Biology subjects

Mülleder, M.

Publications and source records attributed to Mülleder, M..

8 recordsLinked to original sources

bioRxiv2026

A draft atlas of the human plasma proteome at isoform resolution

Key plasma protein, including albumin, complement system proteins, and coagulation factors circulate in biochemically and functionally distinct isoforms, or proteoforms. Despite the importance of these proteoforms being widely accepted, they are challenging to resolve systematically, and as a consequence, we still lack a more complete picture of the total proteoform diversity of the human plasma proteome. Here, we generated 3,114 intact protein fractions by extensively separating plasma according to isoelectric point and molecular weight. We then analysed these fractions by liquid chromatography data-independent acquisition mass spectrometry (DIA-MS) upon tryptic digestions, and combined the resultant data into a multidimensional, proteoform resolved atlas of the human plasma proteome. We report that 5,077 unequivocally detected plasma proteins circulate at least 179,049 distinct proteoforms, of which we detect 44,083, with a median of 11 proteoforms per protein, at high confidence. Substantially increasing the number of experimentally confirmed proteoforms, our atlas implies that the canonical protein forms account for less than half of the total protein mass in plasma. We detect the greatest proteoform diversity among the most abundant plasma proteins and those functioning in nutrient transport, complement and coagulation. Finally, our data clarifies discrepancies between the Olink and SomaScan proteomic platforms, as according to our atlas, these techniques provide correlated values for relatively abundant proteins with low to medium proteoform diversity, but struggle in the quantification of low-abundant proteins and on those which exist in many proteoforms. In sum, our data reveals extensive proteoform diversity of the human plasma proteome, and implies that proteoform diversity represents an enormous untapped reservoir for biomedical research and biomarker discovery.

biochemistry↗

bioRxiv2026

A microbial growth-coupled platform for in vivo interrogation of Rubisco oxygenase activity

Rubisco catalyzes the primary CO2-fixing reaction of the biosphere, yet its competing oxygenation reaction reduces net global carbon fixation and has resisted direct exploration in living cells. Here, we engineer an auxotrophic Escherichia coli strain in which 2-phosphoglycolate, the direct product of Rubisco oxygenation, becomes essential for growth, making bacterial fitness a quantitative proxy for oxygenation flux in vivo. This provides direct access to catalytic selectivity, something previously inaccessible to carboxylation-coupled assays. The platform enables screening of phylogenetically diverse Form II Rubisco and phosphoribulokinase (Prk) variants circumventing protein purification and extensive in vitro characterization. Adaptive laboratory evolution under oxygenation-selective pressure identified two mutations: Rubisco M115I genetically rebalances the in vivo carboxylation/oxygenation trade-off (resulting in 6-fold reduction in kcat,C), while Prk N216T improves overall flux without altering selectivity. This platform makes Rubiscos least-studied catalytic function selectable and evolvable in vivo, opening the carboxylation/oxygenation trade-off to systematic genetic dissection and engineering.

synthetic biology↗

bioRxiv2025

Altered Brain Energy Metabolism in the APPPS1 Alzheimer's Model during anesthesia: Integration of Experimental Data and In Silico Modeling

BackgroundSynaptic transmission and network activity rely on high ATP turnover. Impairments in cerebral energy metabolism are increasingly recognized as central in aging and Alzheimers disease (AD) pathogenesis. Elderly patients and patients with AD are also at elevated risk for perioperative neurological complications, including post-operative delirium and further cognitive deterioration. However, the interaction between metabolic vulnerability and anesthetic exposure remains incompletely understood. MethodsWe investigated cortical metabolic responses and potassium homeostasis in acute brain slices from wild-type (WT) and AD-like APPPS1 transgenic mice, which were either exposed to isoflurane or left untreated. Glia cells were assessed by staining microglia and astrocytes. Measurements of the cerebral metabolic rate of oxygen (CMRO2), extracellular potassium dynamics, and proteomic profiling were integrated with computational modeling to assess oxidative metabolism and anesthetic effects under different conditions. ResultsAPPPS1 mice exhibited reduced CMRO2 and attenuated neuronal activity compared to age-matched WT controls, showing sex-specific differences. Proteomic analysis revealed the downregulation of key mitochondrial and glycolytic enzymes, indicating an impaired ATP- generating capacity. Exposure to isoflurane further suppressed CMRO2, with a more pronounced effect in the APPPS1 brain tissue, while glia cells exhibited no acute changes. Additionally, isoflurane exacerbated deficits in extracellular potassium ([K]) clearance, highlighting impaired ion homeostasis under anesthetic challenge. ConclusionsOur findings demonstrate that AD-like pathology in APPPS1 mice is associated with a significant decline in oxidative metabolism and ATP availability. These deficits are exacerbated by anesthetic exposure, contributing to impaired potassium regulation. This suggests that diminished metabolic flexibility may underlie increased anesthetic vulnerability and postoperative complications in AD.

neuroscience↗

bioRxiv2023

Calcineurin inhibitor nephrotoxicity revisited: perspectives emerging from differential impact on renal compartments

Calcineurin inhibitors (CNI) are the backbone for immunosuppression after solid organ transplantation. Although successful in preventing kidney transplant rejection, their nephrotoxic side effects notoriously contribute to allograft injury despite attempts to optimize their application, often with additional medications. Complex renal parenchymal damage occurs for cyclosporine A (CsA) as well as for the currently favoured tacrolimus (Tac). To test for distinct CsA and Tac damaging patterns, we combined multiomics analysis with histopathology from rat kidneys exposed to continuous CNI delivery. Damage forms varied strikingly. Both drugs caused significant albeit differential damage in vasculature and nephron. The glomerular filtration barrier was more affected by Tac than by CsA, showing prominent deteriorations in pore endothelium and podocytes along with impaired VEGF/VEGFR2 signaling and podocyte-specific gene expression. By contrast, proximal tubule epithelia were more severely affected by CsA than by Tac, revealing lysosomal dysfunction and enhanced apoptosis along with impaired proteostasis and oxidative stress. We conclude that pathogenetic alterations in renal microenvironments are specific for either treatment. Should this translate to the clinical setting, CNI choice should reflect individual risk factors for renal vasculature and tubular epithelia. As a step in this direction, we share products identified from multiomics for differential pathognomonic biomarkers. Translational StatementCalcineurin inhibitors (CNI) are first-choice immunosuppressive agents. Their nephrotoxic side effects may often limit their use. Tacrolimus is currently preferred to cyclosporine although its superiority remains unclear. Within the nephron, damage to the filtration barrier is greater for tacrolimus, whereas cyclosporine side effects locate more to the proximal tubular epithelium when compared in our rodent model. We identify the distinctive location and nature of damage by both drugs and unravel involved mechanisms. By detecting differential protein signatures we make available pathognomonic biomarkers for renal allograft health under CNI treatment.

pathology↗

bioRxiv2022

OxoScan-MS: Oxonium ion scanning mass spectrometry facilitates plasma glycoproteomics in large scale

Protein glycosylation is a complex and heterogeneous post-translational modification. Specifically, the human plasma proteome is rich in glycoproteins, and as protein glycosylation is frequently dysregulated in disease, glycoproteomics is considered an underexplored resource for biomarker discovery. Here, we present OxoScan-MS, a data-independent mass spectrometric acquisition technology and data analysis software that facilitates sensitive, fast, and cost-effective glycoproteome profiling of plasma and serum samples in large cohort studies. OxoScan-MS quantifies glycosylated peptide features by exploiting a scanning quadrupole to assign precursors to oxonium ions, glycopeptide-specific fragments. OxoScan-MS reaches a high level of sensitivity and selectivity in untargeted glycopeptide profiling, such that it can be efficiently used with fast microflow chromatography without a need for experimental enrichment of glycopeptides from neat plasma. We apply OxoScan-MS to profile the plasma glycoproteomic in an inpatient cohort hospitalised due to severe COVID-19, and obtain precise quantities for 1,002 glycopeptide features. We reveal that severe COVID-19 induces differential glycosylation in disease-relevant plasma glycoproteins, including IgA, fibrinogen and alpha-1-antitrypsin. Thus, with OxoScan-MS we present a strategy for quantitatively mapping glycoproteomes that scales to hundreds and thousands of samples, and report glycoproteomic changes in severe COVID-19.

systems biology↗

bioRxiv2022

The Proteomic Landscape of Genome-Wide Genetic Perturbations

Functional genomic strategies help to address the genotype phenotype problem by annotating gene function and regulatory networks. Here, we demonstrate that combining functional genomics with proteomics uncovers general principles of protein expression, and provides new avenues to annotate protein function. We recorded precise proteomes for all non-essential gene knock-outs in Saccharomyces cerevisiae. We find that protein abundance is driven by a complex interplay of i) general biological properties, including translation rate, turnover, and copy number variations, and ii) their genetic, metabolic and physical interactions, including membership in protein complexes. We further show that combining genetic perturbation with proteomics provides complementary dimensions of functional annotation: proteomic profiling, reverse proteomic profiling, profile similarity and protein covariation analysis. Thus, our study generates a resource in which nine million protein quantities are linked to 79% of the yeast coding genome, and shows that functional proteomics reveals principles that govern protein expression. Highlights- Nine million protein quantities recorded in ~4,600 non-essential gene deletions in S. cerevisiae reveal principles of how the proteome responds to genetic perturbation - Genome-scale protein expression is determined by both functional relationships between proteins, as well as common biological responses - Broad protein expression profiles in slow-growing strains can be explained by chromosomal aneuploidies - Protein half-life and ribosome occupancy are predictable from protein abundance changes across knock-outs - Functional proteomics annotates missing gene function in four complementary dimensions

systems biology↗

bioRxiv2022

Inorganic sulfur fixation via a new homocysteine synthase allows yeast cells to cooperatively compensate for methionine auxotrophy

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 an organosulfur-auxotrophy caused by deletion of homocysteine synthase Met17p is overcome when cells are inoculated at high cell density. We discovered that an uncharacterized gene YLL058Wp, herein named Hydrogen sulfide utilizing-1 (HSU1), acts as a homocysteine synthase and allows the cells to substitute for Met17p by re-assimilating hydrosulfide ions leaked from met17{Delta} 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. SummarySulfur limitation activates a dormant hydrogen sulfide fixation route via a novel homocysteine synthase Hsu1p (YLL058Wp).

molecular biology↗

bioRxiv2020

Longitudinal omics in Syrian hamsters integrated with human data unravel complexity of moderate immune responses to SARS-CoV-2

In COVID-19, the immune response largely determines disease severity and is key to therapeutic strategies. Cellular mechanisms contributing to inflammatory lung injury and tissue repair in SARS-CoV-2 infection, particularly endothelial cell involvement, remain ill-defined. We performed detailed spatiotemporal analyses of cellular and molecular processes in SARS-CoV-2 infected Syrian hamsters. Comparison of hamster single-cell sequencing and proteomics with data sets from COVID-19 patients demonstrated inter-species concordance of cellular and molecular host-pathogen interactions. In depth vascular and pulmonary compartment analyses (i) supported the hypothesis that monocyte-derived macrophages dominate inflammation, (ii) revealed endothelial inflammation status and T-cell attraction, and (iii) showed that CD4+ and CD8+ cytotoxic T-cell responses precede viral elimination. Using the Syrian hamster model of self-limited moderate COVID-19, we defined the specific roles of endothelial and epithelial cells, among other myeloid and non-myeloid lung cell subtypes, for determining the disease course.

immunology↗