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Article ; Online: Insights into the sulfur metabolism of Chlorobaculum tepidum by label-free quantitative proteomics.

Lyratzakis, Alexandros / Meier-Credo, Jakob / Langer, Julian D / Tsiotis, Georgios

2023 Volume 23, Issue 10, Page(s) e2200138

Abstract: Chlorobaculum tepidum is an anaerobic green sulfur bacterium which oxidizes sulfide, elemental sulfur, and thiosulfate for photosynthetic growth. It can also oxidize sulfide to produce extracellular ... ...

Abstract	Chlorobaculum tepidum is an anaerobic green sulfur bacterium which oxidizes sulfide, elemental sulfur, and thiosulfate for photosynthetic growth. It can also oxidize sulfide to produce extracellular S
MeSH term(s)	Chlorobi/metabolism ; Oxidation-Reduction ; Proteomics/methods ; Sulfides/metabolism ; Sulfur/metabolism ; Thiosulfates/metabolism ; Photosynthesis
Chemical Substances	Sulfides ; Sulfur (70FD1KFU70) ; Thiosulfates
Language	English
Publishing date	2023-03-10
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.202200138
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Zs.A 5386: 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)
Zs.A 1868: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Dynamic SILAC to Determine Protein Turnover in Neurons and Glia.

Dörrbaum, Aline R / Schuman, Erin M / Langer, Julian D

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

2022 Volume 2603, Page(s) 1–17

Abstract: Cellular protein turnover-the net result of protein synthesis and degradation-is crucial to maintain protein homeostasis and cellular function under steady-state conditions and to enable cells to remodel their proteomes upon a perturbation. In brain ... ...

Abstract	Cellular protein turnover-the net result of protein synthesis and degradation-is crucial to maintain protein homeostasis and cellular function under steady-state conditions and to enable cells to remodel their proteomes upon a perturbation. In brain cells, proteins are continuously turned over at different rates depending on various factors including cell type, subcellular localization, cellular environment, and neuronal activity. Here we describe a workflow for the analysis of protein synthesis, degradation, and turnover in primary cultured rat neurons and glia using dynamic/pulsed SILAC and mass spectrometry.
MeSH term(s)	Rats ; Animals ; Proteome/metabolism ; Proteolysis ; Neuroglia/metabolism ; Neurons/metabolism ; Mass Spectrometry ; Isotope Labeling/methods
Chemical Substances	Proteome
Language	English
Publishing date	2022-11-12
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2863-8_1
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Article ; Online: Conformational changes in mitochondrial complex I of the thermophilic eukaryote

Laube, Eike / Meier-Credo, Jakob / Langer, Julian D / Kühlbrandt, Werner

Science advances

2022 Volume 8, Issue 47, Page(s) eadc9952

Abstract: Mitochondrial complex I is a redox-driven proton pump that generates proton-motive force across the inner mitochondrial membrane, powering oxidative phosphorylation and ATP synthesis in eukaryotes. We report the structure of complex I from the ... ...

Abstract	Mitochondrial complex I is a redox-driven proton pump that generates proton-motive force across the inner mitochondrial membrane, powering oxidative phosphorylation and ATP synthesis in eukaryotes. We report the structure of complex I from the thermophilic fungus
Language	English
Publishing date	2022-11-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adc9952
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Article: Rotational stability of plate haptic toric intraocular lenses after combined 25-gauge vitrectomy and cataract surgery.

Buhl, Lara / Langer, Julian / Kassumeh, Stefan / Kreutzer, Thomas C / Mayer, Wolfgang J / Priglinger, Siegfried G

International journal of ophthalmology

2023 Volume 16, Issue 8, Page(s) 1231–1236

Abstract: Aim: To evaluate the postoperative intraocular lens (IOL) rotational stability and residual refractive astigmatism following combined 25-gauge vitrectomy and cataract surgery with implantation of a plate haptic toric IOL.: Methods: In this ... ...

Abstract	Aim: To evaluate the postoperative intraocular lens (IOL) rotational stability and residual refractive astigmatism following combined 25-gauge vitrectomy and cataract surgery with implantation of a plate haptic toric IOL. Methods: In this retrospective case series, 32 eyes of 32 patients underwent a combined 25-gauge vitrectomy and phacoemulsification for vitreoretinal diseases and cataract with regular corneal astigmatism of at least 1 diopter (D). A plate haptic toric IOL (AT Torbi 709M, Carl Zeiss Meditec AG) was implanted in all eyes. The outcome measures were rotational stability and refractive astigmatism up to 6mo postoperatively as well as the best corrected visual acuity (BCVA). Results: Preoperative refractive astigmatism was 2.14±1.17 D, which was significantly reduced to 0.77±0.37 D six to eight weeks postoperatively and remained stable throughout the observation period (0.67±0.44 D at three months and 0.75±0.25 D at six months; for all groups: Conclusion: Corneal astigmatism is significantly reduced following combined 25-gauge vitrectomy and cataract surgery. The plate haptic toric IOL position and axis remain stable during the observation period of six months.
Language	English
Publishing date	2023-08-18
Publishing country	China
Document type	Journal Article
ZDB-ID	2663246-9
ISSN	2227-4898 ; 2222-3959
ISSN (online)	2227-4898
ISSN	2222-3959
DOI	10.18240/ijo.2023.08.07
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Article ; Online: Dynamic bi-directional phosphorylation events associated with the reciprocal regulation of synapses during homeostatic up- and down-scaling.

Desch, Kristina / Langer, Julian D / Schuman, Erin M

Cell reports

2021 Volume 36, Issue 8, Page(s) 109583

Abstract: Homeostatic synaptic scaling allows for bi-directional adjustment of the strength of synaptic connections in response to changes in their input. Protein phosphorylation modulates many neuronal processes, but it has not been studied on a global scale ... ...

Abstract	Homeostatic synaptic scaling allows for bi-directional adjustment of the strength of synaptic connections in response to changes in their input. Protein phosphorylation modulates many neuronal processes, but it has not been studied on a global scale during synaptic scaling. Here, we use liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses to measure changes in the phosphoproteome in response to up- or down-scaling in cultured cortical neurons over minutes to 24 h. Of ~45,000 phosphorylation events, ~3,300 (associated with 1,285 phosphoproteins) are regulated by homeostatic scaling. Activity-sensitive phosphoproteins are predominantly located at synapses and involved in cytoskeletal reorganization. We identify many early phosphorylation events that could serve as sensors for the activity offset as well as late and/or persistent phosphoregulation that could represent effector mechanisms driving the homeostatic response. Much of the persistent phosphorylation is reciprocally regulated by up- or down-scaling, suggesting that mechanisms underlying these two poles of synaptic regulation make use of a common signaling axis.
MeSH term(s)	Animals ; Chromatography, Liquid/methods ; Excitatory Postsynaptic Potentials/physiology ; Homeostasis/physiology ; Neuronal Plasticity/physiology ; Neurons/metabolism ; Phosphorylation ; Receptors, AMPA/metabolism ; Synapses/metabolism
Chemical Substances	Receptors, AMPA
Language	English
Publishing date	2021-08-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2021.109583
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Article ; Online: VAP spatially stabilizes dendritic mitochondria to locally support synaptic plasticity.

Bapat, Ojasee / Purimetla, Tejas / Kruessel, Sarah / Shah, Monil / Fan, Ruolin / Thum, Christina / Rupprecht, Fiona / Langer, Julian D / Rangaraju, Vidhya

Nature communications

2024 Volume 15, Issue 1, Page(s) 205

Abstract: Synapses are pivotal sites of plasticity and memory formation. Consequently, synapses are energy consumption hotspots susceptible to dysfunction when their energy supplies are perturbed. Mitochondria are stabilized near synapses via the cytoskeleton and ... ...

Abstract	Synapses are pivotal sites of plasticity and memory formation. Consequently, synapses are energy consumption hotspots susceptible to dysfunction when their energy supplies are perturbed. Mitochondria are stabilized near synapses via the cytoskeleton and provide the local energy required for synaptic plasticity. However, the mechanisms that tether and stabilize mitochondria to support synaptic plasticity are unknown. We identified proteins exclusively tethering mitochondria to actin near postsynaptic spines. We find that VAP, the vesicle-associated membrane protein-associated protein implicated in amyotrophic lateral sclerosis, stabilizes mitochondria via actin near the spines. To test if the VAP-dependent stable mitochondrial compartments can locally support synaptic plasticity, we used two-photon glutamate uncaging for spine plasticity induction and investigated the induced and adjacent uninduced spines. We find VAP functions as a spatial stabilizer of mitochondrial compartments for up to ~60 min and as a spatial ruler determining the ~30 μm dendritic segment supported during synaptic plasticity.
MeSH term(s)	Actins/metabolism ; Dendritic Spines/metabolism ; Neuronal Plasticity ; Synapses/metabolism ; Mitochondria/metabolism
Chemical Substances	Actins
Language	English
Publishing date	2024-01-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-44233-8
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Article ; Online: Quantifying phosphorylation dynamics in primary neuronal cultures using LC-MS/MS.

Desch, Kristina / Schuman, Erin M / Langer, Julian D

STAR protocols

2021 Volume 3, Issue 1, Page(s) 101063

Abstract: Cellular processes require tight and coordinated control of protein abundance, localization, and activity. One of the core mechanisms to achieve specific regulation of proteins is protein phosphorylation. Here we present a workflow to monitor protein ... ...

Abstract	Cellular processes require tight and coordinated control of protein abundance, localization, and activity. One of the core mechanisms to achieve specific regulation of proteins is protein phosphorylation. Here we present a workflow to monitor protein abundance and phosphorylation in primary cultured neurons using liquid chromatography-coupled mass spectrometry. Our protocol provides a detailed guide on all steps for detection and label-free-quantification of phosphorylated and unmodified proteins of primary cortical neurons, including primary cell culture, phosphoproteomic sample preparation and data-processing, and evaluation. For complete details on the use and execution of this protocol, please refer to Desch et al. (2021).
MeSH term(s)	Chromatography, Liquid/methods ; Neurons/chemistry ; Phosphorylation ; Proteins/analysis ; Proteomics/methods ; Tandem Mass Spectrometry
Chemical Substances	Proteins
Language	English
Publishing date	2021-12-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2666-1667
ISSN (online)	2666-1667
DOI	10.1016/j.xpro.2021.101063
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Article ; Online: Detection of Known and Novel Small Proteins in Pseudomonas stutzeri Using a Combination of Bottom-Up and Digest-Free Proteomics and Proteogenomics

Meier-Credo, Jakob / Heiniger, Benjamin / Schori, Christian / Rupprecht, Fiona / Michel, Hartmut / Ahrens, Christian H. / Langer, Julian D.

Analytical Chemistry. 2023 Aug. 03, v. 95, no. 32 p.11892-11900

2023

Abstract: Small proteins of around 50 aa in length have been largely overlooked in genetic and biochemical assays due to the inherent challenges with detecting and characterizing them. Recent discoveries of their critical roles in many biological processes have ... ...

Abstract	Small proteins of around 50 aa in length have been largely overlooked in genetic and biochemical assays due to the inherent challenges with detecting and characterizing them. Recent discoveries of their critical roles in many biological processes have led to an increased recognition of the importance of small proteins for basic research and as potential new drug targets. One example is CcoM, a 36 aa subunit of the cbb3-type oxidase that plays an essential role in adaptation to oxygen-limited conditions in Pseudomonas stutzeri (P. stutzeri), a model for the clinically relevant, opportunistic pathogen Pseudomonas aeruginosa. However, as no comprehensive data were available in P. stutzeri, we devised an integrated, generic approach to study small proteins more systematically. Using the first complete genome as basis, we conducted bottom-up proteomics analyses and established a digest-free, direct-sequencing proteomics approach to study cells grown under aerobic and oxygen-limiting conditions. Finally, we also applied a proteogenomics pipeline to identify missed protein-coding genes. Overall, we identified 2921 known and 29 novel proteins, many of which were differentially regulated. Among 176 small proteins 16 were novel. Direct sequencing, featuring a specialized precursor acquisition scheme, exhibited advantages in the detection of small proteins with higher (up to 100%) sequence coverage and more spectral counts, including sequences with high proline content. Three novel small proteins, uniquely identified by direct sequencing and not conserved beyond P. stutzeri, were predicted to form an operon with a conserved protein and may represent de novo genes. These data demonstrate the power of this combined approach to study small proteins in P. stutzeri and show its potential for other prokaryotes.
Keywords	Pseudomonas aeruginosa ; Pseudomonas stutzeri ; analytical chemistry ; drugs ; models ; operon ; opportunistic pathogens ; oxidoreductases ; prokaryotic cells ; proline ; proteomics
Language	English
Dates of publication	2023-0803
Size	p. 11892-11900.
Publishing place	American Chemical Society
Document type	Article ; Online
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c00676
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Proteome Turnover in the Spotlight: Approaches, Applications, and Perspectives.

Ross, Alison Barbara / Langer, Julian David / Jovanovic, Marko

Molecular & cellular proteomics : MCP

2020 Volume 20, Page(s) 100016

Abstract: In all cells, proteins are continuously synthesized and degraded to maintain protein homeostasis and modify gene expression levels in response to stimuli. Collectively, the processes of protein synthesis and degradation are referred to as protein ... ...

Abstract	In all cells, proteins are continuously synthesized and degraded to maintain protein homeostasis and modify gene expression levels in response to stimuli. Collectively, the processes of protein synthesis and degradation are referred to as protein turnover. At a steady state, protein turnover is constant to maintain protein homeostasis, but in dynamic responses, proteins change their rates of synthesis and degradation to adjust their proteomes to internal or external stimuli. Thus, probing the kinetics and dynamics of protein turnover lends insight into how cells regulate essential processes such as growth, differentiation, and stress response. Here, we outline historical and current approaches to measuring the kinetics of protein turnover on a proteome-wide scale in both steady-state and dynamic systems, with an emphasis on metabolic tracing using stable isotope-labeled amino acids. We highlight important considerations for designing proteome turnover experiments, key biological findings regarding the conserved principles of proteome turnover regulation, and future perspectives for both technological and biological investigation.
MeSH term(s)	Amino Acids ; Animals ; Humans ; Isotope Labeling ; Light ; Pharmaceutical Preparations ; Proteome ; Proteomics ; Radioisotopes
Chemical Substances	Amino Acids ; Pharmaceutical Preparations ; Proteome ; Radioisotopes
Language	English
Publishing date	2020-12-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1074/mcp.R120.002190
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Article ; Online: A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry.

Ahrens, Christian H / Wade, Joseph T / Champion, Matthew M / Langer, Julian D

Journal of bacteriology

2021 Volume 204, Issue 1, Page(s) e0035321

Abstract: Small proteins of up to ∼50 amino acids are an abundant class of biomolecules across all domains of life. Yet due to the challenges inherent in their size, they are often missed in genome annotations, and are difficult to identify and characterize using ... ...

Abstract	Small proteins of up to ∼50 amino acids are an abundant class of biomolecules across all domains of life. Yet due to the challenges inherent in their size, they are often missed in genome annotations, and are difficult to identify and characterize using standard experimental approaches. Consequently, we still know few small proteins even in well-studied prokaryotic model organisms. Mass spectrometry (MS) has great potential for the discovery, validation, and functional characterization of small proteins. However, standard MS approaches are poorly suited to the identification of both known and novel small proteins due to limitations at each step of a typical proteomics workflow, i.e., sample preparation, protease digestion, liquid chromatography, MS data acquisition, and data analysis. Here, we outline the major MS-based workflows and bioinformatic pipelines used for small protein discovery and validation. Special emphasis is placed on highlighting the adjustments required to improve detection and data quality for small proteins. We discuss both the unbiased detection of small proteins and the targeted analysis of small proteins of interest. Finally, we provide guidelines to prioritize novel small proteins, and an outlook on methods with particular potential to further improve comprehensive discovery and characterization of small proteins.
MeSH term(s)	Archaea/genetics ; Archaea/metabolism ; Archaeal Proteins/chemistry ; Archaeal Proteins/genetics ; Archaeal Proteins/metabolism ; Bacteria/genetics ; Bacteria/metabolism ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Computational Biology ; Gene Expression Regulation, Archaeal/physiology ; Gene Expression Regulation, Bacterial/physiology ; Mass Spectrometry/methods
Chemical Substances	Archaeal Proteins ; Bacterial Proteins
Language	English
Publishing date	2021-11-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/JB.00353-21
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