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Article ; Online: Isolation of Synaptic Vesicles from Mammalian Brain.

Ganzella, Marcelo / Ninov, Momchil / Riedel, Dietmar / Jahn, Reinhard

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

2022 Volume 2417, Page(s) 131–145

Abstract: Synaptic vesicles (SVs) store neurotransmitters and undergo a fine-tuned regulatory and dynamic cycle of exo- and endocytosis, which is essential for neurotransmission at chemical synapses. The development of protocols for isolating SVs from biological ... ...

Abstract	Synaptic vesicles (SVs) store neurotransmitters and undergo a fine-tuned regulatory and dynamic cycle of exo- and endocytosis, which is essential for neurotransmission at chemical synapses. The development of protocols for isolating SVs from biological extracts was a fundamental accomplishment since it allowed for characterizing the molecular properties of SVs using biochemical methods. In this chapter, we describe a modified procedure for isolating SVs from a few g of rodent brain and that can be completed within ~12 h. The protocol involves the preparation of isolated nerve terminals from which SVs are released by osmotic shock and then enriched via various centrifugation steps, followed by size exclusion chromatography as final purification step. The final vesicle fraction is 22-fold enriched in SVs over the starting material, and the final yield of SVs obtained using this protocol is approximately 20 μg of protein per gram of mouse brain. The degree of contamination by other organelles and particles monitored by morphology and immunolabeling compares well with that of the classical protocols.
MeSH term(s)	Animals ; Brain/metabolism ; Mammals ; Mice ; Neurotransmitter Agents/metabolism ; Synapses/metabolism ; Synaptic Transmission ; Synaptic Vesicles/metabolism
Chemical Substances	Neurotransmitter Agents
Language	English
Publishing date	2022-01-31
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1916-2_11
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Article ; Online: Structures of transcription preinitiation complex engaged with the +1 nucleosome.

Wang, Haibo / Schilbach, Sandra / Ninov, Momchil / Urlaub, Henning / Cramer, Patrick

Nature structural & molecular biology

2022 Volume 30, Issue 2, Page(s) 226–232

Abstract: The preinitiation complex (PIC) assembles on promoters of protein-coding genes to position RNA polymerase II (Pol II) for transcription initiation. Previous structural studies revealed the PIC on different promoters, but did not address how the PIC ... ...

Abstract	The preinitiation complex (PIC) assembles on promoters of protein-coding genes to position RNA polymerase II (Pol II) for transcription initiation. Previous structural studies revealed the PIC on different promoters, but did not address how the PIC assembles within chromatin. In the yeast Saccharomyces cerevisiae, PIC assembly occurs adjacent to the +1 nucleosome that is located downstream of the core promoter. Here we present cryo-EM structures of the yeast PIC bound to promoter DNA and the +1 nucleosome located at three different positions. The general transcription factor TFIIH engages with the incoming downstream nucleosome and its translocase subunit Ssl2 (XPB in human TFIIH) drives the rotation of the +1 nucleosome leading to partial detachment of nucleosomal DNA and intimate interactions between TFIIH and the nucleosome. The structures provide insights into how transcription initiation can be influenced by the +1 nucleosome and may explain why the transcription start site is often located roughly 60 base pairs upstream of the dyad of the +1 nucleosome in yeast.
MeSH term(s)	Humans ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Nucleosomes/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; RNA Polymerase II/metabolism ; DNA/chemistry ; Transcription, Genetic ; DNA Helicases/metabolism ; Transcription Factor TFIIH/metabolism
Chemical Substances	Nucleosomes ; Saccharomyces cerevisiae Proteins ; RNA Polymerase II (EC 2.7.7.-) ; DNA (9007-49-2) ; SSL2 protein, S cerevisiae ; DNA Helicases (EC 3.6.4.-) ; Transcription Factor TFIIH (148710-81-0)
Language	English
Publishing date	2022-11-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/s41594-022-00865-w
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Zs.A 4101: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: A multiplexed parallel reaction monitoring assay to monitor bovine pregnancy-associated glycoproteins throughout pregnancy and after gestation.

Krebs, Tony / Kilic, Isabel / Neuenroth, Lisa / Wasselin, Thierry / Ninov, Momchil / Tetens, Jens / Lenz, Christof

PloS one

2022 Volume 17, Issue 9, Page(s) e0271057

Abstract: Bovine pregnancy-associated glycoproteins (boPAGs) are extensively glycosylated secretory proteins of trophoblast cells. Roughly 20 different boPAG members are known but their distribution patterns and degree of glycosylation during pregnancy are not ... ...

Abstract	Bovine pregnancy-associated glycoproteins (boPAGs) are extensively glycosylated secretory proteins of trophoblast cells. Roughly 20 different boPAG members are known but their distribution patterns and degree of glycosylation during pregnancy are not well characterized. The objective of the present study was the development of a parallel reaction monitoring-based assay for the profiling of different boPAGs during pregnancy and after gestation. Furthermore, we investigated the effects of N-glycosylation on our analytical results. BoPAGs were purified from cotyledons of four different pregnancy stages. The assay detects 25 proteotypic peptides from 18 boPAGs in a single run. The highest abundances were found for boPAG 1 in both, glycosylated and deglycosylated samples. Strongest effects of glycosylation were detected during mid and late pregnancy as well as in afterbirth samples. Furthermore, we identified different boPAG-clusters based on the observed relative protein abundances between glycosylated and deglycosylated samples. A linkage between the impact of glycosylation and potential N-glycosylation sites or phylogenetic relation was not detected. In conclusion, the newly developed parallel reaction monitoring-based assay enables for the first time a comprehensive semi-quantitative profiling of 18 different boPAGs during pregnancy and post-partum on protein level, thereby investigating the influence of glycosylation. The results of this study provide new and important starting points to address further research on boPAGs to better understand their physiological role during pregnancy and for the development of new pregnancy detection tests.
MeSH term(s)	Animals ; Cattle ; Female ; Glycoproteins/metabolism ; Glycosylation ; Phylogeny ; Placenta/metabolism ; Pregnancy ; Trophoblasts/metabolism
Chemical Substances	Glycoproteins
Language	English
Publishing date	2022-09-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0271057
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Article ; Online: Hsp multichaperone complex buffers pathologically modified Tau.

Moll, Antonia / Ramirez, Lisa Marie / Ninov, Momchil / Schwarz, Juliane / Urlaub, Henning / Zweckstetter, Markus

Nature communications

2022 Volume 13, Issue 1, Page(s) 3668

Abstract: Alzheimer's disease is a neurodegenerative disorder in which misfolding and aggregation of pathologically modified Tau is critical for neuronal dysfunction and degeneration. The two central chaperones Hsp70 and Hsp90 coordinate protein homeostasis, but ... ...

Abstract	Alzheimer's disease is a neurodegenerative disorder in which misfolding and aggregation of pathologically modified Tau is critical for neuronal dysfunction and degeneration. The two central chaperones Hsp70 and Hsp90 coordinate protein homeostasis, but the nature of the interaction of Tau with the Hsp70/Hsp90 machinery has remained enigmatic. Here we show that Tau is a high-affinity substrate of the human Hsp70/Hsp90 machinery. Complex formation involves extensive intermolecular contacts, blocks Tau aggregation and depends on Tau's aggregation-prone repeat region. The Hsp90 co-chaperone p23 directly binds Tau and stabilizes the multichaperone/substrate complex, whereas the E3 ubiquitin-protein ligase CHIP efficiently disassembles the machinery targeting Tau to proteasomal degradation. Because phosphorylated Tau binds the Hsp70/Hsp90 machinery but is not recognized by Hsp90 alone, the data establish the Hsp70/Hsp90 multichaperone complex as a critical regulator of Tau in neurodegenerative diseases.
MeSH term(s)	Alzheimer Disease/metabolism ; HSP70 Heat-Shock Proteins/metabolism ; HSP90 Heat-Shock Proteins/metabolism ; Humans ; Molecular Chaperones/metabolism ; Ubiquitin-Protein Ligases/metabolism ; tau Proteins/metabolism
Chemical Substances	HSP70 Heat-Shock Proteins ; HSP90 Heat-Shock Proteins ; Molecular Chaperones ; tau Proteins ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
Language	English
Publishing date	2022-06-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-31396-z
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Article ; Online: Control of intracellular pH and bicarbonate by CO

Grahn, Elena / Kaufmann, Svenja V / Askarova, Malika / Ninov, Momchil / Welp, Luisa M / Berger, Thomas K / Urlaub, Henning / Kaupp, U Benjamin

Nature communications

2023 Volume 14, Issue 1, Page(s) 5395

Abstract: The reaction of ... ...

Abstract	The reaction of CO
MeSH term(s)	Humans ; Male ; Bicarbonates ; Carbon Dioxide ; Semen ; Sperm Motility ; Spermatozoa ; Hydrogen-Ion Concentration
Chemical Substances	Bicarbonates ; Carbon Dioxide (142M471B3J)
Language	English
Publishing date	2023-09-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-40855-0
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Article ; Online: Proteomic Analysis Reveals the Composition of Glutamatergic Organelles of Auditory Inner Hair Cells.

Cepeda, Andreia P / Ninov, Momchil / Neef, Jakob / Parfentev, Iwan / Kusch, Kathrin / Reisinger, Ellen / Jahn, Reinhard / Moser, Tobias / Urlaub, Henning

Molecular & cellular proteomics : MCP

2023 Volume 23, Issue 2, Page(s) 100704

Abstract: In the ear, inner hair cells (IHCs) employ sophisticated glutamatergic ribbon synapses with afferent neurons to transmit auditory information to the brain. The presynaptic machinery responsible for neurotransmitter release in IHC synapses includes ... ...

Abstract	In the ear, inner hair cells (IHCs) employ sophisticated glutamatergic ribbon synapses with afferent neurons to transmit auditory information to the brain. The presynaptic machinery responsible for neurotransmitter release in IHC synapses includes proteins such as the multi-C
MeSH term(s)	Mice ; Animals ; Hair Cells, Auditory, Inner/metabolism ; Proteomics ; Synapses/metabolism ; Synaptic Vesicles/metabolism ; Qa-SNARE Proteins/metabolism ; Membrane Proteins/metabolism
Chemical Substances	Qa-SNARE Proteins ; otoferlin protein, mouse ; Membrane Proteins
Language	English
Publishing date	2023-12-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1016/j.mcpro.2023.100704
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Zs.A 5599: Show issues

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Article ; Online: ATG9 resides on a unique population of small vesicles in presynaptic nerve terminals.

Binotti, Beyenech / Ninov, Momchil / Cepeda, Andreia P / Ganzella, Marcelo / Matti, Ulf / Riedel, Dietmar / Urlaub, Henning / Sambandan, Sivakumar / Jahn, Reinhard

Autophagy

2023 Volume 20, Issue 4, Page(s) 883–901

Abstract: In neurons, autophagosome biogenesis occurs mainly in distal axons, followed by maturation during retrograde transport. Autophagosomal growth depends on the supply of membrane lipids which requires small vesicles containing ATG9, a lipid scramblase ... ...

Abstract	In neurons, autophagosome biogenesis occurs mainly in distal axons, followed by maturation during retrograde transport. Autophagosomal growth depends on the supply of membrane lipids which requires small vesicles containing ATG9, a lipid scramblase essential for macroautophagy/autophagy. Here, we show that ATG9-containing vesicles are enriched in synapses and resemble synaptic vesicles in size and density. The proteome of ATG9-containing vesicles immuno-isolated from nerve terminals showed conspicuously low levels of trafficking proteins except of the AP2-complex and some enzymes involved in endosomal phosphatidylinositol metabolism. Super resolution microscopy of nerve terminals and isolated vesicles revealed that ATG9-containing vesicles represent a distinct vesicle population with limited overlap not only with synaptic vesicles but also other membranes of the secretory pathway, uncovering a surprising heterogeneity in their membrane composition. Our results are compatible with the view that ATG9-containing vesicles function as lipid shuttles that scavenge membrane lipids from various intracellular membranes to support autophagosome biogenesis.
MeSH term(s)	Animals ; Autophagy-Related Proteins/metabolism ; Presynaptic Terminals/metabolism ; Synaptic Vesicles/metabolism ; Synaptic Vesicles/ultrastructure ; Membrane Proteins/metabolism ; Mice ; Autophagy/physiology ; Endosomes/metabolism ; Vesicular Transport Proteins
Chemical Substances	Autophagy-Related Proteins ; Membrane Proteins ; Atg9A protein, mouse ; Vesicular Transport Proteins
Language	English
Publishing date	2023-11-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2454135-7
ISSN	1554-8635 ; 1554-8627
ISSN (online)	1554-8635
ISSN	1554-8627
DOI	10.1080/15548627.2023.2274204
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Article: Allosteric transcription stimulation by RNA polymerase II super elongation complex

Chen, Ying / Vos, Seychelle M. / Dienemann, Christian / Ninov, Momchil / Urlaub, Henning / Cramer, Patrick

Molecular cell. 2021 Aug. 19, v. 81, no. 16

2021

Abstract: The super elongation complex (SEC) contains the positive transcription elongation factor b (P-TEFb) and the subcomplex ELL2-EAF1, which stimulates RNA polymerase II (RNA Pol II) elongation. Here, we report the cryoelectron microscopy (cryo-EM) structure ... ...

Abstract	The super elongation complex (SEC) contains the positive transcription elongation factor b (P-TEFb) and the subcomplex ELL2-EAF1, which stimulates RNA polymerase II (RNA Pol II) elongation. Here, we report the cryoelectron microscopy (cryo-EM) structure of ELL2-EAF1 bound to a RNA Pol II elongation complex at 2.8 Å resolution. The ELL2-EAF1 dimerization module directly binds the RNA Pol II lobe domain, explaining how SEC delivers P-TEFb to RNA Pol II. The same site on the lobe also binds the initiation factor TFIIF, consistent with SEC binding only after the transition from transcription initiation to elongation. Structure-guided functional analysis shows that the stimulation of RNA elongation requires the dimerization module and the ELL2 linker that tethers the module to the RNA Pol II protrusion. Our results show that SEC stimulates elongation allosterically and indicate that this stimulation involves stabilization of a closed conformation of the RNA Pol II active center cleft.
Keywords	DNA-directed RNA polymerase ; RNA ; cryo-electron microscopy ; dimerization ; transcription initiation ; transcriptional elongation factors
Language	English
Dates of publication	2021-0819
Size	p. 3386-3399.e10.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2021.06.019
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Allosteric transcription stimulation by RNA polymerase II super elongation complex.

Chen, Ying / Vos, Seychelle M / Dienemann, Christian / Ninov, Momchil / Urlaub, Henning / Cramer, Patrick

Molecular cell

2021 Volume 81, Issue 16, Page(s) 3386–3399.e10

Abstract	The super elongation complex (SEC) contains the positive transcription elongation factor b (P-TEFb) and the subcomplex ELL2-EAF1, which stimulates RNA polymerase II (RNA Pol II) elongation. Here, we report the cryoelectron microscopy (cryo-EM) structure of ELL2-EAF1 bound to a RNA Pol II elongation complex at 2.8 Å resolution. The ELL2-EAF1 dimerization module directly binds the RNA Pol II lobe domain, explaining how SEC delivers P-TEFb to RNA Pol II. The same site on the lobe also binds the initiation factor TFIIF, consistent with SEC binding only after the transition from transcription initiation to elongation. Structure-guided functional analysis shows that the stimulation of RNA elongation requires the dimerization module and the ELL2 linker that tethers the module to the RNA Pol II protrusion. Our results show that SEC stimulates elongation allosterically and indicate that this stimulation involves stabilization of a closed conformation of the RNA Pol II active center cleft.
MeSH term(s)	Allosteric Regulation/genetics ; Cell Nucleus/genetics ; Cell Nucleus/ultrastructure ; Cryoelectron Microscopy ; Humans ; Molecular Structure ; Multiprotein Complexes/genetics ; Multiprotein Complexes/ultrastructure ; Positive Transcriptional Elongation Factor B/genetics ; Positive Transcriptional Elongation Factor B/ultrastructure ; Protein Binding/genetics ; Protein Conformation ; RNA Polymerase II/genetics ; RNA Polymerase II/ultrastructure ; Transcription Elongation, Genetic ; Transcription Factors/genetics ; Transcription Factors/ultrastructure ; Transcription, Genetic/genetics ; Transcriptional Elongation Factors/genetics ; Transcriptional Elongation Factors/ultrastructure
Chemical Substances	EAF1 protein, human ; ELL2 protein, human ; Multiprotein Complexes ; Transcription Factors ; Transcriptional Elongation Factors ; Positive Transcriptional Elongation Factor B (EC 2.7.11.-) ; RNA Polymerase II (EC 2.7.7.-)
Language	English
Publishing date	2021-07-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2021.06.019
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Zs.A 5055: Show issues

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Article ; Online: The Coding and Small Non-coding Hippocampal Synaptic RNAome.

Epple, Robert / Krüger, Dennis / Berulava, Tea / Brehm, Gerrit / Ninov, Momchil / Islam, Rezaul / Köster, Sarah / Fischer, Andre

Molecular neurobiology

2021 Volume 58, Issue 6, Page(s) 2940–2953

Abstract: Neurons are highly compartmentalized cells that depend on local protein synthesis. Messenger RNAs (mRNAs) have thus been detected in neuronal dendrites, and more recently in the pre- and postsynaptic compartments as well. Other RNA species such as ... ...

Abstract	Neurons are highly compartmentalized cells that depend on local protein synthesis. Messenger RNAs (mRNAs) have thus been detected in neuronal dendrites, and more recently in the pre- and postsynaptic compartments as well. Other RNA species such as microRNAs have also been described at synapses where they are believed to control mRNA availability for local translation. A combined dataset analyzing the synaptic coding and non-coding RNAome via next-generation sequencing approaches is, however, still lacking. Here, we isolate synaptosomes from the hippocampus of young wild-type mice and provide the coding and non-coding synaptic RNAome. These data are complemented by a novel approach for analyzing the synaptic RNAome from primary hippocampal neurons grown in microfluidic chambers. Our data show that synaptic microRNAs control almost the entire synaptic mRNAome, and we identified several hub microRNAs. By combining the in vivo synaptosomal data with our novel microfluidic chamber system, our findings also support the hypothesis that part of the synaptic microRNAome may be supplied to neurons via astrocytes. Moreover, the microfluidic system is suitable for studying the dynamics of the synaptic RNAome in response to stimulation. In conclusion, our data provide a valuable resource and point to several important targets for further research.
MeSH term(s)	Animals ; Hippocampus/metabolism ; Male ; Mice, Inbred C57BL ; MicroRNAs/genetics ; Microfluidics ; Neurons/metabolism ; RNA, Messenger/genetics ; RNA, Untranslated/genetics ; RNA, Untranslated/metabolism ; Synapses/metabolism ; Synaptosomes/metabolism ; Mice
Chemical Substances	MicroRNAs ; RNA, Messenger ; RNA, Untranslated
Language	English
Publishing date	2021-02-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	645020-9
ISSN	1559-1182 ; 0893-7648
ISSN (online)	1559-1182
ISSN	0893-7648
DOI	10.1007/s12035-021-02296-y
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