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Article ; Online: Identification and characterization of sugar-regulated promoters in Chaetomium thermophilum.

Reislöhner, Sven / Schermann, Geza / Kilian, Max / Santamaría-Muñoz, Daniela / Zimmerli, Christian / Kellner, Nikola / Baßler, Jochen / Brunner, Michael / Hurt, Ed

BMC biotechnology

2023 Volume 23, Issue 1, Page(s) 19

Abstract: The thermophilic fungus Chaetomium thermophilum has been used extensively for biochemical and high-resolution structural studies of protein complexes. However, subsequent functional analyses of these assemblies have been hindered owing to the lack of ... ...

Abstract	The thermophilic fungus Chaetomium thermophilum has been used extensively for biochemical and high-resolution structural studies of protein complexes. However, subsequent functional analyses of these assemblies have been hindered owing to the lack of genetic tools compatible with this thermophile, which are typically suited to other mesophilic eukaryotic model organisms, in particular the yeast Saccharomyces cerevisiae. Hence, we aimed to find genes from C. thermophilum that are expressed under the control of different sugars and examine their associated 5' untranslated regions as promoters responsible for sugar-regulated gene expression. To identify sugar-regulated promoters in C. thermophilum, we performed comparative xylose- versus glucose-dependent gene expression studies, which uncovered a number of enzymes with induced expression in the presence of xylose but repressed expression in glucose-supplemented media. Subsequently, we cloned the promoters of the two most stringently regulated genes, the xylosidase-like gene (XYL) and xylitol dehydrogenase (XDH), obtained from this genome-wide analysis in front of a thermostable yellow fluorescent protein (YFP) reporter. With this, we demonstrated xylose-dependent YFP expression by both Western blotting and live-cell imaging fluorescence microscopy. Prompted by these results, we expressed the C. thermophilum orthologue of a well-characterized dominant-negative ribosome assembly factor mutant, under the control of the XDH promoter, which allowed us to induce a nuclear export defect on the pre-60S subunit when C. thermophilum cells were grown in xylose- but not glucose-containing medium. Altogether, our study identified xylose-regulatable promoters in C. thermophilum, which might facilitate functional studies of genes of interest in this thermophilic eukaryotic model organism.
MeSH term(s)	Sugars/metabolism ; Xylose/metabolism ; Chaetomium/genetics ; Chaetomium/metabolism ; Saccharomyces cerevisiae/genetics ; Glucose/metabolism
Chemical Substances	Sugars ; Xylose (A1TA934AKO) ; Glucose (IY9XDZ35W2)
Language	English
Publishing date	2023-07-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2052746-9
ISSN	1472-6750 ; 1472-6750
ISSN (online)	1472-6750
ISSN	1472-6750
DOI	10.1186/s12896-023-00791-9
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Book ; Online ; Thesis: In cellulo architecture of the nuclear pore complex

Zimmerli, Christian Eugen [Verfasser] / Hurt, Ed [Akademischer Betreuer]

2020

Author's details	Christian Eugen Zimmerli ; Betreuer: Ed Hurt
Keywords	Biowissenschaften, Biologie ; Life Science, Biology
Subject code	sg570
Language	English
Publisher	Universitätsbibliothek Heidelberg
Publishing place	Heidelberg
Document type	Book ; Online ; Thesis
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Article ; Online: Insights into chemoselectivity principles in metal oxide affinity chromatography using tailored nanocast metal oxide microspheres and mass spectrometry-based phosphoproteomics.

Leitner, Alexander / Sakeye, Motolani / Zimmerli, Christian Eugen / Smått, Jan-Henrik

The Analyst

2017 Volume 142, Issue 11, Page(s) 1993–2003

Abstract: The ability to comprehensively characterize biological samples, including tissues and body fluids, opens up new possibilities to diagnose and treat diseases and to better understand fundamental biological processes. For this purpose, suitable ... ...

Abstract	The ability to comprehensively characterize biological samples, including tissues and body fluids, opens up new possibilities to diagnose and treat diseases and to better understand fundamental biological processes. For this purpose, suitable experimental workflows need to be designed. In this context, materials with particular chemoselective properties are used for the enrichment of certain classes of (bio)molecules. Metal oxides such as titanium dioxide have become the materials of choice for the large-scale study of protein phosphorylation in phosphoproteomics. Despite their widespread use, the main factors influencing their performance (for example, affinity and specificity) are not completely understood. This understanding is, however, crucial to develop improved materials and methods. Here, we used the nanocasting method to prepare microspheres of seven metal oxides with comparable textural properties, allowing an objective comparison of the materials and their binding properties. We evaluated these materials with samples of different complexity, ranging from synthetic peptides to whole cell lysates, using liquid chromatography-tandem mass spectrometry as a readout. A set of more than 7000 identified phosphopeptides allowed us to study differences between the metal oxide sorbents in detail. Importantly, the performance of the affinity materials was found to be mainly correlated with the oxides' isoelectric points (IEPs), with the materials that enriched the highest number of phosphopeptides having an IEP of around 6. This included the widely used TiO
Language	English
Publishing date	2017-05-30
Publishing country	England
Document type	Journal Article
ZDB-ID	210747-8
ISSN	1364-5528 ; 0003-2654
ISSN (online)	1364-5528
ISSN	0003-2654
DOI	10.1039/c7an00570a
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Article ; Online: Convolutional networks for supervised mining of molecular patterns within cellular context.

de Teresa-Trueba, Irene / Goetz, Sara K / Mattausch, Alexander / Stojanovska, Frosina / Zimmerli, Christian E / Toro-Nahuelpan, Mauricio / Cheng, Dorothy W C / Tollervey, Fergus / Pape, Constantin / Beck, Martin / Diz-Muñoz, Alba / Kreshuk, Anna / Mahamid, Julia / Zaugg, Judith B

Nature methods

2023 Volume 20, Issue 2, Page(s) 284–294

Abstract: Cryo-electron tomograms capture a wealth of structural information on the molecular constituents of cells and tissues. We present DeePiCt (deep picker in context), an open-source deep-learning framework for supervised segmentation and macromolecular ... ...

Abstract	Cryo-electron tomograms capture a wealth of structural information on the molecular constituents of cells and tissues. We present DeePiCt (deep picker in context), an open-source deep-learning framework for supervised segmentation and macromolecular complex localization in cryo-electron tomography. To train and benchmark DeePiCt on experimental data, we comprehensively annotated 20 tomograms of Schizosaccharomyces pombe for ribosomes, fatty acid synthases, membranes, nuclear pore complexes, organelles, and cytosol. By comparing DeePiCt to state-of-the-art approaches on this dataset, we show its unique ability to identify low-abundance and low-density complexes. We use DeePiCt to study compositionally distinct subpopulations of cellular ribosomes, with emphasis on their contextual association with mitochondria and the endoplasmic reticulum. Finally, applying pre-trained networks to a HeLa cell tomogram demonstrates that DeePiCt achieves high-quality predictions in unseen datasets from different biological species in a matter of minutes. The comprehensively annotated experimental data and pre-trained networks are provided for immediate use by the community.
MeSH term(s)	Humans ; HeLa Cells ; Mitochondria ; Ribosomes ; Electron Microscope Tomography/methods ; Endoplasmic Reticulum ; Image Processing, Computer-Assisted/methods
Language	English
Publishing date	2023-01-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2169522-2
ISSN	1548-7105 ; 1548-7091
ISSN (online)	1548-7105
ISSN	1548-7091
DOI	10.1038/s41592-022-01746-2
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Article ; Online: Dual roles of mTORC1-dependent activation of the ubiquitin-proteasome system in muscle proteostasis.

Kaiser, Marco S / Milan, Giulia / Ham, Daniel J / Lin, Shuo / Oliveri, Filippo / Chojnowska, Kathrin / Tintignac, Lionel A / Mittal, Nitish / Zimmerli, Christian E / Glass, David J / Zavolan, Mihaela / Rüegg, Markus A

Communications biology

2022 Volume 5, Issue 1, Page(s) 1141

Abstract: Muscle size is controlled by the PI3K-PKB/Akt-mTORC1-FoxO pathway, which integrates signals from growth factors, energy and amino acids to activate protein synthesis and inhibit protein breakdown. While mTORC1 activity is necessary for PKB/Akt-induced ... ...

Abstract	Muscle size is controlled by the PI3K-PKB/Akt-mTORC1-FoxO pathway, which integrates signals from growth factors, energy and amino acids to activate protein synthesis and inhibit protein breakdown. While mTORC1 activity is necessary for PKB/Akt-induced muscle hypertrophy, its constant activation alone induces muscle atrophy. Here we show that this paradox is based on mTORC1 activity promoting protein breakdown through the ubiquitin-proteasome system (UPS) by simultaneously inducing ubiquitin E3 ligase expression via feedback inhibition of PKB/Akt and proteasome biogenesis via Nuclear Factor Erythroid 2-Like 1 (Nrf1). Muscle growth was restored by reactivation of PKB/Akt, but not by Nrf1 knockdown, implicating ubiquitination as the limiting step. However, both PKB/Akt activation and proteasome depletion by Nrf1 knockdown led to an immediate disruption of proteome integrity with rapid accumulation of damaged material. These data highlight the physiological importance of mTORC1-mediated PKB/Akt inhibition and point to juxtaposed roles of the UPS in atrophy and proteome integrity.
MeSH term(s)	Mechanistic Target of Rapamycin Complex 1/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Ubiquitin/metabolism ; Proto-Oncogene Proteins c-akt/metabolism ; Proteostasis ; Proteome/metabolism ; Muscle, Skeletal/metabolism
Chemical Substances	Mechanistic Target of Rapamycin Complex 1 (EC 2.7.11.1) ; Proteasome Endopeptidase Complex (EC 3.4.25.1) ; Ubiquitin ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; Proteome
Language	English
Publishing date	2022-10-27
Publishing country	England
Document type	Journal Article
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-022-04097-y
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Article ; Online: AI-based structure prediction empowers integrative structural analysis of human nuclear pores.

Mosalaganti, Shyamal / Obarska-Kosinska, Agnieszka / Siggel, Marc / Taniguchi, Reiya / Turoňová, Beata / Zimmerli, Christian E / Buczak, Katarzyna / Schmidt, Florian H / Margiotta, Erica / Mackmull, Marie-Therese / Hagen, Wim J H / Hummer, Gerhard / Kosinski, Jan / Beck, Martin

Science (New York, N.Y.)

2022 Volume 376, Issue 6598, Page(s) eabm9506

Abstract: INTRODUCTION The eukaryotic nucleus pro-tects the genome and is enclosed by the two membranes of the nuclear envelope. Nuclear pore complexes (NPCs) perforate the nuclear envelope to facilitate nucleocytoplasmic transport. With a molecular weight of ∼120 ...

Abstract	INTRODUCTION The eukaryotic nucleus pro-tects the genome and is enclosed by the two membranes of the nuclear envelope. Nuclear pore complexes (NPCs) perforate the nuclear envelope to facilitate nucleocytoplasmic transport. With a molecular weight of ∼120 MDa, the human NPC is one of the larg-est protein complexes. Its ~1000 proteins are taken in multiple copies from a set of about 30 distinct nucleoporins (NUPs). They can be roughly categorized into two classes. Scaf-fold NUPs contain folded domains and form a cylindrical scaffold architecture around a central channel. Intrinsically disordered NUPs line the scaffold and extend into the central channel, where they interact with cargo complexes. The NPC architecture is highly dynamic. It responds to changes in nuclear envelope tension with conforma-tional breathing that manifests in dilation and constriction movements. Elucidating the scaffold architecture, ultimately at atomic resolution, will be important for gaining a more precise understanding of NPC function and dynamics but imposes a substantial chal-lenge for structural biologists. RATIONALE Considerable progress has been made toward this goal by a joint effort in the field. A synergistic combination of complementary approaches has turned out to be critical. In situ structural biology techniques were used to reveal the overall layout of the NPC scaffold that defines the spatial reference for molecular modeling. High-resolution structures of many NUPs were determined in vitro. Proteomic analysis and extensive biochemical work unraveled the interaction network of NUPs. Integra-tive modeling has been used to combine the different types of data, resulting in a rough outline of the NPC scaffold. Previous struc-tural models of the human NPC, however, were patchy and limited in accuracy owing to several challenges: (i) Many of the high-resolution structures of individual NUPs have been solved from distantly related species and, consequently, do not comprehensively cover their human counterparts. (ii) The scaf-fold is interconnected by a set of intrinsically disordered linker NUPs that are not straight-forwardly accessible to common structural biology techniques. (iii) The NPC scaffold intimately embraces the fused inner and outer nuclear membranes in a distinctive topol-ogy and cannot be studied in isolation. (iv) The conformational dynamics of scaffold NUPs limits the resolution achievable in structure determination. RESULTS In this study, we used artificial intelligence (AI)-based prediction to generate an exten-sive repertoire of structural models of human NUPs and their subcomplexes. The resulting models cover various domains and interfaces that so far remained structurally uncharac-terized. Benchmarking against previous and unpublished x-ray and cryo-electron micros-copy structures revealed unprecedented accu-racy. We obtained well-resolved cryo-electron tomographic maps of both the constricted and dilated conformational states of the hu-man NPC. Using integrative modeling, we fit-ted the structural models of individual NUPs into the cryo-electron microscopy maps. We explicitly included several linker NUPs and traced their trajectory through the NPC scaf-fold. We elucidated in great detail how mem-brane-associated and transmembrane NUPs are distributed across the fusion topology of both nuclear membranes. The resulting architectural model increases the structural coverage of the human NPC scaffold by about twofold. We extensively validated our model against both earlier and new experimental data. The completeness of our model has enabled microsecond-long coarse-grained molecular dynamics simulations of the NPC scaffold within an explicit membrane en-vironment and solvent. These simulations reveal that the NPC scaffold prevents the constriction of the otherwise stable double-membrane fusion pore to small diameters in the absence of membrane tension. CONCLUSION Our 70-MDa atomically re-solved model covers >90% of the human NPC scaffold. It captures conforma-tional changes that occur during dilation and constriction. It also reveals the precise anchoring sites for intrinsically disordered NUPs, the identification of which is a prerequisite for a complete and dy-namic model of the NPC. Our study exempli-fies how AI-based structure prediction may accelerate the elucidation of subcellular ar-chitecture at atomic resolution. [Figure: see text].
MeSH term(s)	Active Transport, Cell Nucleus ; Artificial Intelligence ; Cryoelectron Microscopy ; Humans ; Molecular Dynamics Simulation ; Nuclear Pore/chemistry ; Nuclear Pore Complex Proteins/chemistry ; Proteomics
Chemical Substances	Nuclear Pore Complex Proteins
Language	English
Publishing date	2022-06-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abm9506
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Article ; Online: Benchmarking tomographic acquisition schemes for high-resolution structural biology.

Turoňová, Beata / Hagen, Wim J H / Obr, Martin / Mosalaganti, Shyamal / Beugelink, J Wouter / Zimmerli, Christian E / Kräusslich, Hans-Georg / Beck, Martin

Nature communications

2020 Volume 11, Issue 1, Page(s) 876

Abstract: Cryo electron tomography with subsequent subtomogram averaging is a powerful technique to structurally analyze macromolecular complexes in their native context. Although close to atomic resolution in principle can be obtained, it is not clear how ... ...

Abstract	Cryo electron tomography with subsequent subtomogram averaging is a powerful technique to structurally analyze macromolecular complexes in their native context. Although close to atomic resolution in principle can be obtained, it is not clear how individual experimental parameters contribute to the attainable resolution. Here, we have used immature HIV-1 lattice as a benchmarking sample to optimize the attainable resolution for subtomogram averaging. We systematically tested various experimental parameters such as the order of projections, different angular increments and the use of the Volta phase plate. We find that although any of the prominently used acquisition schemes is sufficient to obtain subnanometer resolution, dose-symmetric acquisition provides considerably better outcome. We discuss our findings in order to provide guidance for data acquisition. Our data is publicly available and might be used to further develop processing routines.
MeSH term(s)	Benchmarking ; Cryoelectron Microscopy/methods ; Cryoelectron Microscopy/standards ; Databases, Factual ; Electron Microscope Tomography/methods ; Electron Microscope Tomography/standards ; HIV-1/chemistry ; HIV-1/ultrastructure ; Macromolecular Substances/chemistry ; Macromolecular Substances/ultrastructure ; Models, Molecular ; Molecular Biology/methods ; Molecular Biology/standards ; Virion/chemistry ; Virion/ultrastructure
Chemical Substances	Macromolecular Substances
Language	English
Publishing date	2020-02-13
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/s41467-020-14535-2
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Article ; Online: Nuclear pores dilate and constrict in cellulo.

Zimmerli, Christian E / Allegretti, Matteo / Rantos, Vasileios / Goetz, Sara K / Obarska-Kosinska, Agnieszka / Zagoriy, Ievgeniia / Halavatyi, Aliaksandr / Hummer, Gerhard / Mahamid, Julia / Kosinski, Jan / Beck, Martin

Science (New York, N.Y.)

2021 Volume 374, Issue 6573, Page(s) eabd9776

Abstract: In eukaryotic cells, nuclear pore complexes (NPCs) fuse the inner and outer nuclear membranes and mediate nucleocytoplasmic exchange. They are made of 30 different nucleoporins and form a cylindrical architecture around an aqueous central channel. This ... ...

Abstract	In eukaryotic cells, nuclear pore complexes (NPCs) fuse the inner and outer nuclear membranes and mediate nucleocytoplasmic exchange. They are made of 30 different nucleoporins and form a cylindrical architecture around an aqueous central channel. This architecture is highly dynamic in space and time. Variations in NPC diameter have been reported, but the physiological circumstances and the molecular details remain unknown. Here, we combined cryo–electron tomography with integrative structural modeling to capture a molecular movie of the respective large-scale conformational changes in cellulo. Although NPCs of exponentially growing cells adopted a dilated conformation, they reversibly constricted upon cellular energy depletion or conditions of hypertonic osmotic stress. Our data point to a model where the nuclear envelope membrane tension is linked to the conformation of the NPC.
MeSH term(s)	Active Transport, Cell Nucleus ; Biomechanical Phenomena ; Cryoelectron Microscopy ; Cytoplasm/metabolism ; Energy Metabolism ; Image Processing, Computer-Assisted ; Imaging, Three-Dimensional ; Models, Biological ; Nuclear Envelope/physiology ; Nuclear Envelope/ultrastructure ; Nuclear Pore/physiology ; Nuclear Pore/ultrastructure ; Nuclear Pore Complex Proteins/chemistry ; Osmotic Pressure ; Schizosaccharomyces/growth & development ; Schizosaccharomyces/ultrastructure ; Schizosaccharomyces pombe Proteins/chemistry ; Stress, Physiological
Chemical Substances	Nuclear Pore Complex Proteins ; Schizosaccharomyces pombe Proteins
Language	English
Publishing date	2021-12-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abd9776
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Article ; Online: Cone-shaped HIV-1 capsids are transported through intact nuclear pores.

Zila, Vojtech / Margiotta, Erica / Turoňová, Beata / Müller, Thorsten G / Zimmerli, Christian E / Mattei, Simone / Allegretti, Matteo / Börner, Kathleen / Rada, Jona / Müller, Barbara / Lusic, Marina / Kräusslich, Hans-Georg / Beck, Martin

Cell

2021 Volume 184, Issue 4, Page(s) 1032–1046.e18

Abstract: Human immunodeficiency virus (HIV-1) remains a major health threat. Viral capsid uncoating and nuclear import of the viral genome are critical for productive infection. The size of the HIV-1 capsid is generally believed to exceed the diameter of the ... ...

Abstract	Human immunodeficiency virus (HIV-1) remains a major health threat. Viral capsid uncoating and nuclear import of the viral genome are critical for productive infection. The size of the HIV-1 capsid is generally believed to exceed the diameter of the nuclear pore complex (NPC), indicating that capsid uncoating has to occur prior to nuclear import. Here, we combined correlative light and electron microscopy with subtomogram averaging to capture the structural status of reverse transcription-competent HIV-1 complexes in infected T cells. We demonstrated that the diameter of the NPC in cellulo is sufficient for the import of apparently intact, cone-shaped capsids. Subsequent to nuclear import, we detected disrupted and empty capsid fragments, indicating that uncoating of the replication complex occurs by breaking the capsid open, and not by disassembly into individual subunits. Our data directly visualize a key step in HIV-1 replication and enhance our mechanistic understanding of the viral life cycle.
MeSH term(s)	Active Transport, Cell Nucleus ; Capsid/metabolism ; Capsid/ultrastructure ; Cryoelectron Microscopy ; HEK293 Cells ; HIV Infections/virology ; HIV-1/metabolism ; HIV-1/ultrastructure ; Humans ; Models, Biological ; Nuclear Pore/metabolism ; Nuclear Pore/ultrastructure ; Nuclear Pore/virology ; Reverse Transcription ; Virion/metabolism ; Virus Internalization ; mRNA Cleavage and Polyadenylation Factors/metabolism
Chemical Substances	cleavage factor Im, human ; mRNA Cleavage and Polyadenylation Factors
Language	English
Publishing date	2021-02-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2021.01.025
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Article ; Online: In-cell architecture of the nuclear pore and snapshots of its turnover.

Allegretti, Matteo / Zimmerli, Christian E / Rantos, Vasileios / Wilfling, Florian / Ronchi, Paolo / Fung, Herman K H / Lee, Chia-Wei / Hagen, Wim / Turoňová, Beata / Karius, Kai / Börmel, Mandy / Zhang, Xiaojie / Müller, Christoph W / Schwab, Yannick / Mahamid, Julia / Pfander, Boris / Kosinski, Jan / Beck, Martin

Nature

2020 Volume 586, Issue 7831, Page(s) 796–800

Abstract: Nuclear pore complexes (NPCs) fuse the inner and outer membranes of the nuclear envelope. They comprise hundreds of nucleoporins (Nups) that assemble into multiple subcomplexes and form large central channels for nucleocytoplasmic ... ...

Abstract	Nuclear pore complexes (NPCs) fuse the inner and outer membranes of the nuclear envelope. They comprise hundreds of nucleoporins (Nups) that assemble into multiple subcomplexes and form large central channels for nucleocytoplasmic exchange
MeSH term(s)	Autophagy ; Cryoelectron Microscopy ; Models, Molecular ; Nuclear Pore/chemistry ; Nuclear Pore/metabolism ; Nuclear Pore/ultrastructure ; Nuclear Pore Complex Proteins/metabolism ; Saccharomyces cerevisiae/cytology ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae/ultrastructure ; Saccharomyces cerevisiae Proteins/metabolism ; Tomography
Chemical Substances	NUP116 protein, S cerevisiae ; NUP159 protein, S cerevisiae ; Nuclear Pore Complex Proteins ; Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2020-09-02
Publishing country	England
Document type	Journal Article ; 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/s41586-020-2670-5
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