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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Synaptic Neurosci.</journal-id>
<journal-title>Frontiers in Synaptic Neuroscience</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Synaptic Neurosci.</abbrev-journal-title>
<issn pub-type="epub">1663-3563</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fnsyn.2022.855673</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Synaptic Neuroscience</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Identification of Synaptic DGK&#x03B8; Interactors That Stimulate DGK&#x03B8; Activity</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name><surname>Barber</surname> <given-names>Casey N.</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Goldschmidt</surname> <given-names>Hana L.</given-names></name>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Ma</surname> <given-names>Qianqian</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Devine</surname> <given-names>Lauren R.</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/1372690/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Cole</surname> <given-names>Robert N.</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/935015/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Huganir</surname> <given-names>Richard L.</given-names></name>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/210551/overview"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name><surname>Raben</surname> <given-names>Daniel M.</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="corresp" rid="c001"><sup>&#x002A;</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/357142/overview"/>
</contrib>
</contrib-group>
<aff id="aff1"><sup>1</sup><institution>Department of Biological Chemistry, Johns Hopkins University School of Medicine</institution>, <addr-line>Baltimore, MD</addr-line>, <country>United States</country></aff>
<aff id="aff2"><sup>2</sup><institution>Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine</institution>, <addr-line>Baltimore, MD</addr-line>, <country>United States</country></aff>
<author-notes>
<fn fn-type="edited-by"><p>Edited by: Henrique Prado von Gersdorff, Oregon Health &#x0026; Science University, United States</p></fn>
<fn fn-type="edited-by"><p>Reviewed by: Natalia L. Kononenko, University of Cologne, Germany; Nicolas Vitale, Centre National de la Recherche Scientifique (CNRS), France</p></fn>
<corresp id="c001">&#x002A;Correspondence: Daniel M. Raben, <email>draben@jhmi.edu</email></corresp>
</author-notes>
<pub-date pub-type="epub">
<day>27</day>
<month>04</month>
<year>2022</year>
</pub-date>
<pub-date pub-type="collection">
<year>2022</year>
</pub-date>
<volume>14</volume>
<elocation-id>855673</elocation-id>
<history>
<date date-type="received">
<day>15</day>
<month>01</month>
<year>2022</year>
</date>
<date date-type="accepted">
<day>16</day>
<month>03</month>
<year>2022</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#x00A9; 2022 Barber, Goldschmidt, Ma, Devine, Cole, Huganir and Raben.</copyright-statement>
<copyright-year>2022</copyright-year>
<copyright-holder>Barber, Goldschmidt, Ma, Devine, Cole, Huganir and Raben</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/"><p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p></license>
</permissions>
<abstract>
<p>Lipids and their metabolic enzymes are a critical point of regulation for the membrane curvature required to induce membrane fusion during synaptic vesicle recycling. One such enzyme is diacylglycerol kinase &#x03B8; (DGK&#x03B8;), which produces phosphatidic acid (PtdOH) that generates negative membrane curvature. Synapses lacking DGK&#x03B8; have significantly slower rates of endocytosis, implicating DGK&#x03B8; as an endocytic regulator. Importantly, DGK&#x03B8; kinase activity is required for this function. However, protein regulators of DGK&#x03B8;&#x2019;s kinase activity in neurons have never been identified. In this study, we employed APEX2 proximity labeling and mass spectrometry to identify endogenous interactors of DGK&#x03B8; in neurons and assayed their ability to modulate its kinase activity. Seven endogenous DGK&#x03B8; interactors were identified and notably, synaptotagmin-1 (Syt1) increased DGK&#x03B8; kinase activity 10-fold. This study is the first to validate endogenous DGK&#x03B8; interactors at the mammalian synapse and suggests a coordinated role between DGK&#x03B8;-produced PtdOH and Syt1 in synaptic vesicle recycling.</p>
</abstract>
<kwd-group>
<kwd>neurotransmission</kwd>
<kwd>synapse</kwd>
<kwd>lipids</kwd>
<kwd>synaptic vesicles</kwd>
<kwd>Syt1</kwd>
<kwd>APEX2</kwd>
<kwd>proximity labeling</kwd>
</kwd-group>
<contract-sponsor id="cn001">National Institutes of Health<named-content content-type="fundref-id">10.13039/100000002</named-content></contract-sponsor>
<counts>
<fig-count count="6"/>
<table-count count="0"/>
<equation-count count="0"/>
<ref-count count="62"/>
<page-count count="15"/>
<word-count count="9987"/>
</counts>
</article-meta>
</front>
<body>
<sec id="S1" sec-type="intro">
<title>Introduction</title>
<p>Neurotransmission occurs at each of the brain&#x2019;s nearly 100 trillion synapses and governs every aspect of human life from movement to emotional processing to learning and memory (<xref ref-type="bibr" rid="B46">Schweizer and Ryan, 2006</xref>; <xref ref-type="bibr" rid="B14">Eroglu and Barres, 2010</xref>). Because dysregulation of neurotransmission can, therefore, result in a variety of neurological dysfunctions, the synaptic vesicle cycle must be tightly coordinated by a variety of proteins and enzymes (<xref ref-type="bibr" rid="B50">S&#x00FC;dhof, 1995</xref>; <xref ref-type="bibr" rid="B40">Puchkov and Haucke, 2013</xref>).</p>
<p>Recently, lipids have emerged as a new critical point of regulation of neurotransmission, such as phosphatidic acid (PtdOH) because of its roles in many cellular signaling pathways and membrane rearrangements (<xref ref-type="bibr" rid="B44">Rohrbough and Broadie, 2005</xref>; <xref ref-type="bibr" rid="B55">Thakur et al., 2019</xref>; <xref ref-type="bibr" rid="B54">Tanguy et al., 2021</xref>). Because PtdOH is a cone-shaped lipid, it induces negative membrane curvature necessary for synaptic vesicle fusion (<xref ref-type="bibr" rid="B35">McMahon and Boucrot, 2015</xref>; <xref ref-type="bibr" rid="B52">Tanguy et al., 2019</xref>). PtdOH is also negatively charged and has a relatively small phosphomonoester headgroup, making it a popular binding partner for many proteins such as the plasma membrane-associated SNARE protein syntaxin-1 and N-ethylmaleimide sensitive fusion protein (NSF) (<xref ref-type="bibr" rid="B62">Zhukovsky et al., 2019</xref>). A mutation in syntaxin-1 that prevents PtdOH-binding results in a significant effect on evoked exocytosis in chromaffin and PC12 cells (<xref ref-type="bibr" rid="B55">Thakur et al., 2019</xref>; <xref ref-type="bibr" rid="B62">Zhukovsky et al., 2019</xref>; <xref ref-type="bibr" rid="B53">Tanguy et al., 2020</xref>). <italic>In vitro</italic>, PtdOH regulates the membrane insertion and activity of dynamin-1 (<xref ref-type="bibr" rid="B7">Burger et al., 2000</xref>). It is hypothesized that the local production of PtdOH in the active zone or periactive zone by PtdOH-producing lipid-metabolizing enzymes serves as an additional step of regulation to synaptic vesicle fusion and fission (<xref ref-type="bibr" rid="B50">S&#x00FC;dhof, 1995</xref>; <xref ref-type="bibr" rid="B44">Rohrbough and Broadie, 2005</xref>).</p>
<p>Diacylglycerol kinase theta (DGK&#x03B8;) is a lipid-metabolizing enzyme that phosphorylates diacylglycerol to produce PtdOH (<xref ref-type="bibr" rid="B19">Goto and Kondo, 1999</xref>; <xref ref-type="bibr" rid="B58">Tu-Sekine and Raben, 2011</xref>; <xref ref-type="bibr" rid="B57">Tu-Sekine et al., 2016</xref>; <xref ref-type="bibr" rid="B45">Sakane et al., 2020</xref>). There are 10 mammalian DGK isoforms (&#x03B1;, &#x03B2;, &#x03B3;, &#x03B4;, &#x03B7;, &#x03BA;, &#x03B5;, &#x03B6;, &#x03B9;, &#x03B8;) expressed in the central nervous system (CNS), which are categorized according to their domain structure (<xref ref-type="bibr" rid="B2">Barber and Raben, 2020</xref>). DGK&#x03B8; is a Type V DGK, containing three C1 domains, a central PH domain, followed by the catalytic domain. Multiple DGKs have known functions within the CNS (<xref ref-type="bibr" rid="B56">Topham and Prescott, 2009</xref>). For example, DGK&#x03B1; is selectively expressed in oligodendrocytes and is thought to be involved in the production of myelin (<xref ref-type="bibr" rid="B19">Goto and Kondo, 1999</xref>). DGK&#x03B2; is expressed postsynaptically in pyramidal excitatory neurons and evidence suggests a functional role in long-term potentiation. DGKs &#x03B4; and &#x03B7; are thought to have roles in neurodegenerative and psychiatric diseases, such as epilepsy and bipolar disease, respectively (<xref ref-type="bibr" rid="B8">Caricasole et al., 2002</xref>; <xref ref-type="bibr" rid="B3">Baum et al., 2008</xref>). Additionally, DGK&#x03B6; contains a PDZ domain, is known to bind to the postsynaptic scaffolding protein PSD-95 and data suggests a role for DGK&#x03B6; in dendritic spine maintenance (<xref ref-type="bibr" rid="B28">Kim et al., 2009</xref>).</p>
<p>DGK&#x03B8; is predominantly expressed in excitatory neurons throughout all parts of the mammalian brain (<xref ref-type="bibr" rid="B25">Ishisaka and Hara, 2014</xref>). It is expressed throughout the cytosol both pre- and postsynaptically (<xref ref-type="bibr" rid="B18">Goldschmidt et al., 2016</xref>; <xref ref-type="bibr" rid="B2">Barber and Raben, 2020</xref>). Importantly, it has been shown that DGK&#x03B8; knockout (KO) neurons had significantly slower rates of synaptic vesicle endocytosis in response to depolarization as compared to wild-type (WT) neurons. The rates further slowed in response to stronger stimulation. Interestingly, rates of exocytosis were unaffected in DGK&#x03B8; KO neurons compared to WT neurons (<xref ref-type="bibr" rid="B18">Goldschmidt et al., 2016</xref>). This suggests that DGK&#x03B8; kinase activity regulates synaptic vesicle endocytosis. The mechanism underlying the regulation of this enzyme in neurons is unclear. Previously, <italic>in vitro</italic> studies with purified DGK&#x03B8; revealed that proteins with polybasic regions could activate the enzyme (<xref ref-type="bibr" rid="B59">Tu-Sekine and Raben, 2012</xref>), but identification of endogenous protein activators of DGK&#x03B8; in neurons has never been explored.</p>
<p>In the current study, we used proximity labeling and mass spectrometry to identify endogenous regulators of DGK&#x03B8;&#x2019;s kinase activity using an APEX2-tagged DGK&#x03B8; in primary cortical neuron cultures, with an emphasis on synaptic bouton or vesicle proteins. The potential interactions were confirmed biochemically and each interactor was examined for its ability to stimulate DGK&#x03B8; activity <italic>in vitro</italic>. We found that several well-known protein regulators of the synaptic vesicle cycle interact with DGK&#x03B8;, and that some of these proteins also stimulate DGK&#x03B8; activity, such as synaptogyrin-1 (Syngr1) and CaMKII&#x03B1;. Importantly, synaptotagmin-1 (Syt1) interacts with DGK&#x03B8; and increases DGK&#x03B8; activity 10-fold. Taken together, these results suggest that DGK&#x03B8; interacts with and is modulated by key synaptic vesicle recycling proteins to regulate the dynamics of synaptic vesicle recycling.</p>
</sec>
<sec id="S2" sec-type="materials|methods">
<title>Materials and Methods</title>
<sec id="S2.SS1">
<title>Reagents</title>
<table-wrap position="float" id="T1">
<table cellspacing="5" cellpadding="5" frame="hsides" rules="groups">
<thead>
<tr>
<td valign="top" align="left">Primary Antibodies</td>
<td valign="top" align="left">Source</td>
<td valign="top" align="center">Product Number</td>
<td valign="top" align="center">IF Dilution</td>
<td valign="top" align="center">WB Dilution</td>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">Chicken anti-GFP</td>
<td valign="top" align="left">Abcam</td>
<td valign="top" align="center">ab13970</td>
<td valign="top" align="center">1:1000</td>
<td valign="top" align="center">&#x2013;</td>
</tr>
<tr>
<td valign="top" align="left">Mouse anti-DGK&#x03B8;</td>
<td valign="top" align="left">BD Biosciences</td>
<td valign="top" align="center">610931</td>
<td valign="top" align="center">1:100</td>
<td valign="top" align="center">1:100</td>
</tr>
<tr>
<td valign="top" align="left">Guinea pig anti-vGlut1</td>
<td valign="top" align="left">Synaptic Systems</td>
<td valign="top" align="center">135304</td>
<td valign="top" align="center">1:2500</td>
<td valign="top" align="center">&#x2013;</td>
</tr>
<tr>
<td valign="top" align="left">Rabbit anti-DsRed</td>
<td valign="top" align="left">Clontech</td>
<td valign="top" align="center">632496</td>
<td valign="top" align="center">1:1000</td>
<td valign="top" align="center">&#x2013;</td>
</tr>
<tr>
<td valign="top" align="left">Mouse anti-GFP N86/8</td>
<td valign="top" align="left">NeuroMab</td>
<td valign="top" align="center">75-131</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:1000</td>
</tr>
<tr>
<td valign="top" align="left">Mouse anti-tubulin</td>
<td valign="top" align="left">Sigma-Aldrich</td>
<td valign="top" align="center">T8328</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:1000</td>
</tr>
<tr>
<td valign="top" align="left">Rabbit anti-dynamin1</td>
<td valign="top" align="left">Synaptic Systems</td>
<td valign="top" align="center">115003</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:1000</td>
</tr>
<tr>
<td valign="top" align="left">Rabbit anti-synaptogyrin1</td>
<td valign="top" align="left">Synaptic Systems</td>
<td valign="top" align="center">103003</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:1000</td>
</tr>
<tr>
<td valign="top" align="left">Rabbit anti-munc18-1</td>
<td valign="top" align="left">Cell Signaling Technology</td>
<td valign="top" align="center">13414P</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:1000</td>
</tr>
<tr>
<td valign="top" align="left">Rabbit anti-munc18-1</td>
<td valign="top" align="left">Synaptic Systems</td>
<td valign="top" align="center">116003</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:1000</td>
</tr>
<tr>
<td valign="top" align="left">Mouse anti-clathrin heavy chain1</td>
<td valign="top" align="left">BD Biosciences</td>
<td valign="top" align="center">610500</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:2000</td>
</tr>
<tr>
<td valign="top" align="left">Rabbit anti-synaptotagmin1</td>
<td valign="top" align="left">Cell Signaling Technology</td>
<td valign="top" align="center">14558S</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:1000</td>
</tr>
<tr>
<td valign="top" align="left">Rabbit anti-camk2a</td>
<td valign="top" align="left">Cell Signaling Technology</td>
<td valign="top" align="center">D10C11</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:1000</td>
</tr>
<tr>
<td valign="top" align="left">Rabbit anti-hspa8</td>
<td valign="top" align="left">Aviva Systems Biology</td>
<td valign="top" align="center">ARP48445_P050</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:1000</td>
</tr>
<tr>
<td valign="top" align="left">Rabbit anti-syntaxin7</td>
<td valign="top" align="left">Synaptic Systems</td>
<td valign="top" align="center">110073</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:1000</td>
</tr>
<tr>
<td valign="top" align="left">Mouse anti-synaptojanin1</td>
<td valign="top" align="left">BD Biosciences</td>
<td valign="top" align="center">612248</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:1000</td>
</tr>
<tr>
<td valign="top" align="left">Rabbit anti-SNAP25</td>
<td valign="top" align="left">Cell Signaling Technology</td>
<td valign="top" align="center">3926S</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:1000</td>
</tr>
<tr>
<td valign="top" align="left">Rabbit anti-PKCa</td>
<td valign="top" align="left">Cell Signaling Technology</td>
<td valign="top" align="center">59754S</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:5000</td>
</tr>
<tr>
<td valign="top" align="left">Rabbit anti-basp1</td>
<td valign="top" align="left">Aviva Systems Biology</td>
<td valign="top" align="center">ARP59932_P050</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:1000</td>
</tr>
<tr>
<td valign="top" align="left">Rabbit anti-cofilin1</td>
<td valign="top" align="left">Cell Signaling Technology</td>
<td valign="top" align="center">5175T</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:1000</td>
</tr>
<tr>
<td valign="top" align="left">Mouse anti-HA ascites</td>
<td valign="top" align="left">Homemade</td>
<td valign="top" align="center">N/A</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:2500</td>
</tr>
<tr>
<td valign="top" align="left">Mouse anti-myc ascites</td>
<td valign="top" align="left">Homemade</td>
<td valign="top" align="center">N/A</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:2000</td>
</tr>
<tr>
<td valign="top" align="left">Rabbit anti-clathrin heavy chain1</td>
<td valign="top" align="left">Cell Signaling Technology</td>
<td valign="top" align="center">4796T</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:1000</td>
</tr>
<tr>
<td valign="top" align="left">Rabbit anti-myc serum</td>
<td valign="top" align="left">Homemade</td>
<td valign="top" align="center">N/A</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:5000</td>
</tr>
<tr>
<td valign="top" align="left" colspan="5"><hr/></td>
</tr>
<tr>
<td valign="top" align="left"><bold>Secondary Antibodies</bold></td>
<td valign="top" align="left"><bold>Source</bold></td>
<td valign="top" align="center"><bold>Product Number</bold></td>
<td/>
<td/>
</tr>
<tr>
<td valign="top" align="left" colspan="5"><hr/></td>
</tr>
<tr>
<td valign="top" align="left">IRDye 800CW goat anti-rabbit IgG</td>
<td valign="top" align="left">LICOR</td>
<td valign="top" align="center">926-32211</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:10,000</td>
</tr>
<tr>
<td valign="top" align="left">IRDye 800CW goat anti-mouse IgG</td>
<td valign="top" align="left">LICOR</td>
<td valign="top" align="center">926-32210</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:10,000</td>
</tr>
<tr>
<td valign="top" align="left">IRDye 680LT goat anti-rabbit IgG</td>
<td valign="top" align="left">LICOR</td>
<td valign="top" align="center">926-68021</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:10,000</td>
</tr>
<tr>
<td valign="top" align="left">IRDye 680LT goat anti-mouse IgG</td>
<td valign="top" align="left">LICOR</td>
<td valign="top" align="center">926-68020</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:10,000</td>
</tr>
<tr>
<td valign="top" align="left">IRDye 680LT streptavidin</td>
<td valign="top" align="left">LICOR</td>
<td valign="top" align="center">926-68031</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:10,000</td>
</tr>
<tr>
<td valign="top" align="left">IRDye 800CW streptavidin</td>
<td valign="top" align="left">LICOR</td>
<td valign="top" align="center">926-32230</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1:10,000</td>
</tr>
<tr>
<td valign="top" align="left">Goat anti-Guinea Pig Alexa Fluor 647</td>
<td valign="top" align="left">Invitrogen</td>
<td valign="top" align="center">A21450</td>
<td valign="top" align="center">1:500</td>
<td valign="top" align="center">&#x2013;</td>
</tr>
<tr>
<td valign="top" align="left">Goat anti-Mouse Alexa Fluor 647</td>
<td valign="top" align="left">Invitrogen</td>
<td valign="top" align="center">A21236</td>
<td valign="top" align="center">1:500</td>
<td valign="top" align="center">&#x2013;</td>
</tr>
<tr>
<td valign="top" align="left">Goat anti-Chicken DyLight 488</td>
<td valign="top" align="left">Invitrogen</td>
<td valign="top" align="center">SA5-10070</td>
<td valign="top" align="center">1:500</td>
<td valign="top" align="center">&#x2013;</td>
</tr>
<tr>
<td valign="top" align="left">Goat anti-Mouse Alexa Fluor 568</td>
<td valign="top" align="left">Invitrogen</td>
<td valign="top" align="center">A11004</td>
<td valign="top" align="center">1:500</td>
<td valign="top" align="center">&#x2013;</td>
</tr>
<tr>
<td valign="top" align="left">Goat anti-Rabbit Alexa Fluor 568</td>
<td valign="top" align="left">Invitrogen</td>
<td valign="top" align="center">A11036</td>
<td valign="top" align="center">1:500</td>
<td valign="top" align="center">&#x2013;</td>
</tr>
<tr>
<td valign="top" align="left" colspan="5"><hr/></td>
</tr>
<tr>
<td valign="top" align="left"><bold>Purified Proteins</bold></td>
<td valign="top" align="left"><bold>Source</bold></td>
<td valign="top" align="center"><bold>Product Number</bold></td>
<td/>
<td/>
</tr>
<tr>
<td valign="top" align="left" colspan="5"><hr/></td>
</tr>
<tr>
<td valign="top" align="left">Camk2a</td>
<td valign="top" align="left">Origene</td>
<td valign="top" align="center">TP318186</td>
<td/>
<td/>
</tr>
<tr>
<td valign="top" align="left">Hspa8</td>
<td valign="top" align="left">Origene</td>
<td valign="top" align="center">TP302209</td>
<td/>
<td/>
</tr>
<tr>
<td valign="top" align="left">Synaptogyrin-1</td>
<td valign="top" align="left">Origene</td>
<td valign="top" align="center">TP300562</td>
<td/>
<td/>
</tr>
<tr>
<td valign="top" align="left">Dynamin-1</td>
<td valign="top" align="left">Origene</td>
<td valign="top" align="center">TP306284</td>
<td/>
<td/>
</tr>
<tr>
<td valign="top" align="left">Munc18-1</td>
<td valign="top" align="left">Origene</td>
<td valign="top" align="center">TP318471</td>
<td/>
<td/>
</tr>
<tr>
<td valign="top" align="left">Syntaxin-7</td>
<td valign="top" align="left">NovoPro Bioscience</td>
<td valign="top" align="center">502965-20</td>
<td/>
<td/>
</tr>
<tr>
<td valign="top" align="left" colspan="5"><hr/></td>
</tr>
<tr>
<td valign="top" align="left"><bold>Other Reagents</bold></td>
<td valign="top" align="left"><bold>Source</bold></td>
<td valign="top" align="center"><bold>Product Number</bold></td>
<td/>
<td/>
</tr>
<tr>
<td valign="top" align="left" colspan="5"><hr/></td>
</tr>
<tr>
<td valign="top" align="left">Biotinyl tyramide</td>
<td valign="top" align="left">Chemodex</td>
<td valign="top" align="center">B0270</td>
<td/>
<td/>
</tr>
<tr>
<td valign="top" align="left">Trypsin</td>
<td valign="top" align="left">Worthington</td>
<td valign="top" align="center">LS003741</td>
<td/>
<td/>
</tr>
<tr>
<td valign="top" align="left">Streptavidin beads</td>
<td valign="top" align="left">Pierce</td>
<td valign="top" align="center">88817</td>
<td/>
<td/>
</tr>
<tr>
<td valign="top" align="left">Hydrogen peroxide</td>
<td valign="top" align="left">Sigma-Aldrich</td>
<td valign="top" align="center">H1009-100ML</td>
<td/>
<td/>
</tr>
<tr>
<td valign="top" align="left">1,1,1,3,3,3-Hexafluoro-2-propanol</td>
<td valign="top" align="left">Acros Organics</td>
<td valign="top" align="center">AC445820100</td>
<td/>
<td/>
</tr>
<tr>
<td valign="top" align="left">Sodium ascorbate</td>
<td valign="top" align="left">Spectrum</td>
<td valign="top" align="center">S1349</td>
<td/>
<td/>
</tr>
</tbody>
</table></table-wrap>
<table-wrap position="float" id="T2">
<table cellspacing="5" cellpadding="5" frame="hsides" rules="groups">
<tbody>
<tr>
<td valign="top" align="left"><bold>Primary Antibodies</bold></td>
<td valign="top" align="left"><bold>Source</bold></td>
<td valign="top" align="center"><bold>Product Number</bold></td>
</tr>
<tr>
<td valign="top" align="left">Sodium azide</td>
<td valign="top" align="left">Thermo Fisher Scientific</td>
<td valign="top" align="center">14314</td>
</tr>
<tr>
<td valign="top" align="left">Trolox</td>
<td valign="top" align="left">Acros Organics</td>
<td valign="top" align="center">53188-07-1</td>
</tr>
<tr>
<td valign="top" align="left">Iodoacetamide</td>
<td valign="top" align="left">Sigma-Aldrich</td>
<td valign="top" align="center">I6125-25G</td>
</tr>
<tr>
<td valign="top" align="left">DTT</td>
<td valign="top" align="left">Pierce</td>
<td valign="top" align="center">A39255</td>
</tr>
<tr>
<td valign="top" align="left">Biotin</td>
<td valign="top" align="left">Sigma-Aldrich</td>
<td valign="top" align="center">B4501-1G</td>
</tr>
<tr>
<td valign="top" align="left">Lipofectamine 2000</td>
<td valign="top" align="left">Invitrogen</td>
<td valign="top" align="center">11668-019</td>
</tr>
<tr>
<td valign="top" align="left"></td>
<td valign="top" align="left"/><td valign="top" align="left"/></tr>
</tbody>
</table></table-wrap>
</sec>
<sec id="S2.SS2">
<title>Plasmids</title>
<table-wrap position="float" id="T3">
<table cellspacing="5" cellpadding="5" frame="hsides" rules="groups">
<thead>
<tr>
<td valign="top" align="left">Plasmid</td>
<td valign="top" align="left">Source</td>
<td valign="top" align="center">Product Number</td>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">pRK5-myc-DGK&#x03B8;</td>
<td valign="top" align="left">Homemade</td>
<td valign="top" align="center">N/A</td>
</tr>
<tr>
<td valign="top" align="left">pCAG_DGK&#x03B8;-GFP-APEX2</td>
<td valign="top" align="left">Homemade</td>
<td valign="top" align="center">N/A</td>
</tr>
<tr>
<td valign="top" align="left">LCK-myr-mCherry</td>
<td valign="top" align="left">Homemade</td>
<td valign="top" align="center">N/A</td>
</tr>
<tr>
<td valign="top" align="left">pcDNA3.1 HA-dynamin1</td>
<td valign="top" align="left">Addgene</td>
<td valign="top" align="center">34682</td>
</tr>
<tr>
<td valign="top" align="left">pCAG-mGFP-Camk2a</td>
<td valign="top" align="left">Addgene</td>
<td valign="top" align="center">127389</td>
</tr>
<tr>
<td valign="top" align="left">pcDNA3.1 GFP-HSPA8</td>
<td valign="top" align="left">Addgene</td>
<td valign="top" align="center">121161</td>
</tr>
<tr>
<td valign="top" align="left">pCAG-Syt1-pH</td>
<td valign="top" align="left">Homemade</td>
<td valign="top" align="center">N/A</td>
</tr>
<tr>
<td valign="top" align="left">pCMV5-HA-Stx7</td>
<td valign="top" align="left">MRC PPU Reagents and Services</td>
<td valign="top" align="center">26785</td>
</tr>
<tr>
<td valign="top" align="left">pCMV5-HA-CLTC</td>
<td valign="top" align="left">MRC PPU Reagents and Services</td>
<td valign="top" align="center">31877</td>
</tr>
<tr>
<td valign="top" align="left">pCMV5-Syngr1-GFP</td>
<td valign="top" align="left">Provided by Raffaella de Pace, NIH/NICHD</td>
<td valign="top" align="center">N/A</td>
</tr>
<tr>
<td valign="top" align="left">pCMV5-HA-Munc18-1b</td>
<td valign="top" align="left">Provided by Jacqueline Burr&#x00E9;, Cornell</td>
<td valign="top" align="center">N/A</td>
</tr>
<tr>
<td valign="top" align="left">pCMV5-Munc18-1b-GFP</td>
<td valign="top" align="left">Provided by Jacqueline Burr&#x00E9;, Cornell</td>
<td valign="top" align="center">N/A</td>
</tr>
<tr>
<td valign="top" align="left"></td>
<td valign="top" align="left"/><td valign="top" align="left"/></tr>
</tbody>
</table></table-wrap>
</sec>
<sec id="S2.SS3">
<title>Neuron Culture</title>
<p>All animal protocols were approved by the Johns Hopkins University Animal Care and Use Committee. To prepare primary neuron cultures, WT embryonic day 16 (E16) rat pups were removed from sacrificed Sprague Dawley mothers. Cortices were dissected from pup brains and incubated in dissection media with papain and DNase for 25 min at 37&#x00B0;C and then fully dissociated by gentle trituration. Neurons to be used for APEX2 labeling were then electroporated with the Rat Nucleofector Kit (Amaxa) with 4 &#x03BC;g pCAG_DGK&#x03B8;-GFP-APEX2 and plated on poly-L-lysine (PLL)-coated 10 cm dishes in Neurobasal Plus medium supplemented with 5% horse serum, 50 U/mL penicillin, 50 U/mL streptomycin, 2 mM Glutamax and 2% b27 Plus at 10 e<sup>6</sup> cells/dish. WT neurons were plated in the same media at 4 e<sup>6</sup> cells/dish. At DIV4, all neurons were fed with serum-reduced (2% horse serum) media supplemented with fluoro-deoxyuridine (FDU) to prevent the proliferation of glial cells. Following this, neurons were fed about every 4 days with Neurobasal Plus medium supplemented with 50 U/mL penicillin, 50 U/mL streptomycin, 2 mM Glutamax, and 2% b27 plus. For most experiments, neurons were grown until DIV21 in a 37&#x00B0;C incubator (5%CO<sub>2</sub>).</p>
</sec>
<sec id="S2.SS4">
<title>Neuron Immunofluorescence</title>
<p>For immunofluorescence experiments, WT rat neurons were plated on PLL-coated 18 mm glass coverslips placed in the wells of a 12 well plate. On DIV19, neurons were transfected with a combination of 0.5 &#x03BC;g pCAG_DGK&#x03B8;-GFP-APEX2, 0.5 &#x03BC;g LCK-myr-mCherry, or 0.5 &#x03BC;g pRK5-myc-DGK&#x03B8;. To accomplish this, Lipofectamine 2000 (L2K) was diluted in Neurobasal media and incubated for 5 min. DNA was diluted in Neurobasal media and then combined at a 1:1 ratio with the L2K/Neurobasal dilution and incubated for 15 min at room temperature (RT). 1 mL of media was gently removed from each well of cells to be transfected and saved. The transfection mixture was then added dropwise to cells and incubated for about 13 min at 37&#x00B0;C, 5%CO<sub>2</sub>. Following this incubation, the transfection media was aspirated and replaced with 1 mL of the saved media. The next day, the neurons were fixed for staining. Coverslips were washed 1&#x00D7; with phosphate-buffered saline (PBS) and then incubated with parafix (4% paraformaldehyde + 4% sucrose in PBS) for 15 min at RT and washed 3&#x00D7; with PBS. They were permeabilized for 10 min with 0.25% Triton-X in PBS and washed 3&#x00D7; with PBS. To reduce non-specific antibody binding, coverslips were incubated with 10% bovine serum albumin (BSA) at 37&#x00B0;C (5%CO<sub>2</sub>) for 1 h. Coverslips were then incubated with primary antibodies diluted in 3% BSA overnight at 4&#x00B0;C. The next day, coverslips were washed 3&#x00D7; with PBS and incubated with secondary antibodies (goat conjugated Alexa Fluor 647, 568, or 488) diluted in 3% BSA in PBS +0.1% Triton-X (PBST) for 1 h at RT. Subsequently, they were washed 3&#x00D7; with PBS and mounted on glass slides with Fluoromount-G and stored at 4&#x00B0;C. Images were obtained with an 800-laser scanning confocal microscope (Zeiss) and images were analyzed with ImageJ.</p>
</sec>
<sec id="S2.SS5">
<title>Western Blot Analysis</title>
<p>All SDS-PAGE gels were performed with Bolt 8% Bis-Tris mini protein gels. Eluates from streptavidin pulldowns and CoIPs were loaded directly on gels. Input samples and other neuronal or HEK lysate samples were diluted with water and 4&#x00D7; Laemmli buffer with 10% &#x03B2;-mercaptoethanol and boiled for 5 min at 100&#x00B0;C before loading on gels. Proteins were transferred to nitrocellulose membranes with the Bio-Rad Mini <italic>Trans-</italic>Blot system and blocked with 3% BSA for 1 h. Blots were incubated with primary antibodies diluted in 3% BSA in PBST on a 4&#x00B0;C rocker overnight. The next day, blots were washed 3&#x00D7; with PBST and incubated with LICOR IRDye-conjugated secondary antibodies for 1 h at RT. Afterward blots were washed 3&#x00D7; with PBST before infrared imaging with an Odyssey Imaging System.</p>
</sec>
<sec id="S2.SS6">
<title>APEX2 Proximity Labeling</title>
<p>At DIV21, neurons expressing pCAG_DGK&#x03B8;-GFP-APEX2 were incubated with aCSF supplemented with 500 &#x03BC;M biotin-phenol for 30 min at 37&#x00B0;C. Control neurons not incubated with biotin-phenol were incubated with non-supplemented aCSF for 30 min at 37&#x00B0;C. Immediately after incubation, aCSF was aspirated and 10 mL of 50 mM KCl in aCSF was added to each dish to induce depolarization for 30 s (non-depolarized neurons did not receive this treatment). Following depolarization, 1 mM H<sub>2</sub>O<sub>2</sub> was added to each dish of cells for 1 min to catalyze the APEX2 labeling reaction. After 1 min, aCSF containing biotin-phenol and H<sub>2</sub>O<sub>2</sub> was aspirated and quencher solution (10 mM sodium ascorbate, 5 mM Trolox, 10 mM sodium azide in DPBS) was added to each dish of cells to quench the labeling reaction. Neurons were washed with this solution 4&#x00D7;. Following the last wash, neurons were harvested in 1 mL RIPA containing protease inhibitors, each of the quenchers, and 50 mM TEABC. Each lysate was incubated on a rotator at 4&#x00B0;C for 20 min and then centrifuged at 17,000 &#x00D7; <italic>g</italic> for 5 min. The supernatant was transferred to a new tube and placed at &#x2212;20&#x00B0;C until preparation for proteomic analysis.</p>
</sec>
<sec id="S2.SS7">
<title>Mass Spectrometry Sample Preparation</title>
<p>Neurons (&#x223C;50 e<sup>6</sup> cells total) from five 10 cm dishes were lysed in RIPA buffer. Proteins in lysates were reduced in 10 mM DTT at 56&#x00B0;C for 30 min and alkylated with 30 mM IAA at RT in the dark for 30 min prior to proteolysis with 1:20 dilution of 1 mg/mL trypsin (Worthington): protein in 50 mM TEABC buffer at 37&#x00B0;C on a shaker overnight. Following trypsin digestion, peptides were precipitated and acidified by adding 20% TFA in dH<sub>2</sub>0 to pH4 and incubated at RT for 10 min. Subsequently, lysates were spun at 10,000 &#x00D7; <italic>g</italic> for 10 min at RT to pellet debris, undigested proteins, and membranes. The supernatant was loaded on a 30 mg Waters Oasis plate (WAT058951) to bind and desalt the peptides according to the manufacturer&#x2019;s instructions. The peptides were eluted with 2&#x00D7; washes of 500 &#x03BC;L 60% trifluoroacetic acid and subsequently dried in a speed vacuum.</p>
<p>To prepare streptavidin beads, Pierce magnetic streptavidin beads were washed 3&#x00D7; with PBS. A 1:8 ratio was used (mL beads: mg protein). The dried peptides were resuspended completely in 1 mL RIPA and combined with beads. The peptide-bead mixture was incubated overnight on a 4&#x00B0;C rotator. The next day, the beads were washed 4&#x00D7; with 1 mL 1% SDS, 5&#x00D7; 1 mL 5% acetonitrile in dH<sub>2</sub>0, and 3&#x00D7; 1 mL dH<sub>2</sub>0. Washes were performed by pipetting with low retention tips and after each wash, samples were transferred to a new Eppendorf tube. After the last wash, biotinylated peptides were eluted from streptavidin beads with neat hexafluoroisopropanol (HFIP). For each sample, 600 &#x03BC;L HFIP was added to the tube, incubated for 5 min at RT, then placed on a magnetic rack and the liquid was pipetted off and transferred to a new tube. This was done a second time and the supernatants were combined into one tube for each sample and then dried in a speed vacuum. The dried peptides were kept in &#x2212;20&#x00B0;C until mass spectrometry analysis.</p>
</sec>
<sec id="S2.SS8">
<title>Mass Spectrometry</title>
<p>Peptides were resuspended in 200 &#x03BC;L of 0.1% trifluoroacetic acid loaded and desalted on a Waters Oasis plate C18. After desalting with 0.1%TFA, peptides were eluted in basic (10 mM TEAB) in steps at 5, 10, 25, and 75% acetonitrile. Fractions were dried and rehydrated with 2% acetonitrile, 0.1% formic acid. Each peptide fraction was resuspended in 20 &#x03BC;L loading buffer (2% acetonitrile in 0.1% formic acid) and analyzed by reverse phase liquid chromatography interfaced with tandem mass spectrometry (LC/MSMS) using an Easy-LC 1200 HPLC system<sup><xref ref-type="fn" rid="footnote1">1</xref></sup> interfaced with an Orbitrap Fusion Lumos Tribrid Mass Spectrometer (Lumos, see text footnote 1). Peptides (20% each fraction) were loaded onto a C18 trap (S-10 &#x03BC;M, 120 &#x00C5;, 75 &#x03BC;m &#x00D7; 2 cm, YMC, Japan) and subsequently separated on an in-house packed PicoFrit column (75 &#x03BC;m &#x00D7; 200 mm, 15 &#x03BC;, +/&#x2212;1 &#x03BC;m tip, New Objective) with C18 phase (ReproSil-Pur C18-AQ, 3 &#x03BC;m, 120 &#x00C5;<sup><xref ref-type="fn" rid="footnote2">2</xref></sup>) using 2&#x2013;90% acetonitrile gradient at 300 nl/min over 120 min. Eluting peptides were sprayed at 2.0 kV directly into the Lumos. Survey scans (full MS) were acquired from 350 to 1,400 m/z with data dependent monitoring with a 3 s cycle time. Each precursor individually isolated in a 1.2 Da window and fragmented using HCD activation collision energy 30 and 15 s dynamic exclusion, first mass being 120 m/z. Precursor and the fragment ions were analyzed at resolutions 120,000 and 50,000, respectively, with automatic gain control (AGC) target values at 4 e<sup>5</sup> with 50 ms maximum injection time (IT) and 1 e<sup>5</sup> with 54 ms maximum IT, respectively.</p>
<p>Isotopically resolved masses in precursor (MS) and fragmentation (MS/MS) spectra were processed in Proteome Discoverer (PD) software (v2.4, Thermo Scientific). All data were searched using Mascot (2.6.2<sup><xref ref-type="fn" rid="footnote3">3</xref></sup>) against a custom database (191113 entries, including custom sequence with DGK&#x03B8;-GFP-APEX2 protein plus Rattus) using trypsin as the enzyme, 2 missed cleavages, precursor and fragment tolerances or 6 ppm and 0.01 Da, respectively. Variable modifications included Asn and Gln deamidation, Met oxidation, and Cys carbamidomethylation as static modification. Target decoy PSM (peptide spectrum match) validator was used, and any low-scoring spectra were sent to a custom BYONIC search against SwissProt_Rat_032019_8060entries_DGK_Apex database. The enzyme was specified as trypsin, with 2 missed cleavages, precursor and fragment tolerances or 6 and 8 ppm, respectively. Total common modifications 2 max, rare modifications 1 max. Fixed modification of Carbamidomethyl / +57.021464 @ C, Dynamic Modifications of Oxidation / +15.994915 @ M | common1, Deamidated / +0.984016 @ N, Q | common1, Carbamyl / +43.005814 @ K, R | rare1, Acetyl / +42.010565 @ NTerm, Protein NTerm, K | common2, Acetyl / +42.010565 @ NTerm, Protein NTerm, K | common2, Phospho / +79.966331 @ S, T, Y | rare1, Trioxidation / +47.984744 @ W | rare1, Gln- &#x003E; pyro-Glu / &#x2212;17.026549 @ NTerm Q | common2, Formyl / +27.994915 @ NTerm, K, S, T | rare1, Dimethyl / +28.0313 @ K, R | rare1, Biotin Tyramide / +361.1460 @ Y | rare1, Biotin Tyramide_Plus1 / +362.149 @ Y | rare1.</p>
<p>Spectra and peptides with high confidence (1% FDR) were used for feature mapping and alignment, RT up to 10 min, Mass tolerance 10 ppm, min S/N threshold 5. Quantification calculated from precursor intensity, using unique peptides only. No scaling or normalization, protein abundance calculated from summed abundances, top 3, pair wise ratio based. Hypothesis test was set to <italic>t</italic>-test (background based).</p>
</sec>
<sec id="S2.SS9">
<title>Streptavidin Pulldowns</title>
<p>For streptavidin pulldowns to confirm biotinylation of proteins, APEX2 labeled neuronal lysates were combined with magnetic streptavidin beads that had been washed 2&#x00D7; with RIPA. Following addition of the lysate to the beads, RIPA was added to the lysate-bead mixture to facilitate mixing and samples were incubated overnight on a 4&#x00B0;C rotator. The following day, the flow-through was pipetted off the magnetic beads and the beads were washed 2&#x00D7; 1 mL RIPA, 1&#x00D7; 1 mL 1 M KCl, 1&#x00D7; 1 mL 0.1 M Na<sub>2</sub>CO<sub>3</sub>, 1&#x00D7; 1 mL 2 M urea in 10 mM Tris&#x2013;HCl pH8, 2&#x00D7; 1 mL RIPA. To elute biotinylated proteins from the beads, Laemmli sample buffer containing 6 mM biotin and 60 mM dithiothreitol (DTT) was added to the beads and incubated at 100&#x00B0;C for 15 min. Afterward, the supernatant was collected from the magnetic beads and loaded on gel for Western blot analysis.</p>
</sec>
<sec id="S2.SS10">
<title>Coimmunoprecipitation</title>
<p>All CoIPs were performed using HEK293FT cells. Cells were seeded on 10 cm dishes in DMEM supplemented with 10% fetal bovine serum and 1% Pen-Strep. Transfection was performed when the cells reached about 80% confluency. Lipofectamine 2000 (L2K) was diluted in Opti-MEM and incubated for 5 min at RT. 4 &#x03BC;g of pRK5-myc-DGK&#x03B8; alone or 4 &#x03BC;g pRK5-myc-DGK&#x03B8; plus 4 &#x03BC;g of each potential interactor DNA were diluted in Opti-MEM. The DNA and L2K were mixed at a 1:1 ratio and incubated for 15 min at RT. Afterward, the DNA/L2K mixture was added to cells dropwise and the cells were placed in the incubator (37&#x00B0;C, 5% CO<sub>2</sub>) for 2 h. Then, the media containing the transfection mixture was aspirated completely from plates and fresh HEK cell media was replaced. The cells were harvested after 2 days. Before lysis, cells were washed 2&#x00D7; with PBS. After the final wash was aspirated, the cells were lysed in 1 mL CoIP buffer (1% NP40, 5 mM NaF, 5 mM NaPPi, 1 mM EDTA, 1 mM EGTA in 1&#x00D7; PBS) and placed on 4&#x00B0;C rotator for 20 min. The lysates were then centrifuged at 17,000 &#x00D7; <italic>g</italic> for 5 min and the supernatant was transferred to a new tube.</p>
<p>To begin CoIPs, lysates were first precleared by incubating with protein A/G beads for 1 h on 4&#x00B0;C rotator to reduce non-specific binding. After incubation, samples were centrifuged at 10,000 &#x00D7; <italic>g</italic> and the supernatant was collected and transferred to a new tube. Subsequently, 2 &#x03BC;L of rabbit anti-myc or mouse anti-myc ascites antibodies were added to each sample and incubated overnight on 4&#x00B0;C rotator. The next day, protein A/G beads were added to each antibody/lysate mixture and incubated for 2 h on RT rotator. The flow-through was then removed and beads were gently washed 3&#x00D7; with CoIP buffer by pipetting. After the final wash, beads were incubated in elution buffer (50% CoIP buffer, 50% 4&#x00D7; Laemmli sample buffer) at RT for 15 min and then at 100&#x00B0;C for 15 min. Samples were then briefly centrifuged and the supernatant was transferred to a new tube. Samples were kept at &#x2212;20&#x00B0;C until samples were analyzed for the presence of the interactor by Western blot analyses.</p>
</sec>
<sec id="S2.SS11">
<title>DGK&#x03B8; Activation Assay</title>
<p>The ADP-Glo Assay (Promega) was used to examine the ability of each DGK&#x03B8; interactor to stimulate DGK&#x03B8; activity (<xref ref-type="bibr" rid="B1">Balzano et al., 2011</xref>; <xref ref-type="bibr" rid="B38">Nagaraj et al., 2017</xref>). This assay kit employs a fluorescent reagent to quantify the amount of ADP generated by DGK&#x03B8;&#x2019;s kinase reaction. The reaction mix consists of 10 ng/&#x03BC;L purified DGK&#x03B8;, 0.5 mM of the water-soluble DAG substrate 1,2-dihexanoyl-sn-glycerol (Dic6), 1 mM ATP, 3 mM MgCl<sub>2</sub>, and 500 ng/&#x03BC;L of the potential activator. The reaction mixture was incubated at 37&#x00B0;C for 10 min and stopped by the addition of an equal volume of the ADP-Glo Reagent. This was incubated at RT for an additional 40 min to deplete the remaining ATP. Kinase Detection Reagent was then added and incubated at RT for 40 min, which converts the kinase-generated ADP to ATP which is quantified using a luciferase/luciferin-based reaction. The resulting luminescence is then measured with a Molecular Devices SpectraMax<sup>&#x00AE;</sup> i3x Multi-Mode Microplate Reader.</p>
</sec>
</sec>
<sec id="S3" sec-type="results">
<title>Results</title>
<sec id="S3.SS1">
<title>Validation of DGK&#x03B8;-GFP-APEX2 Expression and Activity</title>
<p>To gain insight into the mechanism of DGK&#x03B8;&#x2019;s modulatory role in compensatory endocytosis, we performed APEX2 proximity labeling with APEX2-tagged DGK&#x03B8; in cortical rat neurons. Mass spectrometry analysis was used to identify potential interactors, with a particular focus on proteins with a known role in synaptic vesicle recycling. We chose to employ APEX2 proximity labeling because its rapid labeling of proteins (&#x223C;1 min) within a small radius (&#x223C;10 nm) results in specific identification of interactions and has been previously used in multiple similar contexts (<xref ref-type="bibr" rid="B42">Rhee et al., 2013</xref>; <xref ref-type="bibr" rid="B24">Hung et al., 2014</xref>, <xref ref-type="bibr" rid="B23">2016</xref>; <xref ref-type="bibr" rid="B29">Lam et al., 2015</xref>; <xref ref-type="bibr" rid="B31">Loh et al., 2016</xref>; <xref ref-type="bibr" rid="B10">Chung et al., 2017</xref>; <xref ref-type="bibr" rid="B20">Han et al., 2017</xref>; <xref ref-type="bibr" rid="B33">Martell et al., 2017</xref>). To identify specific, functionally relevant DGK&#x03B8; interactors, we depolarized neurons prior to labeling in live cells for some samples.</p>
<p>We first confirmed the expression, localization, and activity of our DGK&#x03B8;-GFP-APEX2 construct (<xref ref-type="fig" rid="F1">Figure 1A</xref>). Mature cortical neurons expressing DGK&#x03B8;-GFP-APEX2 were incubated with biotin-phenol (BP) for 30 min, followed by a 1 min incubation with H<sub>2</sub>O<sub>2</sub> to catalyze the labeling reaction. This was performed with or without KCl to induce depolarization (see section &#x201C;Materials and Methods&#x201D;) (<xref ref-type="fig" rid="F1">Figure 1B</xref>). The DGK&#x03B8;-GFP-APEX2 construct expresses well in neurons in both depolarized and non-depolarized neurons, as evidenced by both a GFP and DGK&#x03B8; antibody. The DGK&#x03B8; antibody recognizes the construct at 150 kDa and endogenous DGK&#x03B8; at 100 kDa (<xref ref-type="fig" rid="F1">Figure 1C</xref>). We then tested the BP labeling efficiency of the DGK&#x03B8;-GFP-APEX2 construct in live neurons. The resulting Western blots showed that APEX2 labeling of DGK&#x03B8;-interacting proteins is dependent on BP and H<sub>2</sub>O<sub>2</sub> and there are no significant differences in labeling efficacy between the depolarized and non-depolarized samples. The detection of endogenously biotinylated proteins is seen in the lysates from control reactions, with BP or H<sub>2</sub>O<sub>2</sub> omitted (<xref ref-type="fig" rid="F1">Figure 1D</xref>).</p>
<fig id="F1" position="float">
<label>FIGURE 1</label>
<caption><p>DGK&#x03B8;-GFP-APEX2 is expressed ubiquitously throughout neurons and labeling of interactors is dependent on H<sub>2</sub>O<sub>2</sub>. <bold>(A)</bold> DGK&#x03B8;-GFP-APEX2 was cloned into the neuronal expression vector pCAG. <bold>(B)</bold> Cortical neurons (DIV21) expressing DGK&#x03B8;-GFP-APEX2 were incubated with biotin-phenol (BP, 500 &#x03BC;M, 30 min). Depolarized neurons were treated with a 30 s incubation with 50 mM KCl; control neurons were treated with aCSF. The addition of H<sub>2</sub>O<sub>2</sub> (1 mM, 1 min) catalyzes the reaction. Figure made with <ext-link ext-link-type="uri" xlink:href="http://BioRender.com">BioRender.com</ext-link>. <bold>(C)</bold> DIV21 cortical neuron lysates express near equal amounts of DGK&#x03B8;-GFP-APEX2 with and without depolarization. <bold>(D)</bold> DGK&#x03B8;-GFP-APEX2 biotinylated proteins with similar efficacy in depolarized and non-depolarized samples, and labeling is dependent on BP and H<sub>2</sub>O<sub>2</sub>. <bold>(E)</bold> In cortical neurons (DIV19), DGK&#x03B8;-GFP-APEX2 is localized throughout the cell, in spines, and colocalizes with vGlut1 and DGK&#x03B8; overexpression. Scale bars represent 20 and 5 &#x03BC;m (cropped region).</p></caption>
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<p>To examine the localization of the construct, mature neuron cultures were transfected with DGK&#x03B8;, DGK&#x03B8;-GFP-APEX2, or mCherry. Neurons were fixed and stained with antibodies against DGK&#x03B8;, GFP, vGlut1, or DsRed. As expected, DGK&#x03B8;-GFP-APEX2 is expressed cytosolically throughout the cell, as evidenced by near-complete colocalization with DGK&#x03B8; and the mCherry cell-fill (<xref ref-type="fig" rid="F1">Figure 1E</xref>, lower panel). DGK&#x03B8;-GFP-APEX2 is also expressed synaptically, illustrated by GFP signal within spines and colocalization with vGlut1 expression (<xref ref-type="fig" rid="F1">Figure 1E</xref>, upper panel). Altogether, these results show that the DGK&#x03B8;-GFP-APEX2 construct expresses well in neurons, co-localizes with overexpressed DGK&#x03B8;, robustly labels proteins, and that labeling is dependent on H<sub>2</sub>O<sub>2</sub>.</p>
</sec>
<sec id="S3.SS2">
<title>Mass Spectrometry Identification of DGK&#x03B8;-GFP-APEX2 Labeled Proteins</title>
<p>To capture changes in DGK&#x03B8; interactions with neuronal activity, we labeled mature neurons expressing DGK&#x03B8;-GFP-APEX2 with and without depolarization. The selection of potential interactors was based on interaction changes dependent on depolarization. To identify DGK&#x03B8; interactors, we conducted three mass spectrometry experiments with the same conditions. The detailed data from each mass spectrometry experiment can be found in <xref ref-type="supplementary-material" rid="TS1">Supplementary Tables 1</xref>&#x2013;<xref ref-type="supplementary-material" rid="TS3">3</xref> and <xref ref-type="supplementary-material" rid="FS1">Supplementary Figure 1</xref>. This data is also publicly available in the Proteomics Identifications Database (PRIDE) at <ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/pride/archive/projects/PXD030495">http://www.ebi.ac.uk/pride/archive/projects/PXD030495</ext-link>.</p>
<p>Because proteins were trypsinized before enrichment with streptavidin, the site of biotinylation is known for each peptide identified. Importantly, multiple biotinylated peptides corresponding to DGK&#x03B8;-GFP-APEX2 were identified in each mass spectrometry experiment, serving as our positive control (<xref ref-type="fig" rid="F2">Figure 2A</xref>). Each experiment produced similar numbers of total biotinylated peptides, &#x223C;2,200&#x2013;2,700, corresponding to &#x223C;550&#x2013;700 proteins (<xref ref-type="fig" rid="F2">Figure 2B</xref>). Importantly, because we employed label-free quantitation, the relative abundance ratio for each biotinylated peptide is calculated as (abundance in KCl samples)/(abundance in control samples). <xref ref-type="fig" rid="F2">Figure 2C</xref> displays the log<sub>2</sub>(abundance ratio) for each identified peptide in one of the three experiments, ranging from those peptides only found in KCl samples, those present in both samples in different amounts, and those peptides only found in control samples. Although some peptides may have only been found in one condition, there were usually other peptides from the same protein that were present in the other condition. Importantly, most of our analysis focused on differences in biotinylation and relative abundance between conditions. There was a high degree of similarity between the data sets from each experiment, increasing confidence in potential DGK&#x03B8; interactors. A total of 51% of all peptides identified were found in all three experiments, with 17% being the largest amount of peptides only identified in 1 experiment (<xref ref-type="fig" rid="F2">Figure 2D</xref>).</p>
<fig id="F2" position="float">
<label>FIGURE 2</label>
<caption><p>Differential labeling of synaptic proteins by DGK&#x03B8;-GFP-APEX2 with KCl. <bold>(A)</bold> Biotinylated tyrosine residues within DGK&#x03B8;-GFP-APEX2, corresponding to peptides identified in one (&#x002A;), two (#), or three (&#x2020;) experiments. <bold>(B)</bold> Mass spectrometry experiments 1 and 3 consisted of three KCl-depolarized samples and three control samples, while experiment 2 consisted of two of each. Each sample contains &#x223C;50 e<sup>6</sup> cells. The three experiments produced similar numbers of total biotinylated peptides and their corresponding proteins. <bold>(C)</bold> The differential labeling of peptides with KCl is illustrated for mass spectrometry experiment 2. All biotinylated peptides identified are graphed by their log<sub>2</sub>(peptide abundance). Peptide abundance is calculated as (relative abundance in KCl-depolarized samples)/(relative abundance in control samples). <bold>(D)</bold> Of the total number of peptides identified from our three mass spectrometry experiments, 51% were found in all three experiments, 22% were found in two of the three experiments, and 27% were found in only one experiment.</p></caption>
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<p>Because the goal of this project is to investigate the mechanism of DGK&#x03B8;&#x2019;s newly discovered regulatory role in endocytosis, we focused our analyses on proteins known to have a role in the synaptic vesicle cycle, particularly synaptic proteins. Many of those proteins had some biotinylated peptides found only within the depolarized samples, such as dynamin-1, heat shock cognate 71 (Hsc70), and syntaxin-binding protein 1 (Munc18-1) (<xref ref-type="fig" rid="F2">Figure 2D</xref>). Other proteins had peptides with a high abundance ratio and a high number of PSMs (peptide-spectrum matches), such as calcium calmodulin-dependent kinase II alpha (CaMKII&#x03B1;). Most of the proteins we identified as potential interactors have biotinylated peptides present in samples with and without depolarization. To select candidate proteins of interest, we first isolated proteins that were biotinylated in at least 2 experiments. Then, we selected proteins with the same biotinylated peptide in the same condition in at least 2 experiments. The final candidate proteins selected were all synaptic or directly involved in vesicle cycling. These proteins either had biotinylated peptides with a relatively high number of PSMs or a significant change in the number of PSMs or the site of biotinylation between depolarized and non-depolarized samples (<xref ref-type="fig" rid="F3">Figure 3A</xref>). Our candidate DGK&#x03B8; interactors consisted of the synaptic vesicle proteins listed in <xref ref-type="fig" rid="F3">Figure 3B</xref>. Also listed are 1 or 2 corresponding peptides (each detected in all 3 experiments) and the number of PSMs for that peptide found in each condition in experiment 1. <xref ref-type="supplementary-material" rid="FS1">Supplementary Figure 1</xref> outlines all of the biotinylated peptides and their number of PSMs for each candidate interactor from each experiment. Cofilin-1, CaMKII&#x03B1;, protein kinase C&#x03B1; (PKC&#x03B1;), Hsc70, synaptogyrin-1, SNAP-25 and synaptojanin-1 had an obvious, significant change in peptides and their number of PSMs between depolarized and non-depolarized conditions, while proteins like brain acid soluble protein 1 (Basp1) had peptides with unusually high numbers of PSMs. Clathrin heavy chain 1, dynamin-1, syntaxin-7, Syt1, and Munc18-1 had a combination of both characteristics (<xref ref-type="fig" rid="F3">Figure 3B</xref> and <xref ref-type="supplementary-material" rid="FS1">Supplementary Figure 1</xref>).</p>
<fig id="F3" position="float">
<label>FIGURE 3</label>
<caption><p>Selection of candidate DGK&#x03B8; proteins of interest. <bold>(A)</bold> Criteria for the selection of candidate DGK&#x03B8;-interacting proteins. <bold>(B)</bold> The selected candidate DGK&#x03B8; interactors and one or two biotinylated peptides (all of which were identified in all three mass spectrometry experiments), with their PSMs in each condition. Site of biotinylation, PSMs, and % protein coverage from mass spectrometry experiment 1.</p></caption>
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</sec>
<sec id="S3.SS3">
<title>Biochemical Validation of Biotinylated Candidate Interactors</title>
<p>Because APEX2 proximity labeling can label transient non-specific interactors, it was essential to further validate the potential interaction between DGK&#x03B8; and our candidate interactors. To biochemically validate that our candidate interactors are biotinylated, we performed streptavidin pulldowns with DGK&#x03B8;-GFP-APEX2-labeled lysates. A streptavidin-conjugated antibody confirmed the presence of biotinylated proteins in the input and pulldown samples from both the depolarized and non-depolarized conditions. Dynamin-1, synaptogyrin-1, Munc18-1, clathrin heavy chain 1, Syt1, CaMKII&#x03B1;, Hsc70, and syntaxin-7 were detected in the eluates from both depolarized and non-depolarized samples (<xref ref-type="fig" rid="F4">Figure 4A</xref>). Basp1, cofilin-1, PKC&#x03B1;, synaptojanin-1 and SNAP-25 were not detected in these eluates, suggesting that they are not biotinylated by DGK&#x03B8;-GFP-APEX2 (<xref ref-type="supplementary-material" rid="FS2">Supplementary Figure 2</xref>). These data suggest that most of our candidate interactors, such as canonical synaptic vesicle recycling proteins Syt1 and Munc18-1, are biotinylated by DGK&#x03B8;-GFP-APEX2, which complements our mass spectrometry results. Therefore, our list of candidate interactors now includes CaMKII&#x03B1;, clathrin heavy chain 1, dynamin-1, Hsc70, synaptogyrin-1, Syt1, syntaxin-7, and Munc18-1.</p>
<fig id="F4" position="float">
<label>FIGURE 4</label>
<caption><p>Validation of candidate DGK&#x03B8;-interacting proteins. <bold>(A)</bold> Streptavidin beads were used to isolate biotinylated proteins from DGK&#x03B8;-GFP-APEX2 labeled cortical neuron lysates (DIV21), and biotinylation was confirmed biochemically for dynamin-1, synaptogyrin-1, Munc18-1, clathrin heavy chain 1, Syt1, CaMKII&#x03B1;, Hsc70, and syntaxin-7. <bold>(B)</bold> DGK&#x03B8; overexpressed in HEK cells is immunoprecipitated with a myc antibody. <bold>(C)</bold> DGK&#x03B8; interacts with Hsc70, CaMKII&#x03B1;, Syt1, synaptogyrin-1, dynamin-1, syntaxin-7, and Munc18-1 when both are overexpressed in HEK cells. Hsc70 interacts with DGK&#x03B8; at its endogenous expression level. <bold>(D)</bold> Clathrin heavy chain 1 does not interact with DGK&#x03B8; when overexpressed in HEK cells. All blots are representative of at least three separate experiments.</p></caption>
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</sec>
<sec id="S3.SS4">
<title>Biochemical Confirmation of the Interaction Between DGK&#x03B8; and Candidate Interactors</title>
<p>To further confirm the interaction between DGK&#x03B8; and our candidate interactors, we performed coimmunoprecipitation (CoIP) experiments in HEK293FT cells. Due to the difficulty in obtaining sufficient amounts of protein in neurons compared to HEK cell cultures, we performed these experiments in HEK cells for simplicity and increased sensitivity. HEK293FT cells were transfected with myc-DGK&#x03B8; alone or together with a candidate interactor. First, we confirmed that our myc antibody efficiently pulled down DGK&#x03B8; in HEK cells. Significant amounts of DGK&#x03B8; were found in eluates from DGK&#x03B8;-overexpressed HEK cell lysates, as visualized by a different myc antibody (<xref ref-type="fig" rid="F4">Figure 4B</xref>). We found that CaMKII&#x03B1;, Syt1, synaptogyrin-1, dynamin-1, syntaxin-7 and Munc18-1 coimmunoprecipitated with DGK&#x03B8; when both DGK&#x03B8; and the candidate interactor are overexpressed in HEK cells. Hsc70 coimmunoprecipitated with DGK&#x03B8; at its own endogenous expression level as well as when overexpressed (<xref ref-type="fig" rid="F4">Figure 4C</xref>). Control pulldowns were conducted using a non-specific mouse IgG and failed to pulldown any of our confirmed DGK&#x03B8; interactors (<xref ref-type="supplementary-material" rid="FS3">Supplementary Figure 3</xref>).</p>
<p>We note that clathrin heavy chain 1 was biotinylated but did not coimmunoprecipitate with DGK&#x03B8; (<xref ref-type="fig" rid="F4">Figure 4D</xref>). This could be because the interaction is specific to neurons or that the proteins are spatially segregated in HEK cells. Further, for both Hsc70 and clathrin heavy chain 1, there was not an obvious difference in expression between endogenous and overexpression of these proteins. We hypothesize that a difference is not visible because the endogenous expression is robust.</p>
<p>Overall, these results confirm our mass spectrometry studies, providing the first evidence that DGK&#x03B8; interacts with Hsc70, CaMKII&#x03B1;, Syt1, synaptogyrin-1, dynamin-1, syntaxin-7 and Munc18-1. All of DGK&#x03B8;&#x2019;s newly confirmed interactors have a known role in synaptic vesicle recycling, lending further support to the hypothesis that DGK&#x03B8; is involved in regulating endocytosis. As we expected the DGK&#x03B8; activators to contain a polybasic region, we also note that Syt1, dynamin-1 and Munc18-1 had the highest percent basicity of the proteins that coimmunoprecipitated with DGK&#x03B8; (<xref ref-type="fig" rid="F5">Figure 5A</xref>).</p>
<fig id="F5" position="float">
<label>FIGURE 5</label>
<caption><p>Syt1 increases DGK&#x03B8; activity 10-fold over DGK&#x03B8; alone. <bold>(A)</bold> List of candidate proteins for which an interaction with DGK&#x03B8; was validated and their function. Syt1 has the highest percent basicity of the confirmed interactors. <bold>(B)</bold> DGK&#x03B8; kinase activity was measured for DGK&#x03B8; alone and for DGK&#x03B8; (10 ng/&#x03BC;L) plus the addition of each confirmed interactor (500 ng/&#x03BC;L). Syt1 increased DGK&#x03B8; activity 10-fold, while syntaxin-7 increased DGK&#x03B8; activity four-fold. Error bars indicate SEM. Graph summarizes data from 2 experiments with three replicates each, <italic>n</italic> = 6, &#x002A;<italic>p</italic> &#x003C; 0.05, &#x002A;&#x002A;&#x002A;<italic>p</italic> &#x003C; 0.0005, &#x002A;&#x002A;&#x002A;&#x002A;<italic>p</italic> &#x003C; 0.0001 against DGK&#x03B8; only, ratio paired <italic>t</italic>-test.</p></caption>
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</sec>
<sec id="S3.SS5">
<title>DGK&#x03B8; Interactors That Stimulate DGK&#x03B8; Activity</title>
<p>Confirmed DGK&#x03B8; interactors were examined for their ability to stimulate DGK&#x03B8;&#x2019;s kinase activity using the ADP-Glo assay (<xref ref-type="bibr" rid="B1">Balzano et al., 2011</xref>; <xref ref-type="bibr" rid="B38">Nagaraj et al., 2017</xref>). In this assay, kinase-generated ADP is converted to ATP which is then quantified via a luciferase/luciferin-based reaction. This reaction was performed with purified DGK&#x03B8; alone (10 ng/&#x03BC;L) and with the addition of the following purified, recombinant proteins of each individual DGK&#x03B8; interactor (500 ng/&#x03BC;L) validated by CoIP as described above: Hsc70, CaMKII&#x03B1;, Syt1, synaptogyrin-1, dynamin-1, syntaxin-7, and Munc18-1. We found that the addition of 500 ng/&#x03BC;L Syt1 produced a 10-fold increase in DGK&#x03B8; activity (arbitrary fluorescence units/50 ng DGK&#x03B8;) over DGK&#x03B8; alone, the largest increase of all our confirmed interactors (No DGK&#x03B8;: 2.44 &#x00B1; 0.09, DGK&#x03B8; only: 15.27 &#x00B1; 1.89, DGK&#x03B8;+Syt1: 149.99 &#x00B1; 21.91, DGK&#x03B8;+Stx7: 56.11 &#x00B1; 19.32, DGK&#x03B8;+Syngr1: 43.95 &#x00B1; 6.35, DGK&#x03B8;+CaMKII&#x03B1;: 37.83 &#x00B1; 4.28, DGK&#x03B8;+Hsc70: 36.29 &#x00B1; 5.69, DGK&#x03B8;+Dnm1: 20.66 &#x00B1; 1.16, DGK&#x03B8;+Munc18-1: 18.00 &#x00B1; 1.07; &#x00D7;10<sup>3</sup> arbitrary fluorescence units, <italic>n</italic> = 6). It is also noteworthy that addition of syntaxin-7 led to a four-fold increase in DGK&#x03B8; activity, while synaptogyrin-1, CaMKII&#x03B1; and Hsc70 all led to a 2.5-fold increase in DGK&#x03B8; activity. Dynamin-1 and Munc18-1 did not cause activation of DGK&#x03B8; (<xref ref-type="fig" rid="F5">Figure 5B</xref>). From this data, we conclude that Syt1 is the most probable DGK&#x03B8; interactor and activator, while syntaxin-7 and synaptogyrin-1, proteins also implicated in vesicle recycling, may also play roles in DGK&#x03B8; activity.</p>
</sec>
</sec>
<sec id="S4" sec-type="discussion">
<title>Discussion</title>
<p>In previous studies, DGK&#x03B8; kinase activity was shown to have a regulatory role in synaptic vesicle endocytosis, particularly during elevated neuronal activity (<xref ref-type="bibr" rid="B18">Goldschmidt et al., 2016</xref>). This role depends on the catalytic activity of DGK&#x03B8;. The mechanism involved in regulating DGK&#x03B8; activity in synaptic boutons has not been explored, but it is known that proteins with polybasic regions activate the enzyme&#x2019;s activity (<xref ref-type="bibr" rid="B59">Tu-Sekine and Raben, 2012</xref>). The current study is the first to identify endogenous DGK&#x03B8; interactors in neurons. Using APEX2 proximity labeling, mass spectrometry analyses, and biochemical analyses we confirmed that DGK&#x03B8; interacts with Hsc70, CaMKII&#x03B1;, Syt1, synaptogyrin-1, dynamin-1, syntaxin-7, and Munc18-1. Importantly, Syt1, syntaxin-7, synaptogyrin-1, Hsc70 and CaMKII&#x03B1; all increased DGK&#x03B8; kinase activity compared to DGK&#x03B8; alone. Notably, Syt1 produced a 10-fold increase in DGK&#x03B8; activity, suggesting Syt1 is the strongest DGK&#x03B8; interactor. Taken together, these results suggest that Syt1 functions at synapses to regulate PtdOH production by DGK&#x03B8;.</p>
<p>Given the role of polybasic regions in modulating DGK&#x03B8; activity (<xref ref-type="bibr" rid="B59">Tu-Sekine and Raben, 2012</xref>), it is of particular note that Syt1 is the interactor with the highest percent basicity. The C2B domain of Syt1 contains a polybasic patch (K324-327) that has been shown to bind acidic phospholipids and regulates synchronous evoked synaptic vesicle release (<xref ref-type="bibr" rid="B9">Chang et al., 2018</xref>). The binding of Ca<sup>2+</sup> to Syt1 results in the hydrophobic amino acids at the ends of the Ca<sup>2+</sup>-binding domains to insert into membranes. This conformational change generates membrane curvature and triggers fusion of synaptic vesicles with the presynaptic membrane (<xref ref-type="bibr" rid="B34">Martens et al., 2007</xref>; <xref ref-type="bibr" rid="B32">Lynch et al., 2008</xref>; <xref ref-type="bibr" rid="B22">Hui et al., 2009</xref>). Importantly, Syt1 also serves as a Ca<sup>2+</sup> sensor for endocytosis and functions to couple and balance endocytosis and exocytosis in the vesicle cycle. It has been proposed that a modulatory protein, such as DGK&#x03B8;, could bind Syt1 during resting states and is released when Syt1 binds Ca<sup>2+</sup>, freeing Syt1 to regulate endocytosis (<xref ref-type="bibr" rid="B61">Yao et al., 2012</xref>; <xref ref-type="bibr" rid="B30">Li et al., 2017</xref>). It is also possible that the interaction between DGK&#x03B8; and Syt1 is crucial to coordinate their activities following depolarization. For example, the binding of Syt1 to DGK&#x03B8; and the subsequent increase of DGK&#x03B8;&#x2019;s kinase activity could produce PtdOH that greatly contributes to the negative membrane curvature necessary for vesicle fusion. It is tempting to speculate that Syt1 is a crucial interactor and activator of DGK&#x03B8;, and together their interaction is important to maintain efficient Ca<sup>2+</sup>-mediated endocytosis (<xref ref-type="fig" rid="F6">Figure 6</xref>). Given Syt1&#x2019;s indispensable role in vesicle recycling, and recent studies that implicate Syt1 in neurodegenerative disease (<xref ref-type="bibr" rid="B6">Brinkmalm et al., 2014</xref>; <xref ref-type="bibr" rid="B17">Gautam et al., 2015</xref>; <xref ref-type="bibr" rid="B49">Shi et al., 2020</xref>), this previously unknown interaction between DGK&#x03B8; and Syt1 strengthens the notion that lipid-metabolizing enzymes are important regulators of neurotransmission.</p>
<fig id="F6" position="float">
<label>FIGURE 6</label>
<caption><p>Model for DGK&#x03B8;&#x2019;s interaction with Syt1. Syt1 is a transmembrane protein on synaptic vesicles and the presynaptic membrane. Perhaps to aid in the membrane deformation required in the fusion and fission of vesicles, Syt1 binds to DGK&#x03B8; and stimulates its kinase activity, producing local hotspots of PtdOH that generate negative membrane curvature. AZ = active zone, EZ = endocytic zone. Figure made with <ext-link ext-link-type="uri" xlink:href="http://BioRender.com">BioRender.com</ext-link>.</p></caption>
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</fig>
<p>While Syt1 is an attractive candidate for the endogenous DGK&#x03B8; activator, other proteins, such as syntaxin-7, may also be involved in regulating the enzyme&#x2019;s activity in neurons. Syntaxin-7 is a SNARE protein mainly localized on early endosomes that is thought to be involved in the homotypic fusion of endocytic organelles and late endosome-lysosome fusion (<xref ref-type="bibr" rid="B39">Prekeris et al., 1999</xref>; <xref ref-type="bibr" rid="B60">Ward et al., 2000</xref>). As endosomes participate in the replenishment of synaptic vesicles during neuronal activity, it is also important to note that syntaxin-7 mediates endosomal membrane fusion in the rapid reproduction of vesicles during high-frequency repetitive stimulation in hippocampal neurons (<xref ref-type="bibr" rid="B37">Mori et al., 2021</xref>). Considering syntaxin-7 also greatly increased DGK&#x03B8; activity, perhaps there is a role for the interaction of DGK&#x03B8; and syntaxin-7 in bulk membrane endocytosis following periods of high stimulation. Previous work showed that DGK&#x03B8; KO neurons possess increasingly slower rates of endocytosis with high frequency stimulation (<xref ref-type="bibr" rid="B18">Goldschmidt et al., 2016</xref>). It is generally thought that during periods of high stimulation, bulk membrane endocytosis of large endosomes occurs to balance membrane homeostasis with the high rates of exocytosis (<xref ref-type="bibr" rid="B11">Clayton et al., 2008</xref>). It is possible that during periods of high frequency stimulation, DGK&#x03B8; activated by syntaxin-7, contributes PtdOH in the formation of large endosomes during bulk endocytosis. This interaction could implicate DGK&#x03B8; in bulk endocytosis and the generation of PtdOH in the membrane curvature of large endosome formation.</p>
<p>Synaptogyrin-1 is an integral membrane protein in synaptic vesicles and produced a &#x223C;2.5-fold increase in DGK&#x03B8; activity (<xref ref-type="fig" rid="F5">Figure 5</xref>). Although its neuronal function is still unclear, it is thought to regulate neurotransmitter release and have a role in synaptic plasticity (<xref ref-type="bibr" rid="B4">Belizaire et al., 2004</xref>). Synaptogyrin-1 and synaptophysin KO mice displayed impaired short- and long-term plasticity (<xref ref-type="bibr" rid="B26">Janz et al., 1999</xref>), while overexpression of synaptogyrin-1 in PC12 cells caused inhibition of Ca<sup>2+</sup>-dependent exocytosis (<xref ref-type="bibr" rid="B51">Sugita et al., 1999</xref>). Synaptogyrin-1 peptides had one of the most obvious differences between depolarized and non-depolarized samples in our mass spectrometry studies. The number of PSMs was extraordinarily high in non-depolarized samples compared to depolarized and compared to other peptides from the entire experiment. Although a link between synaptogyrin-1 and DGK&#x03B8; function is not immediately clear, some studies have suggested a role for DGKs in synaptic plasticity (<xref ref-type="bibr" rid="B43">Rodriguez de Turco et al., 2001</xref>; <xref ref-type="bibr" rid="B11">Clayton et al., 2008</xref>; <xref ref-type="bibr" rid="B2">Barber and Raben, 2020</xref>). DGK&#x03B6; directly interacts with PSD-95 in the postsynapse and contributes to dendritic spine maintenance through its production of PtdOH (<xref ref-type="bibr" rid="B28">Kim et al., 2009</xref>). DGK&#x03B6; KO mice exhibit enhanced long-term potentiation (LTP) and attenuated long-term depression (LTD) at pyramidal synapses in the hippocampus (<xref ref-type="bibr" rid="B47">Seo et al., 2012</xref>). One could postulate that the production of PtdOH by DGK&#x03B8; and its interaction with synaptogyrin-1 might influence synaptic plasticity. Similar to its role in synaptic vesicle endocytosis in the presynapse, DGK&#x03B8; could potentially regulate AMPA and NMDA receptor-containing vesicle recycling at the postsynapse.</p>
<p>CaMKII&#x03B1; is the most abundant protein in the neuronal postsynapse, but is also abundant in the presynapse as it associates with synaptic vesicles. Because of its ubiquity, CaMKII&#x03B1; has been implicated in synaptic plasticity, dendritic arbor structure, and density of glutamatergic synapses, among other things (<xref ref-type="bibr" rid="B16">Fink and Meyer, 2002</xref>; <xref ref-type="bibr" rid="B36">Miller et al., 2002</xref>; <xref ref-type="bibr" rid="B21">Hell, 2014</xref>). Given the breadth of its localization and function, it is difficult to speculate a specific role for CaMKII&#x03B1; and DGK&#x03B8;&#x2019;s interaction in the regulation of synaptic vesicle recycling. As with synaptogyrin-1, however, a possible connection between DGK&#x03B8; and synaptic plasticity cannot be ignored. Future studies should focus on identifying the role of DGK&#x03B8; in the postsynapse.</p>
<p>DGK&#x03B8;&#x2019;s interaction with Hsc70 may affect the role of Hsc70 in uncoating clathrin from endocytosed vesicles (<xref ref-type="bibr" rid="B13">Eisenberg and Greene, 2007</xref>; <xref ref-type="bibr" rid="B5">B&#x00F6;cking et al., 2011</xref>). Disruption of DGK&#x03B8;&#x2019;s interaction with Hsc70, for example by decreased levels or absence of DGK&#x03B8;, may slow the rates of clathrin uncoating resulting in slower rates of synaptic vesicle endocytosis as previously observed (<xref ref-type="bibr" rid="B18">Goldschmidt et al., 2016</xref>). DGK&#x03B8; could also participate in the Hsc70-binding of free clathrin after it has disassembled from lattices, to prevent aggregation and quick access for recycling for further rounds of endocytosis. Although several biotinylated peptides from clathrin heavy chain 1 were identified in each of our mass spectrometry experiments (<xref ref-type="fig" rid="F3">Figure 3B</xref>), clathrin heavy chain 1 did not coimmunoprecipitate with DGK&#x03B8; (<xref ref-type="fig" rid="F4">Figure 4D</xref>). The biotinylation we observed could be the result of the close proximity of DGK&#x03B8; and clathrin heavy chain 1, due to DGK&#x03B8;&#x2019;s binding to Hsc70. We cannot rule out the possibility that our APEX2 proximity labeling detects a very transient interaction between DGK&#x03B8; and clathrin heavy chain 1 which is not detectable by coimmunoprecipitation.</p>
<p>Interestingly, confirmed interactors dynamin-1 and Munc18-1 did not stimulate DGK&#x03B8; kinase activity. Munc18-1 binds tightly to syntaxin-1 and is required for SNARE-mediated membrane fusion. Mutations in Munc18-1 cause a defect in the stability of the SNARE bundle and priming of synaptic vesicles (<xref ref-type="bibr" rid="B12">Ferenc et al., 2009</xref>; <xref ref-type="bibr" rid="B27">Jiao et al., 2018</xref>). Dynamin-1 is a GTPase required for functional endocytosis at synapses. It is thought to oligomerize in a circular shape around the neck of endocytic pits and mediate fission of vesicles from the membrane (<xref ref-type="bibr" rid="B48">Sever, 2002</xref>; <xref ref-type="bibr" rid="B41">Raimondi et al., 2011</xref>). Dynamin-1 KO synapses have significantly increased numbers of clathrin-coated vesicles and pits that remain connected to membranes following an action potential, leading to a dramatic endocytic defect (<xref ref-type="bibr" rid="B48">Sever, 2002</xref>; <xref ref-type="bibr" rid="B15">Ferguson et al., 2007</xref>). Our mass spectrometry experiments suggest that both dynamin-1 and Munc18-1 have a stronger interaction with DGK&#x03B8; following depolarization (<xref ref-type="fig" rid="F3">Figure 3B</xref> and <xref ref-type="supplementary-material" rid="FS1">Supplementary Figure 1</xref>). Given that both proteins are in close proximity to membrane deformations, a role for DGK&#x03B8;&#x2019;s interaction should not be discounted. DGK&#x03B8; may play a non-catalytic role in regulation or activation of dynamin-1 or Munc18-1. We should also note that Basp1, cofilin-1, PKC&#x03B1;, SNAP-25, and synaptojanin-1 were eliminated as potential DGK&#x03B8; interactors because we could not biochemically validate their biotinylation. This may be due to very transient interactions between each candidate and DGK&#x03B8; <italic>in vivo.</italic> For example, SNAP-25 may briefly interact with DGK&#x03B8; because of DGK&#x03B8;&#x2019;s interaction with Munc18-1 as they reside in very close proximity.</p>
<p>It is also important to consider the role of DGK&#x03B8;-induced PtdOH in compensatory endocytosis. Indeed, many DGK&#x03B8;-interacting proteins&#x2019; functions involve membrane curvature. For example, curvature is important for the dynamin-1-mediated membrane scission, as well as for membrane fusion by the SNARE protein syntaxin-7 and Munc18-1. It is interesting, therefore, to speculate that DGK&#x03B8; is important for the local production of PtdOH and the generation of that membrane curvature.</p>
<p>Together, we validated that DGK&#x03B8; interacts with important proteins that regulate key steps of vesicle cycling at the presynapse, most notably Syt1. Future work is required to determine how DGK&#x03B8; interacts with the interacting proteins identified in this study and which interactions are essential for efficient neurotransmitter release. The identification of DGK&#x03B8; interactors and activators is crucial for understanding the mechanism of DGK&#x03B8;&#x2019;s role in the synaptic vesicle cycle and neurotransmission in general.</p>
</sec>
<sec id="S5" sec-type="data-availability">
<title>Data Availability Statement</title>
<p>The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/<xref ref-type="supplementary-material" rid="FS1">Supplementary Material</xref>.</p>
</sec>
<sec id="S6">
<title>Ethics Statement</title>
<p>The animal study was reviewed and approved by the Johns Hopkins University Animal Care and Use Committee.</p>
</sec>
<sec id="S7">
<title>Author Contributions</title>
<p>CB, HG, RH, and DR: conceptualization. CB, HG, QM, LD, RC, DR, and RH: methodology. CB: investigation. CB, DR, and LD: writing &#x2013; original draft. CB, HG, RC, DR, and RH: writing, review, and editing draft. DR: funding acquisition. DR and RH: supervision. All authors contributed to the article and approved the submitted version.</p>
</sec>
<sec id="conf1" sec-type="COI-statement">
<title>Conflict of Interest</title>
<p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
<sec id="pudiscl1" sec-type="disclaimer">
<title>Publisher&#x2019;s Note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
</sec>
</body>
<back>
<sec id="S8" sec-type="funding-information">
<title>Funding</title>
<p>This work was supported by RO1NS077923 by the National Institutes of Health to DR, who acquired the funding and contributed to the conceptualization and supervision of this work.</p>
</sec>
<ack>
<p>We thank the members of the RH lab for critical discussions.</p>
</ack>
<sec id="S10" sec-type="supplementary-material">
<title>Supplementary Material</title>
<p>The Supplementary Material for this article can be found online at: <ext-link ext-link-type="uri" xlink:href="https://www.frontiersin.org/articles/10.3389/fnsyn.2022.855673/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fnsyn.2022.855673/full#supplementary-material</ext-link></p>
<supplementary-material xlink:href="Image_1.pdf" id="FS1" mimetype="application/pdf" xmlns:xlink="http://www.w3.org/1999/xlink">
<label>Supplementary Figure 1</label>
<caption><p>Each of the 13 tables corresponds to a protein on our list of candidate DGK&#x03B8; interactors. Each table outlines the peptides that were found within that protein by listing the number of the amino acid that has the biotin tyramide tag. The number of PSMs for each peptide is also listed. Peptides in the KCl column were more abundant in depolarized samples. Peptides in the control column were more abundant in the non-depolarized samples. PSMs were combined for peptides for which the biotin tyramide tag was located within three amino acids. Peptides with 3 or less PSMs were eliminated from this analysis. Blue text = experiment 1, black text = experiment 2, red text = experiment 3.</p></caption>
</supplementary-material>
<supplementary-material xlink:href="Image_2.tiff" id="FS2" mimetype="image/tiff" xmlns:xlink="http://www.w3.org/1999/xlink">
<label>Supplementary Figure 2</label>
<caption><p>Basp1, cofilin-1, PKC&#x03B1;, SNAP-25, and synaptojanin-1 were not detected in our streptavidin pulldown experiments and therefore we were not able to confirm biotinylation biochemically for these proteins. They were eliminated from further analysis. Each blot is representative of at least 3 separate experiments.</p></caption>
</supplementary-material>
<supplementary-material xlink:href="Image_3.tiff" id="FS3" mimetype="image/tiff" xmlns:xlink="http://www.w3.org/1999/xlink">
<label>Supplementary Figure 3</label>
<caption><p>Dynamin-1, synaptogyrin-1, Syt1, CaMKII&#x03B1;, Munc18-1, Hsc70, and syntaxin-7, all biochemically-confirmed DGK&#x03B8;-interacting proteins, did not pull down with DGK&#x03B8; when isolated with a non-specific mouse IgG.</p></caption>
</supplementary-material>
<supplementary-material xlink:href="Table_1.XLSX" id="TS1" mimetype="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet" xmlns:xlink="http://www.w3.org/1999/xlink">
<label>Supplementary Table 1</label>
<caption><p>Detailed data from mass spectrometry experiment 1.</p></caption>
</supplementary-material>
<supplementary-material xlink:href="Table_2.XLSX" id="TS2" mimetype="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet" xmlns:xlink="http://www.w3.org/1999/xlink">
<label>Supplementary Table 2</label>
<caption><p>Detailed data from mass spectrometry experiment 2.</p></caption>
</supplementary-material>
<supplementary-material xlink:href="Table_3.XLSX" id="TS3" mimetype="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet" xmlns:xlink="http://www.w3.org/1999/xlink">
<label>Supplementary Table 3</label>
<caption><p>Detailed data from mass spectrometry experiment 3.</p></caption>
</supplementary-material>
</sec>
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