Nathan McDonald
Basic Life Science Research Associate, Biology
Honors & Awards
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K99 Pathway to Independence Award, NIH NINDS (2021-2023)
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Postdoctoral Research Fellowship, The Helen Hay Whitney Foundation (2019-2021)
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(declined) Ruth L. Kirschstein National Research Service Award F32, NIH NINDS (2018)
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Stanford Training Program in Aging Research T32, NIH NIA (2017)
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Most Outstanding Graduate Student Award, Vanderbilt Department of Cell and Developmental Biology (2016)
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Predoctoral Fellowship, American Heart Association (2015-2016)
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Colonel Robinson Merit Scholarship, University of North Carolina at Chapel Hill (2007-2011)
https://orcid.org/0000-0003-2716-3881Links
Current Research and Scholarly Interests
I am interested in the fundamental cell biology of neurons. In particular, I study how neuronal synapses are formed and function. Synapses are specialized intercellular junctions that facilitate rapid communication between neurons, and thus form the basis of neural circuits and nervous system function.
Within a synapse, synaptic vesicles containing neurotransmitters are released at a specific region termed the active zone. The active zone is composed of a variety of molecules that coordinate the tethering and priming of synaptic vesicles, the recruitment of ion channels to respond to action potentials, and the stabilization of the synapse through transmembrane connections to a postsynaptic cell.
A wide range of transmembrane proteins are capable of initiating synapse formation during development and provide specificity for targeting the proper postsynaptic cell, including Neurexins/Neuroligins, LRRTMs, DIPs/DPRs, and many Ig domain proteins. However, in all synapses, these molecules must signal to build a common active zone core. I am studying how the conserved active zone core assembles downstream of this complexity, a fundamental unresolved question in developmental neurobiology.
To study this problem, I use the simple and stereotyped nervous system of the nematode Caenorhabditis elegans. I use fluorescent imaging of endogenous proteins at single neuron and single synapse resolution, as well as genetic and biochemical methods.
All Publications
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SAD-1 kinase controls presynaptic phase separation by relieving SYD-2/Liprin-α autoinhibition.
PLoS biology
2023; 21 (12): e3002421
Abstract
Neuronal development orchestrates the formation of an enormous number of synapses that connect the nervous system. In developing presynapses, the core active zone structure has been found to assemble through liquid-liquid phase separation. Here, we find that the phase separation of Caenorhabditis elegans SYD-2/Liprin-α, a key active zone scaffold, is controlled by phosphorylation. We identify the SAD-1 kinase as a regulator of SYD-2 phase separation and determine presynaptic assembly is impaired in sad-1 mutants and increased by overactivation of SAD-1. Using phosphoproteomics, we find SAD-1 phosphorylates SYD-2 on 3 sites that are critical to activate phase separation. Mechanistically, SAD-1 phosphorylation relieves a binding interaction between 2 folded domains in SYD-2 that inhibits phase separation by an intrinsically disordered region (IDR). We find synaptic cell adhesion molecules localize SAD-1 to nascent synapses upstream of active zone formation. We conclude that SAD-1 phosphorylates SYD-2 at developing synapses, activating its phase separation and active zone assembly.
View details for DOI 10.1371/journal.pbio.3002421
View details for PubMedID 38048304
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Finding functions of phase separation in the presynapse.
Current opinion in neurobiology
2021; 69: 178–84
Abstract
Synapses are the basic units of neuronal communication. Understanding how synapses assemble and function is therefore essential to understanding nervous systems. Decades of study have identified many molecular components and functional mechanisms of synapses. Recently, an additional level of synaptic protein organization has been identified: phase separation. In the presynapse, components of the central active zone and a synaptic vesicle-clustering factor have been shown to form liquid-liquid phase-separated condensates or hydrogels. New in vivo functional studies have directly tested how phase separation impacts both synapse formation and function. Here, we review this emerging evidence for in vivo functional roles of phase separation at the presynapse and discuss future functional studies necessary to understand its complexity.
View details for DOI 10.1016/j.conb.2021.04.001
View details for PubMedID 33979706
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Opposite Surfaces of the Cdc15 F-BAR Domain Create a Membrane Platform That Coordinates Cytoskeletal and Signaling Components for Cytokinesis
CELL REPORTS
2020; 33 (12): 108526
Abstract
Many eukaryotes assemble an actin- and myosin-based cytokinetic ring (CR) on the plasma membrane (PM) for cell division, but how it is anchored there remains unclear. In Schizosaccharomyces pombe, the F-BAR protein Cdc15 links the PM via its F-BAR domain to proteins in the CR's interior via its SH3 domain. However, Cdc15's F-BAR domain also directly binds formin Cdc12, suggesting that Cdc15 may polymerize a protein network directly adjacent to the membrane. Here, we determine that the F-BAR domain binds Cdc12 using residues on the face opposite its membrane-binding surface. These residues also bind paxillin-like Pxl1, promoting its recruitment with calcineurin to the CR. Mutation of these F-BAR domain residues results in a shallower CR, with components localizing ∼35% closer to the PM than in wild type, and aberrant CR constriction. Thus, F-BAR domains serve as oligomeric membrane-bound platforms that can modulate the architecture of an entire actin structure.
View details for DOI 10.1016/j.celrep.2020.108526
View details for Web of Science ID 000601399100006
View details for PubMedID 33357436
View details for PubMedCentralID PMC7775634
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Assembly of synaptic active zones requires phase separation of scaffold molecules.
Nature
2020
Abstract
The formation of synapses during neuronal development is essential for establishing neural circuits and a nervous system1. Every presynapse builds a core 'active zone' structure, where ion channels cluster and synaptic vesicles release their neurotransmitters2. Although the composition of active zones is well characterized2,3, it is unclear how active-zone proteins assemble together and recruit the machinery required for vesicle release during development. Here we find that the core active-zone scaffold proteins SYD-2(also known asliprin-alpha) and ELKS-1 undergo phase separation during an early stage of synapse development, and later mature into a solid structure. We directly test the in vivo function of phase separation by using mutant SYD-2 and ELKS-1 proteins that specifically lack this activity. These mutant proteins remain enriched at synapses in Caenorhabditis elegans, but show defects in active-zone assembly and synapse function. The defects are rescued by introducing a phase-separation motif from an unrelated protein. In vitro, we reconstitute the SYD-2 and ELKS-1 liquid-phase scaffold, and find that it is competent to bind and incorporate downstream active-zone components. We find that the fluidity of SYD-2 and ELKS-1 condensates is essential for efficient mixing and incorporation of active-zone components. These data reveal that a developmental liquid phase of scaffold molecules is essential for the assembly of the synaptic active zone, before maturation into a stable final structure.
View details for DOI 10.1038/s41586-020-2942-0
View details for PubMedID 33208945
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DYRK kinase Pom1 drives F-BAR protein Cdc15 from the membrane to promote medial division
MOLECULAR BIOLOGY OF THE CELL
2020; 31 (9): 917–29
Abstract
In many organisms, positive and negative signals cooperate to position the division site for cytokinesis. In the rod-shaped fission yeast Schizosaccharomyces pombe, symmetric division is achieved through anillin/Mid1-dependent positive cues released from the central nucleus and negative signals from the DYRK-family polarity kinase Pom1 at cell tips. Here we establish that Pom1's kinase activity prevents septation at cell tips even if Mid1 is absent or mislocalized. We also find that Pom1 phosphorylation of F-BAR protein Cdc15, a major scaffold of the division apparatus, disrupts Cdc15's ability to bind membranes and paxillin, Pxl1, thereby inhibiting Cdc15's function in cytokinesis. A Cdc15 mutant carrying phosphomimetic versions of Pom1 sites or deletion of Cdc15 binding partners suppresses division at cell tips in cells lacking both Mid1 and Pom1 signals. Thus, inhibition of Cdc15-scaffolded septum formation at cell poles is a key Pom1 mechanism that ensures medial division.
View details for DOI 10.1091/mbc.E20-01-0026
View details for Web of Science ID 000530663100007
View details for PubMedID 32101481
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The F-BAR Domain of Rga7 Relies on a Cooperative Mechanism of Membrane Binding with a Partner Protein during Fission Yeast Cytokinesis
CELL REPORTS
2019; 26 (10): 2540-+
Abstract
F-BAR proteins bind the plasma membrane (PM) to scaffold and organize the actin cytoskeleton. To understand how F-BAR proteins achieve their PM association, we studied the localization of a Schizosaccharomyces pombe F-BAR protein Rga7, which requires the coiled-coil protein Rng10 for targeting to the division site during cytokinesis. We find that the Rga7 F-BAR domain directly binds a motif in Rng10 simultaneously with the PM, and that an adjacent Rng10 motif independently binds the PM. Together, these multivalent interactions significantly enhance Rga7 F-BAR avidity for membranes at physiological protein concentrations, ensuring the division site localization of Rga7. Moreover, the requirement for the F-BAR domain in Rga7 localization and function in cytokinesis is bypassed by tethering an Rga7 construct lacking its F-BAR to Rng10, indicating that at least some F-BAR domains are necessary but not sufficient for PM targeting and are stably localized to specific cortical positions through adaptor proteins.
View details for DOI 10.1016/j.celrep.2019.01.112
View details for Web of Science ID 000460280800003
View details for PubMedID 30840879
View details for PubMedCentralID PMC6425953
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Nanoscale architecture of the Schizosaccharomyces pombe contractile ring.
eLife
2017; 6
Abstract
The contractile ring is a complex molecular apparatus which physically divides many eukaryotic cells. Despite knowledge of its protein composition, the molecular architecture of the ring is not known. Here we have applied super-resolution microscopy and FRET to determine the nanoscale spatial organization of Schizosaccharomyces pombe contractile ring components relative to the plasma membrane. Similar to other membrane-tethered actin structures, we find proteins localize in specific layers relative to the membrane. The most membrane-proximal layer (0-80 nm) is composed of membrane-binding scaffolds, formin, and the tail of the essential myosin-II. An intermediate layer (80-160 nm) consists of a network of cytokinesis accessory proteins as well as multiple signaling components which influence cell division. Farthest from the membrane (160-350 nm) we find F-actin, the motor domains of myosins, and a major F-actin crosslinker. Circumferentially within the ring, multiple proteins proximal to the membrane form clusters of different sizes, while components farther from the membrane are uniformly distributed. This comprehensive organizational map provides a framework for understanding contractile ring function.
View details for DOI 10.7554/eLife.28865
View details for PubMedID 28914606
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Structural organization of membrane-inserted hexamers formed by Helicobacter pylori VacA toxin
MOLECULAR MICROBIOLOGY
2016; 102 (1): 22-36
Abstract
Helicobacter pylori colonizes the human stomach and is a potential cause of peptic ulceration or gastric adenocarcinoma. H. pylori secretes a pore-forming toxin known as vacuolating cytotoxin A (VacA). The 88 kDa secreted VacA protein, composed of an N-terminal p33 domain and a C-terminal p55 domain, assembles into water-soluble oligomers. The structural organization of membrane-bound VacA has not been characterized in any detail and the role(s) of specific VacA domains in membrane binding and insertion are unclear. We show that membrane-bound VacA organizes into hexameric oligomers. Comparison of the two-dimensional averages of membrane-bound and soluble VacA hexamers generated using single particle electron microscopy reveals a structural difference in the central region of the oligomers (corresponding to the p33 domain), suggesting that membrane association triggers a structural change in the p33 domain. Analyses of the isolated p55 domain and VacA variants demonstrate that while the p55 domain can bind membranes, the p33 domain is required for membrane insertion. Surprisingly, neither VacA oligomerization nor the presence of putative transmembrane GXXXG repeats in the p33 domain is required for membrane insertion. These findings provide new insights into the process by which VacA binds and inserts into the lipid bilayer to form membrane channels.
View details for DOI 10.1111/mmi.13443
View details for Web of Science ID 000384807900002
View details for PubMedID 27309820
View details for PubMedCentralID PMC5035229
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The Tubulation Activity of a Fission Yeast F-BAR Protein Is Dispensable for Its Function in Cytokinesis
CELL REPORTS
2016; 14 (3): 534-546
Abstract
F-BAR proteins link cellular membranes to the actin cytoskeleton in many biological processes. Here we investigated the function of the Schizosaccharomyces pombe Imp2 F-BAR domain in cytokinesis and find that it is critical for Imp2's role in contractile ring constriction and disassembly. To understand mechanistically how the F-BAR domain functions, we determined its structure, elucidated how it interacts with membranes, and identified an interaction between dimers that allows helical oligomerization and membrane tubulation. Using mutations that block either membrane binding or tubulation, we find that membrane binding is required for Imp2's cytokinetic function but that oligomerization and tubulation, activities often deemed central to F-BAR protein function, are dispensable. Accordingly, F-BARs that do not have the capacity to tubulate membranes functionally substitute for the Imp2 F-BAR, establishing that its major role is as a cell-cycle-regulated bridge between the membrane and Imp2 protein partners, rather than as a driver of membrane curvature.
View details for DOI 10.1016/j.celrep.2015.12.062
View details for Web of Science ID 000368701600014
View details for PubMedID 26776521
View details for PubMedCentralID PMC4731314
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Characterization of Cytokinetic F-BARs and Other Membrane-Binding Proteins.
Methods in molecular biology (Clifton, N.J.)
2016; 1369: 181-189
Abstract
Multiple membrane-binding proteins are key players in cytokinesis in yeast and other organisms. In vivo techniques for analyzing protein-membrane interactions are currently limited. In vitro assays allow characterization of the biochemical properties of these proteins to build a mechanistic understanding of protein-membrane interactions during cytokinesis. Here, we describe two in vitro assays to characterize FCH-Bin/Amphyphysin/RVS (F-BAR) domains and other protein's interactions with membranes: liposome co-pelleting and giant unilamellar vesicle fluorescent binding.
View details for DOI 10.1007/978-1-4939-3145-3_13
View details for PubMedID 26519313
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Linking up at the BAR: Oligomerization and F-BAR protein function
CELL CYCLE
2016; 15 (15): 1977-1985
Abstract
As cells grow, move, and divide, they must reorganize and rearrange their membranes and cytoskeleton. The F-BAR protein family links cellular membranes with actin cytoskeletal rearrangements in processes including endocytosis, cytokinesis, and cell motility. Here we review emerging information on mechanisms of F-BAR domain oligomerization and membrane binding, and how these activities are coordinated with additional domains to accomplish scaffolding and signaling functions.
View details for DOI 10.1080/15384101.2016.1190893
View details for Web of Science ID 000382232900012
View details for PubMedID 27245932
View details for PubMedCentralID PMC4968964
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Oligomerization but Not Membrane Bending Underlies the Function of Certain F-BAR Proteins in Cell Motility and Cytokinesis
DEVELOPMENTAL CELL
2015; 35 (6): 725-736
Abstract
F-BAR proteins function in diverse cellular processes by linking membranes to the actin cytoskeleton. Through oligomerization, multiple F-BAR domains can bend membranes into tubules, though the physiological importance of F-BAR-to-F-BAR assemblies is not yet known. Here, we investigate the F-BAR domain of the essential cytokinetic scaffold, Schizosaccharomyces pombe Cdc15, during cytokinesis. Challenging a widely held view that membrane deformation is a fundamental property of F-BARs, we report that the Cdc15 F-BAR binds, but does not deform, membranes in vivo or in vitro, and six human F-BAR domains-including those from Fer and RhoGAP4-share this property. Nevertheless, tip-to-tip interactions between F-BAR dimers are critical for Cdc15 oligomerization and high-avidity membrane binding, stabilization of contractile ring components at the medial cortex, and the fidelity of cytokinesis. F-BAR oligomerization is also critical for Fer and RhoGAP4 physiological function, demonstrating its broad importance to F-BAR proteins that function without membrane bending.
View details for DOI 10.1016/j.devcel.2015.11.023
View details for Web of Science ID 000366946000012
View details for PubMedID 26702831
View details for PubMedCentralID PMC4691284
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Regulation of contractile ring formation and septation in Schizosaccharomyces pombe
CURRENT OPINION IN MICROBIOLOGY
2015; 28: 46-52
Abstract
The fission yeast Schizosaccharomyces pombe has become a powerful model organism for cytokinesis studies, propelled by pioneering genetic screens in the 1980s and 1990s. S. pombe cells are rod-shaped and divide similarly to mammalian cells, utilizing a medially-placed actin-and myosin-based contractile ring. A cell wall division septum is deposited behind the constricting ring, forming the new ends of each daughter cell. Here we discuss recent advances in our understanding of the regulation of contractile ring formation through formin proteins and the role of the division septum in S. pombe cell division.
View details for DOI 10.1016/j.mib.2015.08.001
View details for Web of Science ID 000367857400007
View details for PubMedID 26340438
View details for PubMedCentralID PMC4688203
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Identification of New Players in Cell Division, DNA Damage Response, and Morphogenesis Through Construction of Schizosaccharomyces pombe Deletion Strains
G3-GENES GENOMES GENETICS
2015; 5 (3): 361-370
Abstract
Many fundamental biological processes are studied using the fission yeast, Schizosaccharomyces pombe. Here we report the construction of a set of 281 haploid gene deletion strains covering many previously uncharacterized genes. This collection of strains was tested for growth under a variety of different stress conditions. We identified new genes involved in DNA metabolism, completion of the cell cycle, and morphogenesis. This subset of nonessential gene deletions will add to the toolkits available for the study of biological processes in S. pombe.
View details for DOI 10.1534/g3.114.015701
View details for Web of Science ID 000350659600005
View details for PubMedCentralID PMC4349090
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The F-BAR Cdc15 promotes contractile ring formation through the direct recruitment of the formin Cdc12
JOURNAL OF CELL BIOLOGY
2015; 208 (4): 391-399
Abstract
In Schizosaccharomyces pombe, cytokinesis requires the assembly and constriction of an actomyosin-based contractile ring (CR). Nucleation of F-actin for the CR requires a single formin, Cdc12, that localizes to the cell middle at mitotic onset. Although genetic requirements for formin Cdc12 recruitment have been determined, the molecular mechanisms dictating its targeting to the medial cortex during cytokinesis are unknown. In this paper, we define a short motif within the N terminus of Cdc12 that binds directly to the F-BAR domain of the scaffolding protein Cdc15. Mutations preventing the Cdc12-Cdc15 interaction resulted in reduced Cdc12, F-actin, and actin-binding proteins at the CR, which in turn led to a delay in CR formation and sensitivity to other perturbations of CR assembly. We conclude that Cdc15 contributes to CR formation and cytokinesis via formin Cdc12 recruitment, defining a novel cytokinetic function for an F-BAR domain.
View details for DOI 10.1083/jcb.201411097
View details for Web of Science ID 000349844600004
View details for PubMedID 25688133
View details for PubMedCentralID PMC4332253
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The Cdc15 and Imp2 SH3 domains cooperatively scaffold a network of proteins that redundantly ensure efficient cell division in fission yeast
MOLECULAR BIOLOGY OF THE CELL
2015; 26 (2): 256-269
Abstract
Schizosaccharomyces pombe cdc15 homology (PCH) family members participate in numerous biological processes, including cytokinesis, typically by bridging the plasma membrane via their F-BAR domains to the actin cytoskeleton. Two SH3 domain-containing PCH family members, Cdc15 and Imp2, play critical roles in S. pombe cytokinesis. Although both proteins localize to the contractile ring, with Cdc15 preceding Imp2, only cdc15 is an essential gene. Despite these distinct roles, the SH3 domains of Cdc15 and Imp2 cooperate in the essential process of recruiting other proteins to stabilize the contractile ring. To better understand the connectivity of this SH3 domain-based protein network at the CR and its function, we used a biochemical approach coupled to proteomics to identify additional proteins (Rgf3, Art1, Spa2, and Pos1) that are integrated into this network. Cell biological and genetic analyses of these SH3 partners implicate them in a range of activities that ensure the fidelity of cell division, including promoting cell wall metabolism and influencing cell morphogenesis.
View details for DOI 10.1091/mbc.E14-10-1451
View details for Web of Science ID 000348857200009
View details for PubMedID 25428987
View details for PubMedCentralID PMC4294673
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Convergent Targeting of a Common Host Protein-Network by Pathogen Effectors from Three Kingdoms of Life
CELL HOST & MICROBE
2014; 16 (3): 364-375
Abstract
While conceptual principles governing plant immunity are becoming clear, its systems-level organization and the evolutionary dynamic of the host-pathogen interface are still obscure. We generated a systematic protein-protein interaction network of virulence effectors from the ascomycete pathogen Golovinomyces orontii and Arabidopsis thaliana host proteins. We combined this data set with corresponding data for the eubacterial pathogen Pseudomonas syringae and the oomycete pathogen Hyaloperonospora arabidopsidis. The resulting network identifies host proteins onto which intraspecies and interspecies pathogen effectors converge. Phenotyping of 124 Arabidopsis effector-interactor mutants revealed a correlation between intraspecies and interspecies convergence and several altered immune response phenotypes. Several effectors and the most heavily targeted host protein colocalized in subnuclear foci. Products of adaptively selected Arabidopsis genes are enriched for interactions with effector targets. Our data suggest the existence of a molecular host-pathogen interface that is conserved across Arabidopsis accessions, while evolutionary adaptation occurs in the immediate network neighborhood of effector targets.
View details for DOI 10.1016/j.chom.2014.08.004
View details for Web of Science ID 000342057000013
View details for PubMedID 25211078
View details for PubMedCentralID PMC4191710
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Independently Evolved Virulence Effectors Converge onto Hubs in a Plant Immune System Network
SCIENCE
2011; 333 (6042): 596-601
Abstract
Plants generate effective responses to infection by recognizing both conserved and variable pathogen-encoded molecules. Pathogens deploy virulence effector proteins into host cells, where they interact physically with host proteins to modulate defense. We generated an interaction network of plant-pathogen effectors from two pathogens spanning the eukaryote-eubacteria divergence, three classes of Arabidopsis immune system proteins, and ~8000 other Arabidopsis proteins. We noted convergence of effectors onto highly interconnected host proteins and indirect, rather than direct, connections between effectors and plant immune receptors. We demonstrated plant immune system functions for 15 of 17 tested host proteins that interact with effectors from both pathogens. Thus, pathogens from different kingdoms deploy independently evolved virulence proteins that interact with a limited set of highly connected cellular hubs to facilitate their diverse life-cycle strategies.
View details for DOI 10.1126/science.1203659
View details for Web of Science ID 000293222400053
View details for PubMedID 21798943
View details for PubMedCentralID PMC3170753