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Clathrin IP_mouse sciatic nerve axons_Roylab_UCSD

ABSTRACT: Sciatic nerve axon segments from adult mouse were isolated. Following enzymatic digestion, lysate was subjected to incubation with beads conjugated with either clathrin heavy chain antibody or control IgG antibody for clathrin immunoprecipitation. MudPIT analysis was subsequently performed to identify proteins co-precipitating with clathrin.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Nerve Cord

SUBMITTER: Titus Jung

LAB HEAD: John Yates

PROVIDER: PXD027857 | Pride | 2021-08-12

REPOSITORIES: Pride

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	20130628_exp_01.raw	Raw
	20130628_exp_02.raw	Raw
	20130628_exp_03.raw	Raw
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Publications

Clathrin packets move in slow axonal transport and deliver functional payloads to synapses.

Ganguly Archan A Sharma Rohan R Boyer Nicholas P NP Wernert Florian F Phan Sébastien S Boassa Daniela D Parra Leonardo L Das Utpal U Caillol Ghislaine G Han Xuemei X Yates John R JR Ellisman Mark H MH Leterrier Christophe C Roy Subhojit S

Neuron 20210901 18

In non-neuronal cells, clathrin has established roles in endocytosis, with clathrin cages enclosing plasma membrane infoldings, followed by rapid disassembly and reuse of monomers. However, in neurons, clathrin is conveyed in slow axonal transport over days to weeks, and the underlying transport/targeting mechanisms, mobile cargo structures, and even its precise presynaptic localization and physiologic role are unclear. Combining live imaging, photobleaching/conversion, mass spectrometry, electr ...[more]

PMID: 34534453

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Phosphorylation of CENP-A on serine 7 does not control centromere function

Project description:CENP-A is the histone H3 variant necessary to specify the location of all eukaryoticcentromeres via its CENP-A targeting domain and either one of its terminal regions. In humans, several post-translational modifications occur on CENP-A, but their role in centromere function remains controversial. One of these modifications of CENP-A, phosphorylation on serine 7,has been proposed to control centromere assembly and function. Here, using gene targeting at both endogenous CENP-A alleles and gene replacement in human cells, we demonstrate that a CENP-A variant that cannot be phosphorylated at serine 7 maintains correct CENP-C recruitment, faithful chromosome segregation and long-term cell viability. Thus, we conclude that phosphorylation of CENP-A on serine 7 is dispensable to maintain correct centromere dynamics and function.

2019-01-28 | PXD012163 | Pride

The histone methyltransferase SETD2 couples transcription and splicing by engaging pre-mRNA processing factors through its SHI domain

Project description:The domains of SETD2, a known histone methyltransferase were investigated for specific interaction partners and function using a number of biochemical assays and affinity purification mass spectrometry. The C-terminal domain, named SETD2C, was identified to interact with hnRNP-L through a previously uncharacterized domain. These findings demonstrate the crosstalk between the transcription and splicing machinery.

2021-02-01 | PXD019376 | Pride

The histone methyltransferase SETD2 couples transcription and splicing by engaging pre-mRNA processing factors through its SHI domain

2021-02-01 | PXD022946 | Pride

The histone methyltransferase SETD2 couples transcription and splicing by engaging pre-mRNA processing factors through its SHI domain

2021-02-01 | PXD019538 | Pride

The stoichiometry of the outer kinetochore responds to microtubule-proximal regulation

Project description:The authors of this manuscript suggest the stoichiometry of outer submodules of the budding yeast kinetochore is strongly influenced by factors at the kinetochore-microtubule interface, including Fin1, Dam1, and microtubule tracking. Outer kinetochore stoichiometry is remarkably plastic and responsive to microtubule-proximal regulation.

2020-01-16 | PXD011384 | Pride

Expression data from murine wildtype and Sh3gl1-/- B cells

Project description:We show that antigen internalization depends both on constitutive, clathrin-mediated endocytosis and on antigen-induced, clathrin-independent endocytosis mediated by endophilin A2. Although endophilin A2-mediated endocytosis is dispensable for antigen presentation, it is selectively required for metabolic support of B cell proliferation, in part through regulation of iron uptake. Consequently, endophilin A2 deficient mice show defects in GC B cell responses and production of high-affinity IgG. The requirement for endophilin A2 highlights a unique importance of clathrin-independent intracellular trafficking in GC B cell clonal expansion and antibody responses

2021-07-19 | GSE172295 | GEO

Identification and characterization of proteins that form the inner core Ixodes scapularis tick attachment cement layer.

Project description:Ixodes scapularis and other hard ticks are long-term blood feeders. This feeding behavior is facilitated by a tick secreted bio adhesive (tick cement) that attaches tick mouthparts to skin tissue and prevents the host from dislodging the tick from its feeding site. Understanding tick cement formation is highly sought after as its disruption will prevent tick feeding. This study describes proteins that form the inner core layer of I. scapularis tick cement as disrupting these will stop formation of the outer cortical layer. As the inner core cement layer completes forming by 24 h of attachment, we used laser capture to isolate cement from cryosections of 6 h and 24 h tick attachment sites and to distinguish between early and late inner core cement proteins. LC-MS/MS analysis identified 138 tick cement proteins (TCPs) of which 37 and 35 were unique in cement of 6 and 24 h respectively, and 66 shared proteins. The 138 TCPs are classified in 14 functional categories: cuticular protein (16%), tick specific proteins of unknown function, cytoskeletal proteins, and enzymes (at 13% each), enzymes (10%), antioxidant, glycine rich, scaffolding, heat shock, histone, histamine binding, proteases and protease inhibitors, and miscellaneous (at 3-6% each). Gene ontology analysis confirm that TCPs are enriched for bio adhesive properties. Our data offer insights into yet unknown tick cement bonding patterns and set the foundation for understanding the molecular basis of I. scapularis tick cement formation.

2023-03-11 | PXD038685 | Pride

A human genome-wide screen for regulators of clathrin-coated vesicle formation

Project description:Clathrin-mediated endocytosis is essential for a wide range of cellular functions. We used a multi- step siRNA-based screening strategy to identify novel regulators of the first step of clathrin- mediated endocytosis, formation of clathrin-coated vesicles (CCVs) at the plasma membrane. A primary genome-wide screen identified 334 hits that caused accumulation of CCV cargo on the cell surface. A secondary screen identified 92 hits that inhibited cargo uptake and/or altered the morphology of clathrin-coated structures. The hits include components of four functional complexes: coat proteins, V-ATPase subunits, spliceosome-associated proteins, and acetyltransferase subunits. Electron microscopy revealed that V-ATPase depletion caused the cell to form aberrant non-constricted clathrin-coated structures at the plasma membrane. The V- ATPase knockdown phenotype was rescued by addition of exogenous cholesterol, indicating that the knockdown blocks clathrin-mediated endocytosis by preventing cholesterol from recycling from endosomes back to the plasma membrane. The microarray analysis was performed to test whether the siRNA targets are expressed in the cell lines used in the screen. For the microarray analysis of gene expression, the two cell lines used in the study were analyzed in duplicate: HeLa-YXXÎ¦ and HeLa-FXNPXY (Hela-M cells expressing a CD8-YXXÎ¦ and CD8-FXNPXY constructs respectively). YXXÎ¦ and FXNPXY are motifs for clathrin-mediated endocytosis.

2012-12-01 | E-GEOD-39954 | biostudies-arrayexpress

A human genome-wide screen for regulators of clathrin-coated vesicle formation

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Tick host range adaptation: changes in protein profiles in Ixodes scapularis and Amblyomma americanum saliva during stimulation to feed on different hosts

Project description:Understanding the molecular basis of how the tick adapts to feed on different animal hosts is central to understanding tick and tick-borne disease (TBD) epidemiology. Tick adaptation to feed on vertebrate hosts is regulated by tick secretion of multiple tick saliva proteins (TSPs) and other molecules that regulate tick feeding. This study was initiated to determine if ticks such as Ixodes scapularis and Amblyomma americanum that are adapted to feed on multiple hosts utilized the same sets of proteins to accomplish feeding on all hosts. Our data suggest that ticks of the same species differentially express proteins when feeding on diffent hosts. SDS-PAGE and silver staining analysis revealed unique protein eletrophoretic profile in saliva of Ixodes scapularis and Amblyomma americanum that were stimulated to start feeding on different hosts: rabbits, humans, and dogs. LC-MS/MS sequencing and pairwise analysis of proteins in saliva of I. scapularis and A. americanum ticks that were non-stimulated and those that were stimulated to feed on rabbits, dogs, or humans identified TSPs that were unique to each treatment and those that were common. Overal, we identified a total of 276 and 340 non-redundant I. scapularis and A. americanum TSPs, which we have classified into 28 functional classes that include secreted conserved proteins (unknown functions), proteinase inhibitors, lipocalins, extracellular matrix/cell adhesion, heme/iron metabolism, signal transduction and immunity-related proteins being the most predominant in saliva of unfed ticks. With exception of Rhipicephalus microplus, anti-tick vaccine research relies on feeding lab animals. Data here suggest that lab animal data could result in prioritizing irrelevant targets as some tick genes are unique to ticks fed on lab animals. This study provides the platform that could be utilized to identify relevant target anti-tick vaccine antigens, and will facilitate early stage tick feeding research.

2022-02-28 | PXD007712 | Pride

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