Mie Monti, Reyme Herman, Leonardo Mancini, Charlotte Capitanchik, Karen Davey, Charlotte S Dawson, Jernej Ule, Gavin H Thomas, Anne E Willis, Kathryn S Lilley, Eneko Villanueva
{"title":"Interrogation of RNA-protein interaction dynamics in bacterial growth.","authors":"Mie Monti, Reyme Herman, Leonardo Mancini, Charlotte Capitanchik, Karen Davey, Charlotte S Dawson, Jernej Ule, Gavin H Thomas, Anne E Willis, Kathryn S Lilley, Eneko Villanueva","doi":"10.1038/s44320-024-00031-y","DOIUrl":"10.1038/s44320-024-00031-y","url":null,"abstract":"<p><p>Characterising RNA-protein interaction dynamics is fundamental to understand how bacteria respond to their environment. In this study, we have analysed the dynamics of 91% of the Escherichia coli expressed proteome and the RNA-interaction properties of 271 RNA-binding proteins (RBPs) at different growth phases. We find that 68% of RBPs differentially bind RNA across growth phases and characterise 17 previously unannotated proteins as bacterial RBPs including YfiF, a ncRNA-binding protein. While these new RBPs are mostly present in Proteobacteria, two of them are orthologs of human mitochondrial proteins associated with rare metabolic disorders. Moreover, we reveal novel RBP functions for proteins such as the chaperone HtpG, a new stationary phase tRNA-binding protein. For the first time, the dynamics of the bacterial RBPome have been interrogated, showcasing how this approach can reveal the function of uncharacterised proteins and identify critical RNA-protein interactions for cell growth which could inform new antimicrobial therapies.</p>","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"573-589"},"PeriodicalIF":9.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11066096/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140294055","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Anastasia Razdaibiedina, Alexander Brechalov, Helena Friesen, Mojca Mattiazzi Usaj, Myra Paz David Masinas, Harsha Garadi Suresh, Kyle Wang, Charles Boone, Jimmy Ba, Brenda Andrews
{"title":"PIFiA: self-supervised approach for protein functional annotation from single-cell imaging data.","authors":"Anastasia Razdaibiedina, Alexander Brechalov, Helena Friesen, Mojca Mattiazzi Usaj, Myra Paz David Masinas, Harsha Garadi Suresh, Kyle Wang, Charles Boone, Jimmy Ba, Brenda Andrews","doi":"10.1038/s44320-024-00029-6","DOIUrl":"10.1038/s44320-024-00029-6","url":null,"abstract":"<p><p>Fluorescence microscopy data describe protein localization patterns at single-cell resolution and have the potential to reveal whole-proteome functional information with remarkable precision. Yet, extracting biologically meaningful representations from cell micrographs remains a major challenge. Existing approaches often fail to learn robust and noise-invariant features or rely on supervised labels for accurate annotations. We developed PIFiA (Protein Image-based Functional Annotation), a self-supervised approach for protein functional annotation from single-cell imaging data. We imaged the global yeast ORF-GFP collection and applied PIFiA to generate protein feature profiles from single-cell images of fluorescently tagged proteins. We show that PIFiA outperforms existing approaches for molecular representation learning and describe a range of downstream analysis tasks to explore the information content of the feature profiles. Specifically, we cluster extracted features into a hierarchy of functional organization, study cell population heterogeneity, and develop techniques to distinguish multi-localizing proteins and identify functional modules. Finally, we confirm new PIFiA predictions using a colocalization assay, suggesting previously unappreciated biological roles for several proteins. Paired with a fully interactive website ( https://thecellvision.org/pifia/ ), PIFiA is a resource for the quantitative analysis of protein organization within the cell.</p>","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"521-548"},"PeriodicalIF":9.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11066028/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140110698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Systematic identification of 20S proteasome substrates.","authors":"Monika Pepelnjak, Rivkah Rogawski, Galina Arkind, Yegor Leushkin, Irit Fainer, Gili Ben-Nissan, Paola Picotti, Michal Sharon","doi":"10.1038/s44320-024-00015-y","DOIUrl":"10.1038/s44320-024-00015-y","url":null,"abstract":"<p><p>For years, proteasomal degradation was predominantly attributed to the ubiquitin-26S proteasome pathway. However, it is now evident that the core 20S proteasome can independently target proteins for degradation. With approximately half of the cellular proteasomes comprising free 20S complexes, this degradation mechanism is not rare. Identifying 20S-specific substrates is challenging due to the dual-targeting of some proteins to either 20S or 26S proteasomes and the non-specificity of proteasome inhibitors. Consequently, knowledge of 20S proteasome substrates relies on limited hypothesis-driven studies. To comprehensively explore 20S proteasome substrates, we employed advanced mass spectrometry, along with biochemical and cellular analyses. This systematic approach revealed hundreds of 20S proteasome substrates, including proteins undergoing specific N- or C-terminal cleavage, possibly for regulation. Notably, these substrates were enriched in RNA- and DNA-binding proteins with intrinsically disordered regions, often found in the nucleus and stress granules. Under cellular stress, we observed reduced proteolytic activity in oxidized proteasomes, with oxidized protein substrates exhibiting higher structural disorder compared to unmodified proteins. Overall, our study illuminates the nature of 20S substrates, offering crucial insights into 20S proteasome biology.</p>","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"403-427"},"PeriodicalIF":9.9,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10987551/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139576211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Amrisha Bhosle, Sena Bae, Yancong Zhang, Eunyoung Chun, Julian Avila-Pacheco, Ludwig Geistlinger, Gleb Pishchany, Jonathan N Glickman, Monia Michaud, Levi Waldron, Clary B Clish, Ramnik J Xavier, Hera Vlamakis, Eric A Franzosa, Wendy S Garrett, Curtis Huttenhower
{"title":"Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease.","authors":"Amrisha Bhosle, Sena Bae, Yancong Zhang, Eunyoung Chun, Julian Avila-Pacheco, Ludwig Geistlinger, Gleb Pishchany, Jonathan N Glickman, Monia Michaud, Levi Waldron, Clary B Clish, Ramnik J Xavier, Hera Vlamakis, Eric A Franzosa, Wendy S Garrett, Curtis Huttenhower","doi":"10.1038/s44320-024-00027-8","DOIUrl":"10.1038/s44320-024-00027-8","url":null,"abstract":"<p><p>Microbial biochemistry is central to the pathophysiology of inflammatory bowel diseases (IBD). Improved knowledge of microbial metabolites and their immunomodulatory roles is thus necessary for diagnosis and management. Here, we systematically analyzed the chemical, ecological, and epidemiological properties of ~82k metabolic features in 546 Integrative Human Microbiome Project (iHMP/HMP2) metabolomes, using a newly developed methodology for bioactive compound prioritization from microbial communities. This suggested >1000 metabolic features as potentially bioactive in IBD and associated ~43% of prevalent, unannotated features with at least one well-characterized metabolite, thereby providing initial information for further characterization of a significant portion of the fecal metabolome. Prioritized features included known IBD-linked chemical families such as bile acids and short-chain fatty acids, and less-explored bilirubin, polyamine, and vitamin derivatives, and other microbial products. One of these, nicotinamide riboside, reduced colitis scores in DSS-treated mice. The method, MACARRoN, is generalizable with the potential to improve microbial community characterization and provide therapeutic candidates.</p>","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"338-361"},"PeriodicalIF":8.5,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10987656/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140101972","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Andreas Tsouris, Gauthier Brach, Anne Friedrich, Jing Hou, Joseph Schacherer
{"title":"Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast.","authors":"Andreas Tsouris, Gauthier Brach, Anne Friedrich, Jing Hou, Joseph Schacherer","doi":"10.1038/s44320-024-00021-0","DOIUrl":"10.1038/s44320-024-00021-0","url":null,"abstract":"<p><p>Unraveling the genetic sources of gene expression variation is essential to better understand the origins of phenotypic diversity in natural populations. Genome-wide association studies identified thousands of variants involved in gene expression variation, however, variants detected only explain part of the heritability. In fact, variants such as low-frequency and structural variants (SVs) are poorly captured in association studies. To assess the impact of these variants on gene expression variation, we explored a half-diallel panel composed of 323 hybrids originated from pairwise crosses of 26 natural Saccharomyces cerevisiae isolates. Using short- and long-read sequencing strategies, we established an exhaustive catalog of single nucleotide polymorphisms (SNPs) and SVs for this panel. Combining this dataset with the transcriptomes of all hybrids, we comprehensively mapped SNPs and SVs associated with gene expression variation. While SVs impact gene expression variation, SNPs exhibit a higher effect size with an overrepresentation of low-frequency variants compared to common ones. These results reinforce the importance of dissecting the heritability of complex traits with a comprehensive catalog of genetic variants at the population level.</p>","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"362-373"},"PeriodicalIF":8.5,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10987670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139735665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Javier DelaFuente, Juan Diaz-Colunga, Alvaro Sanchez, Alvaro San Millan
{"title":"Global epistasis in plasmid-mediated antimicrobial resistance.","authors":"Javier DelaFuente, Juan Diaz-Colunga, Alvaro Sanchez, Alvaro San Millan","doi":"10.1038/s44320-024-00012-1","DOIUrl":"10.1038/s44320-024-00012-1","url":null,"abstract":"<p><p>Antimicrobial resistance (AMR) in bacteria is a major public health threat and conjugative plasmids play a key role in the dissemination of AMR genes among bacterial pathogens. Interestingly, the association between AMR plasmids and pathogens is not random and certain associations spread successfully at a global scale. The burst of genome sequencing has increased the resolution of epidemiological programs, broadening our understanding of plasmid distribution in bacterial populations. Despite the immense value of these studies, our ability to predict future plasmid-bacteria associations remains limited. Numerous empirical studies have recently reported systematic patterns in genetic interactions that enable predictability, in a phenomenon known as global epistasis. In this perspective, we argue that global epistasis patterns hold the potential to predict interactions between plasmids and bacterial genomes, thereby facilitating the prediction of future successful associations. To assess the validity of this idea, we use previously published data to identify global epistasis patterns in clinically relevant plasmid-bacteria associations. Furthermore, using simple mechanistic models of antibiotic resistance, we illustrate how global epistasis patterns may allow us to generate new hypotheses on the mechanisms associated with successful plasmid-bacteria associations. Collectively, we aim at illustrating the relevance of exploring global epistasis in the context of plasmid biology.</p>","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"311-320"},"PeriodicalIF":9.9,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10987494/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139972753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States.","authors":"Ludovica Ciampi, Luis Serrano, Manuel Irimia","doi":"10.1038/s44320-024-00020-1","DOIUrl":"10.1038/s44320-024-00020-1","url":null,"abstract":"<p><p>Alternative Splicing (AS) programs serve as instructive signals of cell type specificity, particularly within the brain, which comprises dozens of molecularly and functionally distinct cell types. Among them, retinal photoreceptors stand out due to their unique transcriptome, making them a particularly well-suited system for studying how AS shapes cell type-specific molecular functions. Here, we use the Splicing Regulatory State (SRS) as a novel framework to discuss the splicing factors governing the unique AS pattern of photoreceptors, and how this pattern may aid in the specification of their highly specialized sensory cilia. In addition, we discuss how other sensory cells with ciliated structures, for which data is much scarcer, also rely on specific SRSs to implement a proteome specialized in the detection of sensory stimuli. By reviewing the general rules of cell type- and tissue-specific AS programs, firstly in the brain and subsequently in specialized sensory neurons, we propose a novel paradigm on how SRSs are established and how they can diversify. Finally, we illustrate how SRSs shape the outcome of mutations in splicing factors to produce cell type-specific phenotypes that can lead to various human diseases.</p>","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"296-310"},"PeriodicalIF":9.9,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10987577/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140028437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mira L Burtscher, Stephan Gade, Martin Garrido-Rodriguez, Anna Rutkowska, Thilo Werner, H Christian Eberl, Massimo Petretich, Natascha Knopf, Katharina Zirngibl, Paola Grandi, Giovanna Bergamini, Marcus Bantscheff, Maria Fälth-Savitski, Julio Saez-Rodriguez
{"title":"Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition.","authors":"Mira L Burtscher, Stephan Gade, Martin Garrido-Rodriguez, Anna Rutkowska, Thilo Werner, H Christian Eberl, Massimo Petretich, Natascha Knopf, Katharina Zirngibl, Paola Grandi, Giovanna Bergamini, Marcus Bantscheff, Maria Fälth-Savitski, Julio Saez-Rodriguez","doi":"10.1038/s44320-024-00025-w","DOIUrl":"10.1038/s44320-024-00025-w","url":null,"abstract":"<p><p>Complex disease phenotypes often span multiple molecular processes. Functional characterization of these processes can shed light on disease mechanisms and drug effects. Thermal Proteome Profiling (TPP) is a mass-spectrometry (MS) based technique assessing changes in thermal protein stability that can serve as proxies of functional protein changes. These unique insights of TPP can complement those obtained by other omics technologies. Here, we show how TPP can be integrated with phosphoproteomics and transcriptomics in a network-based approach using COSMOS, a multi-omics integration framework, to provide an integrated view of transcription factors, kinases and proteins with altered thermal stability. This allowed us to recover consequences of Poly (ADP-ribose) polymerase (PARP) inhibition in ovarian cancer cells on cell cycle and DNA damage response as well as interferon and hippo signaling. We found that TPP offers a complementary perspective to other omics data modalities, and that its integration allowed us to obtain a more complete molecular overview of PARP inhibition. We anticipate that this strategy can be used to integrate functional proteomics with other omics to study molecular processes.</p>","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"458-474"},"PeriodicalIF":9.9,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10987601/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140059959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Hats off to 20S proteasome substrate discovery.","authors":"Taylor R Church, Anna Brennan, Seth S Margolis","doi":"10.1038/s44320-024-00028-7","DOIUrl":"10.1038/s44320-024-00028-7","url":null,"abstract":"","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"293-295"},"PeriodicalIF":8.5,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10987484/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140110686","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nina Mitic, Anika Neuschulz, Bastiaan Spanjaard, Julia Schneider, Nora Fresmann, Klara Tereza Novoselc, Taraneh Strunk, Lisa Münster, Pedro Olivares-Chauvet, Jovica Ninkovic, Jan Philipp Junker
{"title":"Dissecting the spatiotemporal diversity of adult neural stem cells.","authors":"Nina Mitic, Anika Neuschulz, Bastiaan Spanjaard, Julia Schneider, Nora Fresmann, Klara Tereza Novoselc, Taraneh Strunk, Lisa Münster, Pedro Olivares-Chauvet, Jovica Ninkovic, Jan Philipp Junker","doi":"10.1038/s44320-024-00022-z","DOIUrl":"10.1038/s44320-024-00022-z","url":null,"abstract":"<p><p>Adult stem cells are important for tissue turnover and regeneration. However, in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here, we dissected the diversity of neural stem cells in the adult zebrafish brain, an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single-cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze the regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells, with some subtypes being restricted to a single brain region, while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation, with different states being involved in proliferative and non-proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for the functional manipulation of neural stem cell subtypes.</p>","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"321-337"},"PeriodicalIF":9.9,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10987636/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139747040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}