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Article: Identification of new ciliary signaling pathways in the brain and insights into neurological disorders.

Loukil, Abdelhalim / Ebright, Emma / Uezu, Akiyoshi / Gao, Yudong / Soderling, Scott H / Goetz, Sarah C

bioRxiv : the preprint server for biology

2023

Abstract: Primary cilia are conserved sensory hubs essential for signaling transduction and embryonic development. Ciliary dysfunction causes a variety of developmental syndromes with neurological features and cognitive impairment, whose basis mostly remains ... ...

Abstract	Primary cilia are conserved sensory hubs essential for signaling transduction and embryonic development. Ciliary dysfunction causes a variety of developmental syndromes with neurological features and cognitive impairment, whose basis mostly remains unknown. Despite connections to neural function, the primary cilium remains an overlooked organelle in the brain. Most neurons have a primary cilium; however, it is still unclear how this organelle modulates brain architecture and function, given the lack of any systemic dissection of neuronal ciliary signaling. Here, we present the first in vivo glance at the molecular composition of cilia in the mouse brain. We have adapted
Language	English
Publishing date	2023-12-21
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.12.20.572700
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Article ; Online: Identifying Synaptic Proteins by In Vivo BioID from Mouse Brain.

Uezu, Akiyoshi / Soderling, Scott

Methods in molecular biology (Clifton, N.J.)

2019 Volume 2008, Page(s) 107–119

Abstract: Two anatomically and functionally distinct types of synapses are present in the central nervous system, excitatory synapses, and inhibitory synapses. Purification and analysis of the protein complex at the excitatory postsynapses have led to fundamental ... ...

Abstract	Two anatomically and functionally distinct types of synapses are present in the central nervous system, excitatory synapses, and inhibitory synapses. Purification and analysis of the protein complex at the excitatory postsynapses have led to fundamental insights into neurobiology. In contrast, the biochemical purification and analysis of the inhibitory postsynaptic density have been largely intractable. The recently developed method called BioID employs the biotin ligase mutant, BirA*, fused to a bait protein to label and capture proximal proteins. We adapted the BioID approach to enable in vivo BioID, or iBioID of inhibitory synaptic complexes in the mouse brain. This protocol describes the iBioID method to allow synaptic bait proteins to target synaptic complexes, label, and purify biotinylated proteins from the mouse brain. This technique can be easily adapted to target other substructures in vivo that have been difficult to purify and analyze in the past.
MeSH term(s)	Animals ; Biotinylation ; Brain/metabolism ; Brain Chemistry ; Carbon-Nitrogen Ligases/chemistry ; Escherichia coli Proteins/chemistry ; Mice ; Nerve Tissue Proteins/analysis ; Nerve Tissue Proteins/metabolism ; Repressor Proteins/chemistry ; Synapses/chemistry ; Synapses/metabolism
Chemical Substances	Escherichia coli Proteins ; Nerve Tissue Proteins ; Repressor Proteins ; Carbon-Nitrogen Ligases (EC 6.3.-) ; birA protein, E coli (EC 6.3.4.15)
Language	English
Publishing date	2019-05-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9537-0_9
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Article ; Online: Map7D2 and Map7D1 facilitate microtubule stabilization through distinct mechanisms in neuronal cells.

Kikuchi, Koji / Sakamoto, Yasuhisa / Uezu, Akiyoshi / Yamamoto, Hideyuki / Ishiguro, Kei-Ichiro / Shimamura, Kenji / Saito, Taro / Hisanaga, Shin-Ichi / Nakanishi, Hiroyuki

Life science alliance

2022 Volume 5, Issue 8

Abstract: Microtubule (MT) dynamics are modulated through the coordinated action of various MT-associated proteins (MAPs). However, the regulatory mechanisms underlying MT dynamics remain unclear. We show that the MAP7 family protein Map7D2 stabilizes MTs to ... ...

Abstract	Microtubule (MT) dynamics are modulated through the coordinated action of various MT-associated proteins (MAPs). However, the regulatory mechanisms underlying MT dynamics remain unclear. We show that the MAP7 family protein Map7D2 stabilizes MTs to control cell motility and neurite outgrowth. Map7D2 directly bound to MTs through its N-terminal half and stabilized MTs in vitro. Map7D2 localized prominently to the centrosome and partially on MTs in mouse N1-E115 neuronal cells, which expresses two of the four MAP7 family members, Map7D2 and Map7D1. Map7D2 loss decreased the resistance to the MT-destabilizing agent nocodazole without affecting acetylated/detyrosinated stable MTs, suggesting that Map7D2 stabilizes MTs via direct binding. In addition, Map7D2 loss increased the rate of random cell migration and neurite outgrowth, presumably by disturbing the balance between MT stabilization and destabilization. Map7D1 exhibited similar subcellular localization and gene knockdown phenotypes to Map7D2. However, in contrast to Map7D2, Map7D1 was required for the maintenance of acetylated stable MTs. Taken together, our data suggest that Map7D2 and Map7D1 facilitate MT stabilization through distinct mechanisms in cell motility and neurite outgrowth.
MeSH term(s)	Animals ; Cell Movement/genetics ; Mice ; Microtubule-Associated Proteins/genetics ; Microtubule-Associated Proteins/metabolism ; Microtubules/metabolism ; Neurons/metabolism ; Nocodazole/metabolism ; Nocodazole/pharmacology
Chemical Substances	Microtubule-Associated Proteins ; Nocodazole (SH1WY3R615)
Language	English
Publishing date	2022-04-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2575-1077
ISSN (online)	2575-1077
DOI	10.26508/lsa.202201390
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Article ; Online: In vivo proximity proteomics of nascent synapses reveals a novel regulator of cytoskeleton-mediated synaptic maturation.

Spence, Erin F / Dube, Shataakshi / Uezu, Akiyoshi / Locke, Margaret / Soderblom, Erik J / Soderling, Scott H

Nature communications

2019 Volume 10, Issue 1, Page(s) 386

Abstract: Excitatory synapse formation during development involves the complex orchestration of both structural and functional alterations at the postsynapse. However, the molecular mechanisms that underlie excitatory synaptogenesis are only partially resolved, in ...

Abstract	Excitatory synapse formation during development involves the complex orchestration of both structural and functional alterations at the postsynapse. However, the molecular mechanisms that underlie excitatory synaptogenesis are only partially resolved, in part because the internal machinery of developing synapses is largely unknown. To address this, we apply a chemicogenetic approach, in vivo biotin identification (iBioID), to discover aspects of the proteome of nascent synapses. This approach uncovered sixty proteins, including a previously uncharacterized protein, CARMIL3, which interacts in vivo with the synaptic cytoskeletal regulator proteins SrGAP3 (or WRP) and actin capping protein. Using new CRISPR-based approaches, we validate that endogenous CARMIL3 is localized to developing synapses where it facilitates the recruitment of capping protein and is required for spine structural maturation and AMPAR recruitment associated with synapse unsilencing. Together these proteomic and functional studies reveal a previously unknown mechanism important for excitatory synapse development in the developing perinatal brain.
MeSH term(s)	Actin Capping Proteins/genetics ; Actin Capping Proteins/metabolism ; Animals ; Biotin ; CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats ; Cytoskeletal Proteins/metabolism ; Cytoskeleton/metabolism ; Dendritic Spines/metabolism ; Excitatory Postsynaptic Potentials/physiology ; GTPase-Activating Proteins ; Gene Expression Regulation ; HEK293 Cells ; Humans ; Mice, Inbred C57BL ; Microfilament Proteins/genetics ; Microfilament Proteins/metabolism ; Microtubules/metabolism ; Neurogenesis/genetics ; Neurogenesis/physiology ; Neurons/metabolism ; Proteome/genetics ; Proteome/metabolism ; Proteomics ; Synapses/genetics ; Synapses/metabolism
Chemical Substances	Actin Capping Proteins ; CARMIL1 protein, human ; Carmil1 protein, mouse ; Cytoskeletal Proteins ; GTPase-Activating Proteins ; Microfilament Proteins ; Proteome ; Srgap3 protein, mouse ; Biotin (6SO6U10H04)
Language	English
Publishing date	2019-01-23
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-019-08288-w
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Article ; Online: Essential role for InSyn1 in dystroglycan complex integrity and cognitive behaviors in mice.

Uezu, Akiyoshi / Hisey, Erin / Kobayashi, Yoshihiko / Gao, Yudong / Bradshaw, Tyler Wa / Devlin, Patrick / Rodriguiz, Ramona / Tata, Purushothama Rao / Soderling, Scott

eLife

2019 Volume 8

Abstract: Human mutations in the dystroglycan complex (DGC) result in not only muscular dystrophy but also cognitive impairments. However, the molecular architecture critical for the synaptic organization of the DGC in neurons remains elusive. Here, we report ... ...

Abstract	Human mutations in the dystroglycan complex (DGC) result in not only muscular dystrophy but also cognitive impairments. However, the molecular architecture critical for the synaptic organization of the DGC in neurons remains elusive. Here, we report Inhibitory Synaptic protein 1 (InSyn1) is a critical component of the DGC whose loss alters the composition of the GABAergic synapses, excitatory/inhibitory balance in vitro and in vivo, and cognitive behavior. Association of InSyn1 with DGC subunits is required for InSyn1 synaptic localization. InSyn1 null neurons also show a significant reduction in DGC and GABA receptor distribution as well as abnormal neuronal network activity. Moreover, InSyn1 null mice exhibit elevated neuronal firing patterns in the hippocampus and deficits in fear conditioning memory. Our results support the dysregulation of the DGC at inhibitory synapses and altered neuronal network activity and specific cognitive tasks via loss of a novel component, InSyn1.
MeSH term(s)	Animals ; Cells, Cultured ; Cognition ; Dystroglycans/metabolism ; GABAergic Neurons/metabolism ; Hippocampus/physiology ; Humans ; Memory ; Mice, Inbred C57BL ; Synapses/metabolism ; Synapsins/metabolism
Chemical Substances	SYN1 protein, human ; Synapsins ; Dystroglycans (146888-27-9)
Language	English
Publishing date	2019-12-12
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.50712
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Article ; Online: In vivo proximity proteomics of nascent synapses reveals a novel regulator of cytoskeleton-mediated synaptic maturation

Erin F. Spence / Shataakshi Dube / Akiyoshi Uezu / Margaret Locke / Erik J. Soderblom / Scott H. Soderling

Nature Communications, Vol 10, Iss 1, Pp 1-

2019 Volume 16

Abstract: The internal molecular mechanisms that underlie excitatory synaptogenesis remain poorly characterized. This study utilizes a chemogenetic approach, in vivo biotin identification (iBioID), to discover previously uncharacterized proteins at nascent ... ...

Abstract	The internal molecular mechanisms that underlie excitatory synaptogenesis remain poorly characterized. This study utilizes a chemogenetic approach, in vivo biotin identification (iBioID), to discover previously uncharacterized proteins at nascent synapses. CARMIL3 is identified as a cytoskeletal protein that facilitates spine maturation and AMPAR recruitment.
Keywords	Science ; Q
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: In vivo proximity proteomics of nascent synapses reveals a novel regulator of cytoskeleton-mediated synaptic maturation

Erin F. Spence / Shataakshi Dube / Akiyoshi Uezu / Margaret Locke / Erik J. Soderblom / Scott H. Soderling

Nature Communications, Vol 10, Iss 1, Pp 1-

2019 Volume 16

Abstract	The internal molecular mechanisms that underlie excitatory synaptogenesis remain poorly characterized. This study utilizes a chemogenetic approach, in vivo biotin identification (iBioID), to discover previously uncharacterized proteins at nascent synapses. CARMIL3 is identified as a cytoskeletal protein that facilitates spine maturation and AMPAR recruitment.
Keywords	Science ; Q
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Chemico-genetic discovery of astrocytic control of inhibition in vivo.

Takano, Tetsuya / Wallace, John T / Baldwin, Katherine T / Purkey, Alicia M / Uezu, Akiyoshi / Courtland, Jamie L / Soderblom, Erik J / Shimogori, Tomomi / Maness, Patricia F / Eroglu, Cagla / Soderling, Scott H

Nature

2020 Volume 588, Issue 7837, Page(s) 296–302

Abstract: Perisynaptic astrocytic processes are an integral part of central nervous system ... ...

Abstract	Perisynaptic astrocytic processes are an integral part of central nervous system synapses
MeSH term(s)	Animals ; Astrocytes/chemistry ; Astrocytes/cytology ; Astrocytes/metabolism ; Cell Adhesion Molecules, Neuronal/metabolism ; Cell Shape ; Female ; GABAergic Neurons/cytology ; GABAergic Neurons/metabolism ; Genetic Complementation Test ; HEK293 Cells ; Humans ; Male ; Mice ; Neural Inhibition ; Neurons/cytology ; Neurons/metabolism ; Proteome/metabolism ; Proteomics ; Synapses/chemistry ; Synapses/metabolism ; gamma-Aminobutyric Acid/metabolism
Chemical Substances	Cell Adhesion Molecules, Neuronal ; Proteome ; gamma-Aminobutyric Acid (56-12-2)
Language	English
Publishing date	2020-11-11
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-020-2926-0
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Article ; Online: Essential role for InSyn1 in dystroglycan complex integrity and cognitive behaviors in mice

Akiyoshi Uezu / Erin Hisey / Yoshihiko Kobayashi / Yudong Gao / Tyler WA Bradshaw / Patrick Devlin / Ramona Rodriguiz / Purushothama Rao Tata / Scott Soderling

eLife, Vol

2019 Volume 8

Abstract	Human mutations in the dystroglycan complex (DGC) result in not only muscular dystrophy but also cognitive impairments. However, the molecular architecture critical for the synaptic organization of the DGC in neurons remains elusive. Here, we report Inhibitory Synaptic protein 1 (InSyn1) is a critical component of the DGC whose loss alters the composition of the GABAergic synapses, excitatory/inhibitory balance in vitro and in vivo, and cognitive behavior. Association of InSyn1 with DGC subunits is required for InSyn1 synaptic localization. InSyn1 null neurons also show a significant reduction in DGC and GABA receptor distribution as well as abnormal neuronal network activity. Moreover, InSyn1 null mice exhibit elevated neuronal firing patterns in the hippocampus and deficits in fear conditioning memory. Our results support the dysregulation of the DGC at inhibitory synapses and altered neuronal network activity and specific cognitive tasks via loss of a novel component, InSyn1.
Keywords	GABA ; inhibitory synapse ; dystrophin/dystroglycan complex ; hippocampus ; InSyn1 ; memory ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	571
Language	English
Publishing date	2019-12-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Plug-and-Play Protein Modification Using Homology-Independent Universal Genome Engineering.

Gao, Yudong / Hisey, Erin / Bradshaw, Tyler W A / Erata, Eda / Brown, Walter E / Courtland, Jamie L / Uezu, Akiyoshi / Xiang, Yu / Diao, Yarui / Soderling, Scott H

Neuron

2019 Volume 103, Issue 4, Page(s) 583–597.e8

Abstract: Analysis of endogenous protein localization, function, and dynamics is fundamental to the study of all cells, including the diversity of cell types in the brain. However, current approaches are often low throughput and resource intensive. Here, we ... ...

Abstract	Analysis of endogenous protein localization, function, and dynamics is fundamental to the study of all cells, including the diversity of cell types in the brain. However, current approaches are often low throughput and resource intensive. Here, we describe a CRISPR-Cas9-based homology-independent universal genome engineering (HiUGE) method for endogenous protein manipulation that is straightforward, scalable, and highly flexible in terms of genomic target and application. HiUGE employs adeno-associated virus (AAV) vectors of autonomous insertional sequences (payloads) encoding diverse functional modifications that can integrate into virtually any genomic target loci specified by easily assembled gene-specific guide-RNA (GS-gRNA) vectors. We demonstrate that universal HiUGE donors enable rapid alterations of proteins in vitro or in vivo for protein labeling and dynamic visualization, neural-circuit-specific protein modification, subcellular rerouting and sequestration, and truncation-based structure-function analysis. Thus, the "plug-and-play" nature of HiUGE enables high-throughput and modular analysis of mechanisms driving protein functions in cellular neurobiology.
MeSH term(s)	Animals ; Brain/cytology ; Brain/metabolism ; CRISPR-Cas Systems ; Cells, Cultured ; Dependovirus/genetics ; Gene Editing/methods ; Gene Knock-In Techniques/methods ; Genetic Vectors/genetics ; Genomics/methods ; Humans ; Immunochemistry/methods ; Inteins ; Mice ; Mutagenesis, Insertional ; Nerve Tissue Proteins/chemistry ; Nerve Tissue Proteins/genetics ; Protein Engineering/methods ; Protein Processing, Post-Translational ; Proteomics ; RNA, Guide, CRISPR-Cas Systems/genetics ; Recombinant Fusion Proteins/genetics ; Sequence Homology, Nucleic Acid
Chemical Substances	Nerve Tissue Proteins ; RNA, Guide, CRISPR-Cas Systems ; Recombinant Fusion Proteins
Language	English
Publishing date	2019-07-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	808167-0
ISSN	1097-4199 ; 0896-6273
ISSN (online)	1097-4199
ISSN	0896-6273
DOI	10.1016/j.neuron.2019.05.047
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