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Book ; Thesis: Die Beeinflussung der mRNA-Expression inflammatorischer Zytokine ko-kultivierter bronchialer Epithelzellen durch humane faser, partikelexponierte Blutmonozyten unter In-vitro-Bedingungen

Messner, Christoph

1998

Author's details	vorgelegt von Christoph Messner
Language	German
Size	VI, 168 Bl., Ill., graph. Darst.
Edition	[Mikrofiche-Ausg.]
Publishing country	Germany
Document type	Book ; Thesis
Thesis / German Habilitation thesis	Mainz, Univ., Diss., 2000
HBZ-ID	HT013308424
Database	Catalogue ZB MED Medicine, Health

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Article ; Online: Cellular control of protein levels: A systems biology perspective.

Munro, Victoria / Kelly, Van / Messner, Christoph B / Kustatscher, Georg

Proteomics

2023 , Page(s) e2200220

Abstract: How cells regulate protein levels is a central question of biology. Over the past decades, molecular biology research has provided profound insights into the mechanisms and the molecular machinery governing each step of the gene expression process, from ... ...

Abstract	How cells regulate protein levels is a central question of biology. Over the past decades, molecular biology research has provided profound insights into the mechanisms and the molecular machinery governing each step of the gene expression process, from transcription to protein degradation. Recent advances in transcriptomics and proteomics have complemented our understanding of these fundamental cellular processes with a quantitative, systems-level perspective. Multi-omic studies revealed significant quantitative, kinetic and functional differences between the genome, transcriptome and proteome. While protein levels often correlate with mRNA levels, quantitative investigations have demonstrated a substantial impact of translation and protein degradation on protein expression control. In addition, protein-level regulation appears to play a crucial role in buffering protein abundances against undesirable mRNA expression variation. These findings have practical implications for many fields, including gene function prediction and precision medicine.
Language	English
Publishing date	2023-11-27
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.202200220
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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: Global analysis of cytosine and adenine DNA modifications across the tree of life.

Varma, Sreejith Jayasree / Calvani, Enrica / Grüning, Nana-Maria / Messner, Christoph B / Grayson, Nicholas / Capuano, Floriana / Mülleder, Michael / Ralser, Markus

eLife

2022 Volume 11

Abstract: Interpreting the function and metabolism of enzymatic DNA modifications requires both position-specific and global quantities. Sequencing-based techniques that deliver the former have become broadly accessible, but analytical methods for the global ... ...

Abstract	Interpreting the function and metabolism of enzymatic DNA modifications requires both position-specific and global quantities. Sequencing-based techniques that deliver the former have become broadly accessible, but analytical methods for the global quantification of DNA modifications have thus far been applied mostly to individual problems. We established a mass spectrometric method for the sensitive and accurate quantification of multiple enzymatic DNA modifications. Then, we isolated DNA from 124 archean, bacterial, fungal, plant, and mammalian species, and several tissues and created a resource of global DNA modification quantities. Our dataset provides insights into the general nature of enzymatic DNA modifications, reveals unique biological cases, and provides complementary quantitative information to normalize and assess the accuracy of sequencing-based detection of DNA modifications. We report that only three of the studied DNA modifications, methylcytosine (5mdC), methyladenine (N6mdA) and hydroxymethylcytosine (5hmdC), were detected above a picomolar detection limit across species, and dominated in higher eukaryotes (5mdC), in bacteria (N6mdA), or the vertebrate central nervous systems (5hmdC). All three modifications were detected simultaneously in only one of the tested species,
MeSH term(s)	5-Methylcytosine/metabolism ; Adenine/metabolism ; Animals ; Cytosine/chemistry ; DNA/metabolism ; DNA Methylation ; Eukaryota/genetics ; Mammals/genetics
Chemical Substances	5-Methylcytosine (6R795CQT4H) ; Cytosine (8J337D1HZY) ; DNA (9007-49-2) ; Adenine (JAC85A2161)
Language	English
Publishing date	2022-07-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.81002
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Article ; Online: Mass spectrometry-based high-throughput proteomics and its role in biomedical studies and systems biology.

Messner, Christoph B / Demichev, Vadim / Wang, Ziyue / Hartl, Johannes / Kustatscher, Georg / Mülleder, Michael / Ralser, Markus

Proteomics

2022 Volume 23, Issue 7-8, Page(s) e2200013

Abstract: There are multiple reasons why the next generation of biological and medical studies require increasing numbers of samples. Biological systems are dynamic, and the effect of a perturbation depends on the genetic background and environment. As a ... ...

Abstract	There are multiple reasons why the next generation of biological and medical studies require increasing numbers of samples. Biological systems are dynamic, and the effect of a perturbation depends on the genetic background and environment. As a consequence, many conditions need to be considered to reach generalizable conclusions. Moreover, human population and clinical studies only reach sufficient statistical power if conducted at scale and with precise measurement methods. Finally, many proteins remain without sufficient functional annotations, because they have not been systematically studied under a broad range of conditions. In this review, we discuss the latest technical developments in mass spectrometry (MS)-based proteomics that facilitate large-scale studies by fast and efficient chromatography, fast scanning mass spectrometers, data-independent acquisition (DIA), and new software. We further highlight recent studies which demonstrate how high-throughput (HT) proteomics can be applied to capture biological diversity, to annotate gene functions or to generate predictive and prognostic models for human diseases.
MeSH term(s)	Humans ; Proteomics/methods ; Systems Biology ; Proteins/analysis ; Mass Spectrometry/methods ; Software
Chemical Substances	Proteins
Language	English
Publishing date	2022-11-18
Publishing country	Germany
Document type	Journal Article ; Review ; 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.202200013
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Article ; Online: Cysteine and iron accelerate the formation of ribose-5-phosphate, providing insights into the evolutionary origins of the metabolic network structure.

Piedrafita, Gabriel / Varma, Sreejith J / Castro, Cecilia / Messner, Christoph B / Szyrwiel, Lukasz / Griffin, Julian L / Ralser, Markus

PLoS biology

2021 Volume 19, Issue 12, Page(s) e3001468

Abstract: The structure of the metabolic network is highly conserved, but we know little about its evolutionary origins. Key for explaining the early evolution of metabolism is solving a chicken-egg dilemma, which describes that enzymes are made from the very same ...

Abstract	The structure of the metabolic network is highly conserved, but we know little about its evolutionary origins. Key for explaining the early evolution of metabolism is solving a chicken-egg dilemma, which describes that enzymes are made from the very same molecules they produce. The recent discovery of several nonenzymatic reaction sequences that topologically resemble central metabolism has provided experimental support for a "metabolism first" theory, in which at least part of the extant metabolic network emerged on the basis of nonenzymatic reactions. But how could evolution kick-start on the basis of a metal catalyzed reaction sequence, and how could the structure of nonenzymatic reaction sequences be imprinted on the metabolic network to remain conserved for billions of years? We performed an in vitro screening where we add the simplest components of metabolic enzymes, proteinogenic amino acids, to a nonenzymatic, iron-driven reaction network that resembles glycolysis and the pentose phosphate pathway (PPP). We observe that the presence of the amino acids enhanced several of the nonenzymatic reactions. Particular attention was triggered by a reaction that resembles a rate-limiting step in the oxidative PPP. A prebiotically available, proteinogenic amino acid cysteine accelerated the formation of RNA nucleoside precursor ribose-5-phosphate from 6-phosphogluconate. We report that iron and cysteine interact and have additive effects on the reaction rate so that ribose-5-phosphate forms at high specificity under mild, metabolism typical temperature and environmental conditions. We speculate that accelerating effects of amino acids on rate-limiting nonenzymatic reactions could have facilitated a stepwise enzymatization of nonenzymatic reaction sequences, imprinting their structure on the evolving metabolic network.
MeSH term(s)	Amino Acids/metabolism ; Catalysis ; Cysteine/chemistry ; Cysteine/metabolism ; Evolution, Molecular ; Glucose/metabolism ; Glycolysis/physiology ; Iron/chemistry ; Iron/metabolism ; Magnetic Resonance Spectroscopy/methods ; Metabolic Networks and Pathways/physiology ; Origin of Life ; Pentose Phosphate Pathway/genetics ; Pentose Phosphate Pathway/physiology ; Ribosemonophosphates/metabolism
Chemical Substances	Amino Acids ; Ribosemonophosphates ; ribose-5-phosphate (4B2428FLTO) ; Iron (E1UOL152H7) ; Glucose (IY9XDZ35W2) ; Cysteine (K848JZ4886)
Language	English
Publishing date	2021-12-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3001468
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Article ; Online: DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput.

Demichev, Vadim / Messner, Christoph B / Vernardis, Spyros I / Lilley, Kathryn S / Ralser, Markus

Nature methods

2019 Volume 17, Issue 1, Page(s) 41–44

Abstract: We present an easy-to-use integrated software suite, DIA-NN, that exploits deep neural networks and new quantification and signal correction strategies for the processing of data-independent acquisition (DIA) proteomics experiments. DIA-NN improves the ... ...

Abstract	We present an easy-to-use integrated software suite, DIA-NN, that exploits deep neural networks and new quantification and signal correction strategies for the processing of data-independent acquisition (DIA) proteomics experiments. DIA-NN improves the identification and quantification performance in conventional DIA proteomic applications, and is particularly beneficial for high-throughput applications, as it is fast and enables deep and confident proteome coverage when used in combination with fast chromatographic methods.
MeSH term(s)	HeLa Cells ; High-Throughput Screening Assays/methods ; Humans ; Mass Spectrometry/methods ; Neural Networks, Computer ; Proteome/analysis ; Proteomics/methods ; Software ; Species Specificity ; Zea mays/metabolism
Chemical Substances	Proteome
Language	English
Publishing date	2019-11-25
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/s41592-019-0638-x
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Zs.A 6022: Show issues

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Article ; Online: Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics.

White, Matthew E H / Sinn, Ludwig R / Jones, D Marc / de Folter, Joost / Aulakh, Simran Kaur / Wang, Ziyue / Flynn, Helen R / Krüger, Lynn / Tober-Lau, Pinkus / Demichev, Vadim / Kurth, Florian / Mülleder, Michael / Blanchard, Véronique / Messner, Christoph B / Ralser, Markus

Nature biomedical engineering

2023 Volume 8, Issue 3, Page(s) 233–247

Abstract: Protein glycosylation, a complex and heterogeneous post-translational modification that is frequently dysregulated in disease, has been difficult to analyse at scale. Here we report a data-independent acquisition technique for the large-scale mass- ... ...

Abstract	Protein glycosylation, a complex and heterogeneous post-translational modification that is frequently dysregulated in disease, has been difficult to analyse at scale. Here we report a data-independent acquisition technique for the large-scale mass-spectrometric quantification of glycopeptides in plasma samples. The technique, which we named 'OxoScan-MS', identifies oxonium ions as glycopeptide fragments and exploits a sliding-quadrupole dimension to generate comprehensive and untargeted oxonium ion maps of precursor masses assigned to fragment ions from non-enriched plasma samples. By applying OxoScan-MS to quantify 1,002 glycopeptide features in the plasma glycoproteomes from patients with COVID-19 and healthy controls, we found that severe COVID-19 induces differential glycosylation in IgA, haptoglobin, transferrin and other disease-relevant plasma glycoproteins. OxoScan-MS may allow for the quantitative mapping of glycoproteomes at the scale of hundreds to thousands of samples.
MeSH term(s)	Humans ; Mass Spectrometry ; Glycosylation ; Glycopeptides/analysis ; Glycopeptides/chemistry ; Glycopeptides/metabolism ; Ions ; COVID-19
Chemical Substances	Glycopeptides ; Ions
Language	English
Publishing date	2023-07-20
Publishing country	England
Document type	Journal Article
ISSN	2157-846X
ISSN (online)	2157-846X
DOI	10.1038/s41551-023-01067-5
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Article ; Online: The proteomic landscape of genome-wide genetic perturbations.

Messner, Christoph B / Demichev, Vadim / Muenzner, Julia / Aulakh, Simran K / Barthel, Natalie / Röhl, Annika / Herrera-Domínguez, Lucía / Egger, Anna-Sophia / Kamrad, Stephan / Hou, Jing / Tan, Guihong / Lemke, Oliver / Calvani, Enrica / Szyrwiel, Lukasz / Mülleder, Michael / Lilley, Kathryn S / Boone, Charles / Kustatscher, Georg / Ralser, Markus

Cell

2023 Volume 186, Issue 9, Page(s) 2018–2034.e21

Abstract: Functional genomic strategies have become fundamental for annotating gene function and regulatory networks. Here, we combined functional genomics with proteomics by quantifying protein abundances in a genome-scale knockout library in Saccharomyces ... ...

Abstract	Functional genomic strategies have become fundamental for annotating gene function and regulatory networks. Here, we combined functional genomics with proteomics by quantifying protein abundances in a genome-scale knockout library in Saccharomyces cerevisiae, using data-independent acquisition mass spectrometry. We find that global protein expression is driven by a complex interplay of (1) general biological properties, including translation rate, protein turnover, the formation of protein complexes, growth rate, and genome architecture, followed by (2) functional properties, such as the connectivity of a protein in genetic, metabolic, and physical interaction networks. Moreover, we show that functional proteomics complements current gene annotation strategies through the assessment of proteome profile similarity, protein covariation, and reverse proteome profiling. Thus, our study reveals principles that govern protein expression and provides a genome-spanning resource for functional annotation.
MeSH term(s)	Proteomics/methods ; Proteome/metabolism ; Genomics/methods ; Genome ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism
Chemical Substances	Proteome
Language	English
Publishing date	2023-04-19
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.2023.03.026
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Article ; Online: QM/MM MD simulations of La(III)-phosphopeptide complexes.

Messner, Christoph B / Bonn, Günther K / Hofer, Thomas S

Molecular bioSystems

2015 Volume 11, Issue 1, Page(s) 232–238

Abstract: Several bioanalytical enrichment techniques are based on the interactions of phosphopeptides with Ln(III) ions. In order to gain an improved understanding of these complexes and the respective ion-peptide interactions, hybrid quantum mechanics/molecular ... ...

Abstract	Several bioanalytical enrichment techniques are based on the interactions of phosphopeptides with Ln(III) ions. In order to gain an improved understanding of these complexes and the respective ion-peptide interactions, hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations of La(III) coordinating to the phosphopeptide VPQLEIVPNSpAEER were conducted. Simulations of di- as well as monoanionic phosphate groups were carried out. The La(III) ion and its first hydration layer, including the sidechain of the phosphoserine residue were treated quantum mechanically at RI-MP2/triple zeta level, whereas the remaining part of the system was treated with classical potentials. The simulation of the dianionic phosphopeptide revealed a 9-fold coordinated La(III) ion, with the phosphopeptide binding bi- as well as monodentate. The mean residence times (τ) of the first shell water molecules were 82 ps and 37 ps for the bi- and monodentate complexes, respectively, which is much higher compared to free La(III) in aqueous solution (τ=17 ps). The simulation of the monoanionic La(III)-phosphopeptide complex revealed a bidentate coordination throughout the 80 ps sampling period. An intramolecular hydrogen bond between the hydrogen of the phosphate group and the backbone was observed and a τ value of 14 ps was obtained, which is much lower as for the dianionic complex.
MeSH term(s)	Lanthanum/chemistry ; Models, Molecular ; Molecular Conformation ; Molecular Dynamics Simulation ; Phosphopeptides/chemistry ; Protein Binding ; Quantum Theory
Chemical Substances	Phosphopeptides ; Lanthanum (6I3K30563S)
Language	English
Publishing date	2015-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2188635-0
ISSN	1742-2051 ; 1742-206X
ISSN (online)	1742-2051
ISSN	1742-206X
DOI	10.1039/c4mb00424h
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Article ; Online: Inorganic sulfur fixation via a new homocysteine synthase allows yeast cells to cooperatively compensate for methionine auxotrophy.

Yu, Jason S L / Heineike, Benjamin M / Hartl, Johannes / Aulakh, Simran K / Correia-Melo, Clara / Lehmann, Andrea / Lemke, Oliver / Agostini, Federica / Lee, Cory T / Demichev, Vadim / Messner, Christoph B / Mülleder, Michael / Ralser, Markus

PLoS biology

2022 Volume 20, Issue 12, Page(s) e3001912

Abstract: The assimilation, incorporation, and metabolism of sulfur is a fundamental process across all domains of life, yet how cells deal with varying sulfur availability is not well understood. We studied an unresolved conundrum of sulfur fixation in yeast, in ... ...

Abstract	The assimilation, incorporation, and metabolism of sulfur is a fundamental process across all domains of life, yet how cells deal with varying sulfur availability is not well understood. We studied an unresolved conundrum of sulfur fixation in yeast, in which organosulfur auxotrophy caused by deletion of the homocysteine synthase Met17p is overcome when cells are inoculated at high cell density. In combining the use of self-establishing metabolically cooperating (SeMeCo) communities with proteomic, genetic, and biochemical approaches, we discovered an uncharacterized gene product YLL058Wp, herein named Hydrogen Sulfide Utilizing-1 (HSU1). Hsu1p acts as a homocysteine synthase and allows the cells to substitute for Met17p by reassimilating hydrosulfide ions leaked from met17Δ cells into O-acetyl-homoserine and forming homocysteine. Our results show that cells can cooperate to achieve sulfur fixation, indicating that the collective properties of microbial communities facilitate their basic metabolic capacity to overcome sulfur limitation.
MeSH term(s)	Cysteine/metabolism ; Cysteine Synthase/genetics ; Cysteine Synthase/metabolism ; Methionine/metabolism ; Proteomics ; Racemethionine ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Sulfur/metabolism
Chemical Substances	Cysteine (K848JZ4886) ; Cysteine Synthase (EC 2.5.1.47) ; MET17 protein, S cerevisiae (EC 2.5.1.47) ; Methionine (AE28F7PNPL) ; O-acetylhomoserine (thiol)-lyase (EC 2.5.1.47) ; Racemethionine (73JWT2K6T3) ; Sulfur (70FD1KFU70) ; YLL058W protein, S cerevisiae (EC 2.5.1.48)
Language	English
Publishing date	2022-12-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3001912
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