Biology subjects

Muenzner, J.

Publications and source records attributed to Muenzner, J..

7 recordsLinked to original sources

bioRxiv2025

The adaptive molecular landscape of reprogrammed telomeric sequences

Telomeric sequences vary across the tree of life and intimately co-evolve with telomere-binding protein complexes. However, the molecular mechanisms allowing organisms to adapt to new telomeric sequences are difficult to gauge from extant species. Here, we reprogrammed multiple yeast lines to human-like telomeric repeats to unveil their molecular and fitness response to novel telomeres. Initially, the exchange of telomere sequences resulted in genome instability, proteome remodelling and severe fitness decline. However, adaptive evolution experiments selected for repeated mutations that drove adaptation to the humanized telomeres. These consisted of the recurrent amplification of the telomere-binding protein TBF1, by complex aneuploidies, or in repeated mutations that attenuate the DNA damage response. Overall, our results outline a response that defines the adaptive molecular landscape to novel telomeric sequences.

evolutionary biology↗

bioRxiv2024

An INS-1 beta-cell proteome highlights the role of fatty acid biosynthesis in glucose-stimulated insulin secretion

Pancreatic beta cells secrete insulin as a response to rising glucose level, a process known as glucose-stimulated insulin secretion (GSIS). In this study, we used liquid chromatography tandem mass spectrometry and data-independent acquisition to acquire proteomes of rat pancreatic INS-1 832/13 beta cells that were short-term stimulated with glucose concentrations ranging from 0 to 20 mM, quantifying the behavior of 3703 proteins across 11 concentrations. Ensemble clustering of proteome profiles revealed unique response patterns of proteins expressed by INS-1 cells. 237 proteins, amongst them proteins associated with vesicular SNARE interactions, protein export, and pancreatic secretion showed an increase in abundance upon glucose stimulation, whilst the majority of proteins, including those associated with metabolic pathways such as glycolysis, the TCA cycle and the respiratory chain, did not respond to rising glucose concentrations. Interestingly, we observe that enzymes participating in fatty acid metabolism, responded distinctly, showing a "switch-on" response upon release of glucose starvation with no further changes in abundance upon increasing glucose levels. We speculate that increased activity of fatty acid metabolic activity might either be part of GSIS by replenishing membrane lipids required for vesicle-mediated exocytosis and/or by providing an electron sink to compensate for the increase in glucose catabolism. Significance of the StudyWe used high-throughput proteomics to capture comprehensive proteome changes 30 minutes post stimulation in the INS-1 832/13 beta cell line. Our study provides insights into the metabolic regulation of glucose-stimulated insulin secretion in pancreatic beta cells, specifically highlighting the early role of fatty acid biosynthesis. These findings suggest a necessary shift in focus from electrochemical to metabolic mechanisms in understanding GSIS, paving the way for future research. As the first to document proteome alterations in the initial phase of GSIS, our study furthermore documents the extent of protein abundance variability when obtaining data after short stimulation times, and therefore highlights the necessity of well-controlled study design and biological replicates. The recorded data set complements existing metabolomic and transcriptomic studies, providing a valuable resource for subsequent investigations.

cell biology↗

bioRxiv2023

Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast

Gene expression varies between individuals and corresponds to a key step linking genotypes to phenotypes. However, our knowledge regarding the species-wide genetic control of protein abundance, including its dependency on transcript levels, is very limited. Here, we have determined quantitative proteomes of a large population of 942 diverse natural Saccharomyces cerevisiae yeast isolates. We found that mRNA and protein abundances are weakly correlated at the population gene level. While the protein co-expression network recapitulates major biological functions, differential expression patterns reveal proteomic signatures related to specific populations. Comprehensive genetic association analyses highlight that genetic variants associated with variation in protein (pQTL) and transcript (eQTL) levels poorly overlap (3.6%). Our results demonstrate that transcriptome and proteome are governed by distinct genetic bases, likely explained by protein turnover. It also highlights the importance of integrating these different levels of gene expression to better understand the genotype-phenotype relationship. HighlightsO_LIAt the level of individual genes, the abundance of transcripts and proteins is weakly correlated within a species ({rho} = 0.165). C_LIO_LIWhile the proteome is not imprinted by population structure, co-expression patterns recapitulate the cellular functional landscape C_LIO_LIWild populations exhibit a higher abundance of respiration-related proteins compared to domesticated populations C_LIO_LILoci that influence protein abundance differ from those that impact transcript levels, likely because of protein turnover C_LI

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

The natural diversity of the yeast proteome reveals chromosome-wide dosage compensation in aneuploids

Aneuploidy, an imbalance in chromosome copy numbers, causes genetic disorders, and drives cancer progression, drug tolerance, and antimicrobial resistance. While aneuploidy can confer stress resistance, it is not well understood how cells overcome the fitness burden caused by aberrant chromosomal copy numbers. Studies using both systematically generated 1-5 and natural aneuploid yeasts 6-8 triggered an intense debate about the role of dosage compensation, concluding that aneuploidy is transmitted to the transcriptome and proteome without significant buffering at the chromosome-wide level, and is, at least in lab strains, associated with significant fitness costs. Conversely, systematic sequencing and phenotyping of large collections of natural isolates revealed that aneuploidy is frequent and has few - if any - fitness costs in nature 9. To address these discrepant findings at the proteomic level, we developed a platform that yields highly precise proteomic measurements across large numbers of genetically diverse samples, and applied it to natural isolates collected as part of the 1011 genomes project 9. For 613 of the isolates, we were able to match the proteomes to their corresponding transcriptomes and genomes, subsequently quantifying the effect of aneuploidy on gene expression by comparing 95 aneuploid with 518 euploid strains. We find, as in previous studies, that aneuploid gene dosage is not buffered chromosome-wide at the transcriptome level. Importantly, in the proteome, we detect an attenuation of aneuploidy by about 25% below the aneuploid gene dosage in natural yeast isolates. Furthermore, this chromosome-wide dosage compensation is associated with the ubiquitin-proteasome system (UPS), which is expressed at higher levels and has increased activity across natural aneuploid strains. Thus, through systematic exploration of the species-wide diversity of the yeast proteome, we shed light on a long-standing debate about the biology of aneuploids, revealing that aneuploidy tolerance is mediated through chromosome-wide dosage compensation at the proteome level.

systems biology↗

bioRxiv2021

pUL21 is a viral phosphatase adaptor that promotes herpes simplex virus replication and spread

The herpes simplex virus (HSV)-1 protein pUL21 is essential for efficient virus replication and dissemination. While pUL21 has been shown to promote multiple steps of virus assembly and spread, the molecular basis of its function remained unclear. Here we identify that pUL21 is a virus-encoded adaptor of protein phosphatase 1 (PP1). pUL21 directs the dephosphorylation of cellular and virus proteins, including components of the viral nuclear egress complex, and we define a conserved non-canonical linear motif in pUL21 that is essential for PP1 recruitment. In vitro evolution experiments reveal that pUL21 directly antagonises the activity of the virus-encoded kinase pUS3, with growth and spread of pUL21 PP1-binding mutant viruses being restored when pUS3 activity is disrupted. This study shows that virus-directed phosphatase activity is essential for efficient herpesvirus assembly and spread, highlighting the fine balance between kinase and phosphatase activity required for optimal virus replication.

microbiology↗

bioRxiv2019

Herpes simplex virus-1 pUL56 degrades GOPC to alter the plasma membrane proteome

Herpesviruses are ubiquitous in the human population and they extensively remodel the cellular environment during infection. Multiplexed quantitative proteomic analysis over a whole time-course of herpes simplex virus (HSV)-1 infection was used to characterize changes in the host-cell proteome and to probe the kinetics of viral protein production. Several host-cell proteins were targeted for rapid degradation by HSV-1, including the cellular trafficking factor GOPC. We identify that the poorly-characterized HSV-1 protein pUL56 binds directly to GOPC, stimulating its ubiquitination and proteasomal degradation. Plasma membrane profiling revealed that pUL56 mediates specific changes to the surface proteome of infected cells, including loss of IL18 receptor and Toll-like receptor 2, and delivery of Toll-like receptor 2 to the cell-surface requires GOPC. Our study highlights an unanticipated and efficient mechanism whereby a single virus protein targets a cellular trafficking factor to modify the abundance of multiple signaling molecules at the surface of infected cells.

microbiology↗