alternative splicing and tissue distribution of transcripts. PLoS One 2010; 5:e11682. [PMID: 20657784 PMCID: PMC2908135 DOI: 10.1371/journal.pone.0011682] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Accepted: 06/20/2010] [Indexed: 01/13/2023] Open
Abstract
Background Intracellular transport of cargoes including organelles, vesicles, signalling molecules, protein complexes, and RNAs, is essential for normal function of eukaryotic cells. The cytoplasmic dynein complex is an important motor that moves cargos along microtubule tracks within the cell. In mammals this multiprotein complex includes dynein intermediate chains 1 and 2 which are encoded by two genes, Dync1i1 and Dync1i2. These proteins are involved in dynein cargo binding and dynein complexes with different intermediate chains bind to specific cargoes, although the mechanisms to achieve this are not known. The DYNC1I1 and DYNC1I2 proteins are translated from different splice isoforms, and specific forms of each protein are essential for the function of different dynein complexes in neurons. Methodology/Principal Findings Here we have undertaken a systematic survey of the dynein intermediate chain splice isoforms in mouse, basing our study on mRNA expression patterns in a range of tissues, and on bioinformatics analysis of mouse, rat and human genomic and cDNA sequences. We found a complex pattern of alternative splicing of both dynein intermediate chain genes, with maximum complexity in the embryonic and adult nervous system. We have found novel transcripts, including some with orthologues in human and rat, and a new promoter and alternative non-coding exon 1 for Dync1i2. Conclusions/Significance These data, including the cloned isoforms will be essential for understanding the role of intermediate chains in the cytoplasmic dynein complex, particularly their role in cargo binding within individual tissues including different brain regions.
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Affiliation(s)
- Anna Kuta
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, United Kingdom
| | - Wenhan Deng
- Biochemistry and Biomedical Science, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Ali Morsi El-Kadi
- Biochemistry and Biomedical Science, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Gareth T. Banks
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, United Kingdom
| | - Majid Hafezparast
- Biochemistry and Biomedical Science, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - K. Kevin Pfister
- Cell Biology Department, School of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Elizabeth M. C. Fisher
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, United Kingdom
- * E-mail:
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58
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Hall J, Song Y, Karplus PA, Barbar E. The crystal structure of dynein intermediate chain-light chain roadblock complex gives new insights into dynein assembly. J Biol Chem 2010; 285:22566-75. [PMID: 20472935 DOI: 10.1074/jbc.m110.103861] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The roadblock/LC7 dynein light chain is a ubiquitous component of all dyneins and is essential for many diverse processes including proper axonal transport and dendrite growth. In addition, LC7 functions in non-dynein transcriptional activation of the transforming growth factor-beta complex. Crystal structures of Drosophila melanogaster LC7 in the apo form and in complex with a segment of the disordered N-terminal domain of dynein intermediate chain (IC) provide the first definitive identification of the IC sequence recognized by LC7. The site, confirmed by isothermal titration calorimetry studies, overlaps the IC sequence considered in the literature to be an IC self-association domain. The IC peptide binds as two amphipathic helices that lie along an extensive hydrophobic cleft on LC7 and ends with a polar side-chain interaction network that includes conserved residues from both proteins. The LC7 recognition sequence on IC and its interface with LC7 are well conserved and are, thus, likely representative of all IC x LC7 structures. Interestingly, the position of bound IC in the IC x LC7 complex mimics a helix that is integrated into the primary structure in distantly related LC7 homologs. The IC x LC7 structure further shows that the naturally occurring robl(Z) deletion mutation contains the majority of the IC binding site and suggests that promotion of IC binding by phosphorylation of LC7 is an indirect effect.
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Affiliation(s)
- Justin Hall
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA
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59
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Benison G, Chiodo M, Karplus PA, Barbar E. Structural, thermodynamic, and kinetic effects of a phosphomimetic mutation in dynein light chain LC8. Biochemistry 2009; 48:11381-9. [PMID: 19863079 PMCID: PMC2821902 DOI: 10.1021/bi901589w] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Dynein light chain LC8 is a small, dimeric, very highly conserved globular protein first identified as an integral part of the dynein and myosin molecular motors but now recognized as a dimerization hub with wider significance. Phosphorylation at Ser88 is thought to be involved in regulating LC8 in the apoptotic pathway. The phosphomimetic Ser88Glu mutation weakens dimerization of LC8 and thus its overall ligand-binding affinity, because only the dimer binds ligands. The 1.9 A resolution crystal structure of dimeric LC8(S88E) bound to a fragment of the ligand Swallow (Swa) presented here shows that the tertiary structure is identical to that of wild-type LC8/Swa, with Glu88 well accommodated sterically at the dimer interface. NMR longitudinal magnetization exchange spectroscopy reveals remarkably slow association kinetics (k(on) approximately 1 s(-1) mM(-1)) in the monomer-dimer equilibrium of both wild-type LC8 and LC8(S88E), possibly due to the strand-swapped architecture of the dimer. The Ser88Glu mutation raises the dimer dissociation constant (K(D)) through a combination of a higher k(off) and lower k(on). Using a minimal model of titration linked to dimerization, we dissect the thermodynamics of dimerization of wild-type LC8 and LC8(S88E) in their various protonation states. When both Glu88 residues are protonated, the LC8(S88E) dimer is nearly as stable as the wild-type dimer, but deprotonation of one Glu88 residue raises K(D) by a factor of 400. We infer that phosphorylation of one subunit of wild-type LC8 raises K(D) by at least as much to prevent dimerization of LC8 at physiological concentrations. Some LC8 binding partners may bind tightly enough to promote dimerization even when one subunit is phosphorylated; thus linkage between phosphorylation and dimerization provides a mechanism for differential regulation of binding of LC8 to its diverse partners.
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Affiliation(s)
- Gregory Benison
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
| | - Marcus Chiodo
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
| | - P. Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
| | - Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
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60
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Dorsett M, Schedl T. A role for dynein in the inhibition of germ cell proliferative fate. Mol Cell Biol 2009; 29:6128-39. [PMID: 19752194 PMCID: PMC2772574 DOI: 10.1128/mcb.00815-09] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Revised: 07/24/2009] [Accepted: 09/08/2009] [Indexed: 01/30/2023] Open
Abstract
During normal development as well as in diseased states such as cancer, extracellular "niches" often provide cues to proximal cells and activate intracellular pathways. Activation of such signaling pathways in turn instructs cellular proliferation and differentiation. In the Caenorhabditis elegans gonad, GLP-1/Notch signaling instructs germ line stem cells to self-renew through mitotic cell division. As germ cells progressively move out of the niche, they differentiate by entering meiosis and eventually form gametes. In this model system, we uncovered an unexpected role for the dynein motor complex in promoting normal differentiation of proliferating germ cells. We demonstrate that dynein light chain 1 (DLC-1) and its partner, dynein heavy chain 1, inhibit the proliferative cell fate, in part through regulation of METT-10, a conserved putative methyltransferase. We show that DLC-1 physically interacts with METT-10 and promotes both its overall levels and nuclear accumulation. Our results add a new dimension to the processes controlled by the dynein motor complex, demonstrating that dynein can act as an antiproliferative factor.
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Affiliation(s)
- Maia Dorsett
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, 63110
| | - Tim Schedl
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, 63110
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61
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Hall J, Karplus PA, Barbar E. Multivalency in the assembly of intrinsically disordered Dynein intermediate chain. J Biol Chem 2009; 284:33115-21. [PMID: 19759397 DOI: 10.1074/jbc.m109.048587] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Dynein light chains are thought to increase binding efficiency of dynein intermediate chain to both dynein heavy chain and dynactin, but their exact role is not clear. Isothermal titration calorimetry and x-ray crystallography reported herein indicate that multivalency effects underlie efficient dynein assembly and regulation. For a ternary complex of a 60-amino acid segment of dynein intermediate chain (IC) bound to two homodimeric dynein light chains Tctex1 and LC8, there is a 50-fold affinity enhancement for the second light chain binding. For a designed IC construct containing two LC8 sites, observed the 1000-fold enhancement reflects a remarkably pure entropic chelate effect of a magnitude commensurate with theoretical predictions. The lower enhancement in wild-type IC is attributed to unfavorable free energy changes associated with incremental interactions of IC with Tctex1. Our results show assembled dynein IC as an elongated, flexible polybivalent duplex, and suggest that polybivalency is an important general mechanism for constructing stable yet reversible and functionally versatile complexes.
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Affiliation(s)
- Justin Hall
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA
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62
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Abstract
NMR is a powerful tool for quantitative measurement of the thermodynamic properties of biological systems. In this review, we discuss the role NMR has played in understanding the various coupled equilibria in dimerization of dynein light chain LC8 and in its interactions with its ligands. LC8, a very highly conserved 89-residue homodimer also known as DYNLL, is an essential component of the dynein and Myosin V molecular motors and is also found in various other complexes. LC8 binds to disordered segments of its partners, promoting them to dimerize and form more ordered structures, often coiled coils. The monomer-dimer equilibrium is controlled by electrostatic interactions at the dimer interface, such as by phosphorylation of residue Ser88, which is a regulatory mechanism for LC8 in vivo. NMR experiments have uncovered several subtle interactions--weak dimerization of a phosphomimetic mutant, and allosteric interaction between the LC8 binding sites--that have been overlooked by other methods. NMR has also provided a residue-specific view of the titration of histidine residues at the LC8 dimer interface, and of a nascent helix in one of the binding partners, the primarily disordered dynein intermediate chain IC74. We give special attention to methods for quantitative interpretation of NMR spectra, an important consideration when using NMR to measure equilibria.
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63
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Palmer KJ, Hughes H, Stephens DJ. Specificity of cytoplasmic dynein subunits in discrete membrane-trafficking steps. Mol Biol Cell 2009; 20:2885-99. [PMID: 19386764 DOI: 10.1091/mbc.e08-12-1160] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The cytoplasmic dynein motor complex is known to exist in multiple forms, but few specific functions have been assigned to individual subunits. A key limitation in the analysis of dynein in intact mammalian cells has been the reliance on gross perturbation of dynein function, e.g., inhibitory antibodies, depolymerization of the entire microtubule network, or the use of expression of dominant negative proteins that inhibit dynein indirectly. Here, we have used RNAi and automated image analysis to define roles for dynein subunits in distinct membrane-trafficking processes. Depletion of a specific subset of dynein subunits, notably LIC1 (DYNC1LI1) but not LIC2 (DYNC1LI2), recapitulates a direct block of ER export, revealing that dynein is required to maintain the steady-state composition of the Golgi, through ongoing ER-to-Golgi transport. Suppression of LIC2 but not of LIC1 results in a defect in recycling endosome distribution and cytokinesis. Biochemical analyses also define the role of each subunit in stabilization of the dynein complex; notably, suppression of DHC1 or IC2 results in concomitant loss of Tctex1. Our data demonstrate that LIC1 and LIC2 define distinct dynein complexes that function at the Golgi versus recycling endosomes, respectively, suggesting that functional populations of dynein mediate discrete intracellular trafficking pathways.
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Affiliation(s)
- Krysten J Palmer
- Cell Biology Laboratories, Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS81TD, United Kingdom
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64
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Ammar ED, Tsai CW, Whitfield AE, Redinbaugh MG, Hogenhout SA. Cellular and molecular aspects of rhabdovirus interactions with insect and plant hosts. ANNUAL REVIEW OF ENTOMOLOGY 2009; 54:447-68. [PMID: 18793103 DOI: 10.1146/annurev.ento.54.110807.090454] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The rhabdoviruses form a large family (Rhabdoviridae) whose host ranges include humans, other vertebrates, invertebrates, and plants. There are at least 90 plant-infecting rhabdoviruses, several of which are economically important pathogens of various crops. All definitive plant-infecting and many vertebrate-infecting rhabdoviruses are persistently transmitted by insect vectors, and a few putative plant rhabdoviruses are transmitted by mites. Plant rhabdoviruses replicate in their plant and arthropod hosts, and transmission by vectors is highly specific, with each virus species transmitted by one or a few related insect species, mainly aphids, leafhoppers, or planthoppers. Here, we provide an overview of plant rhabdovirus interactions with their insect hosts and of how these interactions compare with those of vertebrate-infecting viruses and with the Sigma rhabdovirus that infects Drosophila flies. We focus on cellular and molecular aspects of vector/host specificity, transmission barriers, and virus receptors in the vectors. In addition, we briefly discuss recent advances in understanding rhabdovirus-plant interactions.
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Affiliation(s)
- El-Desouky Ammar
- Department of Entomology, The Ohio State University-OARDC, Wooster, Ohio 44691, USA.
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65
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King SM. Dynein-independent functions of DYNLL1/LC8: redox state sensing and transcriptional control. Sci Signal 2008; 1:pe51. [PMID: 19036713 DOI: 10.1126/scisignal.147pe51] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The highly conserved DYNLL/LC8 proteins promote dimerization of a broad range of targets and are essential for the integrity, activity, or both, of many subcellular systems, such as dyneins, myosin V, and apoptotic factors. Defects in DYNLL/LC8 function lead to severe cellular and developmental phenotypes in multicellular organisms, whereas loss-of-function alleles are lethal. DYNLL/LC8 dimer formation may be controlled by various signaling inputs (including pH changes and phosphorylation), and dimerization has been linked to alterations in the enzymatic activity of neuronal nitric oxide synthase and apoptotic control. A recent report now proposes that DYNLL/LC8-driven interactions are also regulated by changes in cellular redox state, which lead to intermonomer disulfide bond formation and ultimately activation of the transcription factor NF-kappaB.
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Affiliation(s)
- Stephen M King
- Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, CT 06030-3305, USA.
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66
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Hall J, Hall A, Pursifull N, Barbar E. Differences in Dynamic Structure of LC8 Monomer, Dimer, and Dimer−Peptide Complexes. Biochemistry 2008; 47:11940-52. [DOI: 10.1021/bi801093k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Justin Hall
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Andrea Hall
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Nathan Pursifull
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
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67
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The interplay of ligand binding and quaternary structure in the diverse interactions of dynein light chain LC8. J Mol Biol 2008; 384:954-66. [PMID: 18948118 DOI: 10.1016/j.jmb.2008.09.083] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 09/27/2008] [Accepted: 09/29/2008] [Indexed: 11/20/2022]
Abstract
Dynein light chain LC8 is a small, dimeric, and very highly conserved globular protein that is an integral part of the dynein and myosin molecular motors but appears to have a broader role in multiple protein complexes unrelated to molecular motors. LC8 binds to two families of targets: those having a KXTQT sequence fingerprint and those having a GIQVD fingerprint. All known LC8 binding partners containing these fingerprints share a common binding site on LC8 that raises the question of what determines binding specificity. Here, we present the crystal structure of apo-LC8 at 1.7-A resolution, which, when compared with the crystal structures of several LC8 complexes, gives insight into the mechanism underlying the binding diversity of LC8. Peptide binding is associated with a shift in quaternary structure that expands the hydrophobic binding surface available to the ligand, in addition to changes in tertiary structure and ordering of LC8 around the binding groove. The observed quaternary shift suggests a mechanism by which binding at one of the two identical sites can influence binding at the other. NMR spectra of titrations with peptides from each fingerprint family show evidence of allosteric interaction between the two binding sites, to a differing degree in the two ligand families. Allosteric interaction between the binding sites may be a mechanism to promote simultaneous binding of ligands from the same family, providing a physiological role for the two fingerprints.
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68
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Kwon EJ, Bergen JM, Park IK, Pun SH. Peptide-modified vectors for nucleic acid delivery to neurons. J Control Release 2008; 132:230-5. [PMID: 18627784 DOI: 10.1016/j.jconrel.2008.06.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2008] [Revised: 06/05/2008] [Accepted: 06/13/2008] [Indexed: 12/26/2022]
Abstract
Neuron-targeted nucleic acid delivery systems are important technologies for realizing the potential of gene therapy for nervous system disorders. However, neurons are difficult cells to transfect using non-viral vectors due in part to the specific and unique delivery challenges present in these cells. We have investigated several bioactive peptides for their ability to assist in overcoming delivery barriers in mammalian cells. We summarize here our recent progress in developing and applying peptide-modified polycations for nucleic acid delivery. In addition, we present data demonstrating the potential of using multicomponent, peptide-modified polycations for nucleic acid delivery to neurons.
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Affiliation(s)
- E J Kwon
- Department of Bioengineering, University of Washington, Seattle WA 98195, USA
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69
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Barbar E. Dynein Light Chain LC8 Is a Dimerization Hub Essential in Diverse Protein Networks. Biochemistry 2007; 47:503-8. [DOI: 10.1021/bi701995m] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
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70
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Lo KWH, Kogoy JM, Rasoul BA, King SM, Pfister KK. Interaction of the DYNLT (TCTEX1/RP3) light chains and the intermediate chains reveals novel intersubunit regulation during assembly of the dynein complex. J Biol Chem 2007; 282:36871-8. [PMID: 17965411 DOI: 10.1074/jbc.m705991200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cytoplasmic dynein 1 cargo binding domain is formed by five subunits including the intermediate chain and the DYNLT, DYNLL, and DYNLRB light chain families. Six isoforms of the intermediate chain and two isoforms of each of the light chain families have been identified in mammals. There is evidence that different subunit isoforms are involved in regulating dynein function, in particular linking dynein to different cargoes. However, it is unclear how the subunit isoforms are assembled or if there is any specificity to their interactions. Co-immunoprecipitation using DYNLT-specific antibodies reveals that dynein complexes with DYNLT light chains also contain the DYNLL and DYNLRB light chains. The DYNLT light chains, but not DYNLL light chains, associate exclusively with the dynein complex. Yeast two-hybrid and co-immunoprecipitation assays demonstrate that both members of the DYNLT family are capable of forming homodimers and heterodimers. In addition, both homodimers of the DYNLT family bind all six intermediate chain isoforms. However, DYNLT heterodimers do not bind to the intermediate chain. Thus, whereas all combinations of DYNLT light chain dimers can be made, not all of the possible combinations of the isoforms are utilized during the assembly of the dynein complex.
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Affiliation(s)
- Kevin W-H Lo
- Department of Cell Biology, School of Medicine, University of Virginia, Charlottesville, Virginia 22908, USA
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