Structural Features of LC8-Induced Self-Association of Swallow

Kidane, Ariam I.; Song, Yanjun; Nyarko, Afua; Hall, J. Perry; Hare, Michael; Löhr, Frank; Barbar, Elisar

doi:10.1021/bi400642u

Cited by 17 publications

(32 citation statements)

References 43 publications

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“…For an LC8 binding partner called Swallow, also primarily disordered, the two Swallow chains are linked by a weakly predicted coiled-coil N-terminal to the LC8 recognition motif. To determine the origin of LC8 binding enhancement due to Swallow self-association, binding thermodynamics were measured for two Swallow constructs designed to decouple self-association from LC8 binding [8]. Swa DIMER , an engineered variant with coiled-coil stabilizing mutations, is a tightly associated bivalent binding partner with two aligned recognition sequences for LC8, and Swa MONOMER , an engineered variant with coiled-coil destabilizing mutations is a disordered monovalent chain with one LC8 recognition motif.…”

Section: Bivalency Enhances Binding Affinity and Results In Formatmentioning

confidence: 99%

“…The absence of temperature dependence (ΔΔCp of zero) shows that binding enhancement (ΔΔG°) is not due to enthalpic change (ΔΔH° of zero) but due to entropic change (Δ-TΔS° of same value as ΔΔG°). Figures adapted from [5], and [8]. …”

Section: Figurementioning

confidence: 99%

“…Binding enhancement arising from bivalency/polybivalency has been demonstrated in assembly of Swallow/LC8 complex [7, 8], the nuclear pore protein Nup159/LC8 complex [9] and the dynein intermediate chain/light chains complex [4, 5, 10, 11]. A common feature among the three systems is that a segment of their disordered regions has one or more recognition motifs for the hub protein LC8 [12].…”

Section: Introductionmentioning

confidence: 99%

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Polybivalency and disordered proteins in ordering macromolecular assemblies

Barbar¹,

Nyarko²

2015

Seminars in Cell & Developmental Biology

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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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Section: Bivalency Enhances Binding Affinity and Results In Formatmentioning

confidence: 99%

Section: Figurementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Polybivalency and disordered proteins in ordering macromolecular assemblies

Barbar¹,

Nyarko²

2015

Seminars in Cell & Developmental Biology

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“…The growing range of biological functions served by IDP duplex scaffolds is impressive, from dynein assembly and regulation [26, 51–53], to nuclear pores [28, 54], to virus maturation [55, 56]. Additional examples are associated with mRNA localization and lung development [31, 57, 58]. While the full functional implications of IDP duplexes are still under examination in our lab and others, these four intriguing and unique characteristics of IDP duplex structure are well documented.…”

Section: Categories Of Multivalent Idp Assembliesmentioning

confidence: 99%

Multivalent IDP assemblies: Unique properties of LC8‐associated, IDP duplex scaffolds

et al. 2015

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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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“…Promoter-bound CITFA is able, either directly or indirectly, to recruit RNA Pol I and enable transcription initiation. 62; reviewed in references 13 and 20), the Drosophila RNA-binding protein Swallow (24,63), the human motor protein myosin Va (21,22), and the yeast nucleoporin Nup159 (64,65).…”

Section: Figmentioning

confidence: 99%

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

Kirkham

Park

Nguyen

et al. 2016

Molecular and Cellular Biology

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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. Dynein light chain LC8 was originally discovered as a component of the outer arm axonemal dynein in Chlamydomonas reinhardtii (1) but was later found to be present also in cytoplasmic dyneins 1 and 2 (2-4). LC8 is conserved throughout eukaryotic genomes (5). As a part of the dynein motor, LC8 is important for fundamental cellular processes, such as tubulin minus-enddirected intracellular transport, chromatid separation during mitosis, and nuclear migration (6), as well as flagellum-specific functions, namely, motility, intraflagellar transport (7), and ciliogenesis (8, 9). While not essential in Saccharomyces cerevisiae (10), mutation or knockdown of LC8 is embryonic lethal in animals (8,9,11,12). Given that LC8 is more conserved between species than other components of the dynein motor and that LC8 is present in organisms which lack a dynein motor, it was likely that LC8 had nondynein functions (3, 5). LC8 has since been shown to interact with several different proteins and to affect various cellular processes, including protein localization and stability, transcription regulation, and apoptosis (13-15).At physiological pH, LC8 exists almost exclusively as a dimer (16, 17), interacting with partner proteins via two identical sites generated at the dimer interface which bind to diverse short, linear motifs (16,18,19). LC8 promotes the dimerization of its binding partners through aligning dimerization domains present in the partner protein (13,(20)(21)(22). While it was previously hypothesized that LC8 functions as a linker, allowing attachment of the dynein motor to its cargo, the emerging view is that interaction with LC8 induces dimerization, imparting new s...

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Structural Features of LC8-Induced Self-Association of Swallow

Cited by 17 publications

References 43 publications

Polybivalency and disordered proteins in ordering macromolecular assemblies

Polybivalency and disordered proteins in ordering macromolecular assemblies

Multivalent IDP assemblies: Unique properties of LC8‐associated, IDP duplex scaffolds

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

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