Molecular Systems Biology最新文献_第2页

Epigenetic modifications and metabolic gene mutations drive resistance evolution in response to stimulatory antibiotics. 表观遗传修饰和代谢基因突变驱动对刺激性抗生素的抗性进化。

IF 8.5 1区生物学

Molecular Systems Biology Pub Date : 2025-01-16 DOI: 10.1038/s44320-025-00087-4

Hui Lin, Donglin Wang, Qiaojuan Wang, Jie Mao, Lutong Yang, Yaohui Bai, Jiuhui Qu

{"title":"Epigenetic modifications and metabolic gene mutations drive resistance evolution in response to stimulatory antibiotics.","authors":"Hui Lin, Donglin Wang, Qiaojuan Wang, Jie Mao, Lutong Yang, Yaohui Bai, Jiuhui Qu","doi":"10.1038/s44320-025-00087-4","DOIUrl":"https://doi.org/10.1038/s44320-025-00087-4","url":null,"abstract":"The antibiotic resistance crisis, fueled by misuse and bacterial evolution, is a major global health threat. Traditional perspectives tie resistance to drug target mechanisms, viewing antibiotics as mere growth inhibitors. New insights revealed that low-dose antibiotics may also serve as signals, unexpectedly promoting bacterial growth. Yet, the development of resistance under these conditions remains unknown. Our study investigated resistance evolution under stimulatory antibiotics and uncovered new genetic mechanisms of resistance linked to metabolic remodeling. We documented a shift from a fast, reversible mechanism driven by methylation in central metabolic pathways to a slower, stable mechanism involving mutations in key metabolic genes. Both mechanisms contribute to a metabolic profile transition from glycolysis to rapid gluconeogenesis. In addition, our findings demonstrated that rising environmental temperatures associated with metabolic evolution accelerated this process, increasing the prevalence of metabolic gene mutations, albeit with a trade-off in interspecific fitness. These findings expand beyond the conventional understanding of resistance mechanisms, proposing a broader metabolic mechanism within the selective window of stimulatory sub-MIC antibiotics, particularly in the context of climate change.","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":""},"PeriodicalIF":8.5,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks. 代谢突变通过途径特异性瓶颈降低大肠杆菌的抗生素敏感性。

IF 8.5 1区生物学

Molecular Systems Biology Pub Date : 2025-01-02 DOI: 10.1038/s44320-024-00084-z

Paul Lubrano, Fabian Smollich, Thorben Schramm, Elisabeth Lorenz, Alejandra Alvarado, Seraina Carmen Eigenmann, Amelie Stadelmann, Sevvalli Thavapalan, Nils Waffenschmidt, Timo Glatter, Nadine Hoffmann, Jennifer Müller, Silke Peter, Knut Drescher, Hannes Link

{"title":"Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks.","authors":"Paul Lubrano, Fabian Smollich, Thorben Schramm, Elisabeth Lorenz, Alejandra Alvarado, Seraina Carmen Eigenmann, Amelie Stadelmann, Sevvalli Thavapalan, Nils Waffenschmidt, Timo Glatter, Nadine Hoffmann, Jennifer Müller, Silke Peter, Knut Drescher, Hannes Link","doi":"10.1038/s44320-024-00084-z","DOIUrl":"10.1038/s44320-024-00084-z","url":null,"abstract":"Metabolic variation across pathogenic bacterial strains can impact their susceptibility to antibiotics and promote the evolution of antimicrobial resistance (AMR). However, little is known about how metabolic mutations influence metabolism and which pathways contribute to antibiotic susceptibility. Here, we measured the antibiotic susceptibility of 15,120 Escherichia coli mutants, each with a single amino acid change in one of 346 essential proteins. Across all mutants, we observed modest increases of the minimal inhibitory concentration (twofold to tenfold) without any cases of major resistance. Most mutants that showed reduced susceptibility to either of the two tested antibiotics carried mutations in metabolic genes. The effect of metabolic mutations on antibiotic susceptibility was antibiotic- and pathway-specific: mutations that reduced susceptibility against the β-lactam antibiotic carbenicillin converged on purine nucleotide biosynthesis, those against the aminoglycoside gentamicin converged on the respiratory chain. In addition, metabolic mutations conferred tolerance to carbenicillin by reducing growth rates. These results, along with evidence that metabolic bottlenecks are common among clinical E. coli isolates, highlight the contribution of metabolic mutations for AMR.","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":""},"PeriodicalIF":8.5,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142922180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enhancers and genome conformation provide complex transcriptional control of a herpesviral gene. 增强子和基因组构象为疱疹病毒基因提供了复杂的转录控制。

IF 8.5 1区生物学

Molecular Systems Biology Pub Date : 2025-01-01 Epub Date: 2024-11-19 DOI: 10.1038/s44320-024-00075-0

David W Morgens, Leah Gulyas, Xiaowen Mao, Alejandro Rivera-Madera, Annabelle S Souza, Britt A Glaunsinger

{"title":"Enhancers and genome conformation provide complex transcriptional control of a herpesviral gene.","authors":"David W Morgens, Leah Gulyas, Xiaowen Mao, Alejandro Rivera-Madera, Annabelle S Souza, Britt A Glaunsinger","doi":"10.1038/s44320-024-00075-0","DOIUrl":"10.1038/s44320-024-00075-0","url":null,"abstract":"Complex transcriptional control is a conserved feature of both eukaryotes and the viruses that infect them. Despite viral genomes being smaller and more gene dense than their hosts, we generally lack a sense of scope for the features governing the transcriptional output of individual viral genes. Even having a seemingly simple expression pattern does not imply that a gene's underlying regulation is straightforward. Here, we illustrate this by combining high-density functional genomics, expression profiling, and viral-specific chromosome conformation capture to define with unprecedented detail the transcriptional regulation of a single gene from Kaposi's sarcoma-associated herpesvirus (KSHV). We used as our model KSHV ORF68 - which has simple, early expression kinetics and is essential for viral genome packaging. We first identified seven cis-regulatory regions involved in ORF68 expression by densely tiling the ~154 kb KSHV genome with dCas9 fused to a transcriptional repressor domain (CRISPRi). A parallel Cas9 nuclease screen indicated that three of these regions act as promoters of genes that regulate ORF68. RNA expression profiling demonstrated that three more of these regions act by either repressing or enhancing other distal viral genes involved in ORF68 transcriptional regulation. Finally, we tracked how the 3D structure of the viral genome changes during its lifecycle, revealing that these enhancing regulatory elements are physically closer to their targets when active, and that disrupting some elements caused large-scale changes to the 3D genome. These data enable us to construct a complete model revealing that the mechanistic diversity of this essential regulatory circuit matches that of human genes.","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"30-58"},"PeriodicalIF":8.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11696879/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142676266","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}

引用次数: 0

Global atlas of predicted functional domains in Legionella pneumophila Dot/Icm translocated effectors. 嗜肺军团菌 Dot/Icm 易位效应因子中预测功能域的全球图谱。

IF 8.5 1区生物学

Molecular Systems Biology Pub Date : 2025-01-01 Epub Date: 2024-11-19 DOI: 10.1038/s44320-024-00076-z

Deepak T Patel, Peter J Stogios, Lukasz Jaroszewski, Malene L Urbanus, Mayya Sedova, Cameron Semper, Cathy Le, Abraham Takkouche, Keita Ichii, Julie Innabi, Dhruvin H Patel, Alexander W Ensminger, Adam Godzik, Alexei Savchenko

{"title":"Global atlas of predicted functional domains in Legionella pneumophila Dot/Icm translocated effectors.","authors":"Deepak T Patel, Peter J Stogios, Lukasz Jaroszewski, Malene L Urbanus, Mayya Sedova, Cameron Semper, Cathy Le, Abraham Takkouche, Keita Ichii, Julie Innabi, Dhruvin H Patel, Alexander W Ensminger, Adam Godzik, Alexei Savchenko","doi":"10.1038/s44320-024-00076-z","DOIUrl":"10.1038/s44320-024-00076-z","url":null,"abstract":"Legionella pneumophila utilizes the Dot/Icm type IVB secretion system to deliver hundreds of effector proteins inside eukaryotic cells to ensure intracellular replication. Our understanding of the molecular functions of the largest pathogenic arsenal known to the bacterial world remains incomplete. By leveraging advancements in 3D protein structure prediction, we provide a comprehensive structural analysis of 368 L. pneumophila effectors, representing a global atlas of predicted functional domains summarized in a database ( https://pathogens3d.org/legionella-pneumophila ). Our analysis identified 157 types of diverse functional domains in 287 effectors, including 159 effectors with no prior functional annotations. Furthermore, we identified 35 cryptic domains in 30 effector models that have no similarity with experimentally structurally characterized proteins, thus, hinting at novel functionalities. Using this analysis, we demonstrate the activity of thirteen functional domains, including three cryptic domains, predicted in L. pneumophila effectors to cause growth defects in the Saccharomyces cerevisiae model system. This illustrates an emerging strategy of exploring synergies between predictions and targeted experimental approaches in elucidating novel effector activities involved in infection.","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"59-89"},"PeriodicalIF":8.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11696984/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142676352","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}

引用次数: 0

Redesigning error control in cross-linking mass spectrometry enables more robust and sensitive protein-protein interaction studies. 在交联质谱中重新设计误差控制使蛋白质相互作用的研究更加稳健和敏感。

IF 8.5 1区生物学

Molecular Systems Biology Pub Date : 2025-01-01 Epub Date: 2024-12-09 DOI: 10.1038/s44320-024-00079-w

Boris Bogdanow, Max Ruwolt, Julia Ruta, Lars Mühlberg, Cong Wang, Wen-Feng Zeng, Arne Elofsson, Fan Liu

{"title":"Redesigning error control in cross-linking mass spectrometry enables more robust and sensitive protein-protein interaction studies.","authors":"Boris Bogdanow, Max Ruwolt, Julia Ruta, Lars Mühlberg, Cong Wang, Wen-Feng Zeng, Arne Elofsson, Fan Liu","doi":"10.1038/s44320-024-00079-w","DOIUrl":"10.1038/s44320-024-00079-w","url":null,"abstract":"Cross-linking mass spectrometry (XL-MS) allows characterizing protein-protein interactions (PPIs) in native biological systems by capturing cross-links between different proteins (inter-links). However, inter-link identification remains challenging, requiring dedicated data filtering schemes and thorough error control. Here, we benchmark existing data filtering schemes combined with error rate estimation strategies utilizing concatenated target-decoy protein sequence databases. These workflows show shortcomings either in sensitivity (many false negatives) or specificity (many false positives). To ameliorate the limited sensitivity without compromising specificity, we develop an alternative target-decoy search strategy using fused target-decoy databases. Furthermore, we devise a different data filtering scheme that takes the inter-link context of the XL-MS dataset into account. Combining both approaches maintains low error rates and minimizes false negatives, as we show by mathematical simulations, analysis of experimental ground-truth data, and application to various biological datasets. In human cells, inter-link identifications increase by 75% and we confirm their structural accuracy through proteome-wide comparisons to AlphaFold2-derived models. Taken together, target-decoy fusion and context-sensitive data filtering deepen and fine-tune XL-MS-based interactomics.","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"90-106"},"PeriodicalIF":8.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11696718/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142801791","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}

引用次数: 0

State of the interactomes: an evaluation of molecular networks for generating biological insights. 相互作用组的状态：对产生生物学见解的分子网络的评估。

IF 8.5 1区生物学

Molecular Systems Biology Pub Date : 2025-01-01 Epub Date: 2024-12-09 DOI: 10.1038/s44320-024-00077-y

Sarah N Wright, Scott Colton, Leah V Schaffer, Rudolf T Pillich, Christopher Churas, Dexter Pratt, Trey Ideker

{"title":"State of the interactomes: an evaluation of molecular networks for generating biological insights.","authors":"Sarah N Wright, Scott Colton, Leah V Schaffer, Rudolf T Pillich, Christopher Churas, Dexter Pratt, Trey Ideker","doi":"10.1038/s44320-024-00077-y","DOIUrl":"10.1038/s44320-024-00077-y","url":null,"abstract":"Advancements in genomic and proteomic technologies have powered the creation of large gene and protein networks (\"interactomes\") for understanding biological systems. However, the proliferation of interactomes complicates the selection of networks for specific applications. Here, we present a comprehensive evaluation of 45 current human interactomes, encompassing protein-protein interactions as well as gene regulatory, signaling, colocalization, and genetic interaction networks. Our analysis shows that large composite networks such as HumanNet, STRING, and FunCoup are most effective for identifying disease genes, while smaller networks such as DIP, Reactome, and SIGNOR demonstrate stronger performance in interaction prediction. Our study provides a benchmark for interactomes across diverse biological applications and clarifies factors that influence network performance. Furthermore, our evaluation pipeline paves the way for continued assessment of emerging and updated interaction networks in the future.","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"1-29"},"PeriodicalIF":8.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11697402/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142801792","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}

引用次数: 0

Bacterial live therapeutics for human diseases. 治疗人类疾病的活细菌疗法。

IF 8.5 1区生物学

Molecular Systems Biology Pub Date : 2024-12-01 Epub Date: 2024-10-23 DOI: 10.1038/s44320-024-00067-0

Elisabet Frutos-Grilo, Yamile Ana, Javier Gonzalez-de Miguel, Marcel Cardona-I-Collado, Irene Rodriguez-Arce, Luis Serrano

引用次数: 0

Understanding the biological processes of kidney carcinogenesis: an integrative multi-omics approach. 了解肾癌发生的生物学过程：一种综合的多组学方法。

IF 8.5 1区生物学

Molecular Systems Biology Pub Date : 2024-12-01 Epub Date: 2024-11-26 DOI: 10.1038/s44320-024-00072-3

Ricardo Cortez Cardoso Penha, Alexandra Sexton Oates, Sergey Senkin, Hanla A Park, Joshua Atkins, Ivana Holcatova, Anna Hornakova, Slavisa Savic, Simona Ognjanovic, Beata Świątkowska, Jolanta Lissowska, David Zaridze, Anush Mukeria, Vladimir Janout, Amelie Chabrier, Vincent Cahais, Cyrille Cuenin, Ghislaine Scelo, Matthieu Foll, Zdenko Herceg, Paul Brennan, Karl Smith-Byrne, Nicolas Alcala, James D Mckay

{"title":"Understanding the biological processes of kidney carcinogenesis: an integrative multi-omics approach.","authors":"Ricardo Cortez Cardoso Penha, Alexandra Sexton Oates, Sergey Senkin, Hanla A Park, Joshua Atkins, Ivana Holcatova, Anna Hornakova, Slavisa Savic, Simona Ognjanovic, Beata Świątkowska, Jolanta Lissowska, David Zaridze, Anush Mukeria, Vladimir Janout, Amelie Chabrier, Vincent Cahais, Cyrille Cuenin, Ghislaine Scelo, Matthieu Foll, Zdenko Herceg, Paul Brennan, Karl Smith-Byrne, Nicolas Alcala, James D Mckay","doi":"10.1038/s44320-024-00072-3","DOIUrl":"10.1038/s44320-024-00072-3","url":null,"abstract":"Biological mechanisms related to cancer development can leave distinct molecular fingerprints in tumours. By leveraging multi-omics and epidemiological information, we can unveil relationships between carcinogenesis processes that would otherwise remain hidden. Our integrative analysis of DNA methylome, transcriptome, and somatic mutation profiles of kidney tumours linked ageing, epithelial-mesenchymal transition (EMT), and xenobiotic metabolism to kidney carcinogenesis. Ageing process was represented by associations with cellular mitotic clocks such as epiTOC2, SBS1, telomere length, and PBRM1 and SETD2 mutations, which ticked faster as tumours progressed. We identified a relationship between BAP1 driver mutations and the epigenetic upregulation of EMT genes (IL20RB and WT1), correlating with increased tumour immune infiltration, advanced stage, and poorer patient survival. We also observed an interaction between epigenetic silencing of the xenobiotic metabolism gene GSTP1 and tobacco use, suggesting a link to genotoxic effects and impaired xenobiotic metabolism. Our pan-cancer analysis showed these relationships in other tumour types. Our study enhances the understanding of kidney carcinogenesis and its relation to risk factors and progression, with implications for other tumour types.","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"1282-1302"},"PeriodicalIF":8.5,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11612429/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142730720","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}

引用次数: 0

Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting. 细胞下 mRNA 动力学建模显示，核保留是限制速率的因素。

IF 8.5 1区生物学

Molecular Systems Biology Pub Date : 2024-12-01 Epub Date: 2024-11-15 DOI: 10.1038/s44320-024-00073-2

David Steinbrecht, Igor Minia, Miha Milek, Johannes Meisig, Nils Blüthgen, Markus Landthaler

{"title":"Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting.","authors":"David Steinbrecht, Igor Minia, Miha Milek, Johannes Meisig, Nils Blüthgen, Markus Landthaler","doi":"10.1038/s44320-024-00073-2","DOIUrl":"10.1038/s44320-024-00073-2","url":null,"abstract":"Eukaryotic mRNAs are transcribed, processed, translated, and degraded in different subcellular compartments. Here, we measured mRNA flow rates between subcellular compartments in mouse embryonic stem cells. By combining metabolic RNA labeling, biochemical fractionation, mRNA sequencing, and mathematical modeling, we determined the half-lives of nuclear pre-, nuclear mature, cytosolic, and membrane-associated mRNAs from over 9000 genes. In addition, we estimated transcript elongation rates. Many matured mRNAs have long nuclear half-lives, indicating nuclear retention as the rate-limiting step in the flow of mRNAs. In contrast, mRNA transcripts coding for transcription factors show fast kinetic rates, and in particular short nuclear half-lives. Differentially localized mRNAs have distinct rate constant combinations, implying modular regulation. Membrane stability is high for membrane-localized mRNA and cytosolic stability is high for cytosol-localized mRNA. mRNAs encoding target signals for membranes have low cytosolic and high membrane half-lives with minor differences between signals. Transcripts of nuclear-encoded mitochondrial proteins have long nuclear retention and cytoplasmic kinetics that do not reflect co-translational targeting. Our data and analyses provide a useful resource to study spatiotemporal gene expression regulation.","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"1346-1371"},"PeriodicalIF":8.5,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611909/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142639366","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}

引用次数: 0

Deep quantification of substrate turnover defines protease subsite cooperativity. 底物周转的深度定量确定了蛋白酶亚位点的合作性。

IF 8.5 1区生物学

Molecular Systems Biology Pub Date : 2024-12-01 Epub Date: 2024-10-28 DOI: 10.1038/s44320-024-00071-4

Rajani Kanth Gudipati, Dimos Gaidatzis, Jan Seebacher, Sandra Muehlhaeusser, Georg Kempf, Simone Cavadini, Daniel Hess, Charlotte Soneson, Helge Großhans

{"title":"Deep quantification of substrate turnover defines protease subsite cooperativity.","authors":"Rajani Kanth Gudipati, Dimos Gaidatzis, Jan Seebacher, Sandra Muehlhaeusser, Georg Kempf, Simone Cavadini, Daniel Hess, Charlotte Soneson, Helge Großhans","doi":"10.1038/s44320-024-00071-4","DOIUrl":"10.1038/s44320-024-00071-4","url":null,"abstract":"Substrate specificity determines protease functions in physiology and in clinical and biotechnological applications, yet quantitative cleavage information is often unavailable, biased, or limited to a small number of events. Here, we develop qPISA (quantitative Protease specificity Inference from Substrate Analysis) to study Dipeptidyl Peptidase Four (DPP4), a key regulator of blood glucose levels. We use mass spectrometry to quantify >40,000 peptides from a complex, commercially available peptide mixture. By analyzing changes in substrate levels quantitatively instead of focusing on qualitative product identification through a binary classifier, we can reveal cooperative interactions within DPP4's active pocket and derive a sequence motif that predicts activity quantitatively. qPISA distinguishes DPP4 from the related C. elegans DPF-3 (a DPP8/9-orthologue), and we relate the differences to the structural features of the two enzymes. We demonstrate that qPISA can direct protein engineering efforts like the stabilization of GLP-1, a key DPP4 substrate used in the treatment of diabetes and obesity. Thus, qPISA offers a versatile approach for profiling protease and especially exopeptidase specificity, facilitating insight into enzyme mechanisms and biotechnological and clinical applications.","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"1303-1328"},"PeriodicalIF":8.5,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11612144/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142522489","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}

引用次数: 0