Juanita Lara-Gutiérrez, Jen Nguyen, Matthew R. McIlvin, Ichiko Sugiyama, Zachary C. Landry, Uria Alcolombri, Sammy Pontrelli, Joaquín Jiménez-Martínez, Uwe Sauer, Terence Hwa, Johannes M. Keegstra, Mak A. Saito, Roman Stocker
In natural environments, bacteria often encounter low concentrations of nutrient mixtures that are continuously replenished by physical processes such as fluid flow. Studying bacterial physiology under such conditions is experimentally challenging because it is difficult to maintain steady, low nutrient concentrations with rapid renewal. Most studies on nutrient limitation have used approaches such as the chemostat, which rely on long renewal times to sustain low concentrations. We developed a Millifluidic Continuous Culture Device (MCCD), inspired by microfluidics, that enables bacterial cultivation in nutrient mixtures at low micromolar concentrations with rapid renewal driven by fluid flow. Unlike microfluidic systems, the MCCD retains sufficient culture volume to support batch-scale ‘omic analyses. Using the MCCD, we cultured Escherichia coli in a mixture of amino acids and nucleobases at three concentration ranges spanning a fivefold difference in growth rates. Surprisingly, at the lowest concentration range, cells exhibited proteomic signatures of iron limitation despite equal total ferrous iron across conditions. Uptake experiments with labeled iron–histidine and iron–cysteine complexes confirmed that amino acids facilitated ferrous iron acquisition. Under continuous flow, siderophores were washed out, rendering this pathway ineffective and revealing a previously unrecognized mechanism of iron acquisition via soluble ferrous iron–amino acid complexes. These findings highlight the importance of studying bacterial physiology at low nutrient concentrations and also suggest a broader role for other organic substrates capable of complexing iron as potential iron sources in environments with rapid renewal.
{"title":"Bacterial iron acquisition by Escherichia coli is facilitated by amino acid complexation in a rapid-renewal environment","authors":"Juanita Lara-Gutiérrez, Jen Nguyen, Matthew R. McIlvin, Ichiko Sugiyama, Zachary C. Landry, Uria Alcolombri, Sammy Pontrelli, Joaquín Jiménez-Martínez, Uwe Sauer, Terence Hwa, Johannes M. Keegstra, Mak A. Saito, Roman Stocker","doi":"10.1073/pnas.2520431123","DOIUrl":"https://doi.org/10.1073/pnas.2520431123","url":null,"abstract":"In natural environments, bacteria often encounter low concentrations of nutrient mixtures that are continuously replenished by physical processes such as fluid flow. Studying bacterial physiology under such conditions is experimentally challenging because it is difficult to maintain steady, low nutrient concentrations with rapid renewal. Most studies on nutrient limitation have used approaches such as the chemostat, which rely on long renewal times to sustain low concentrations. We developed a Millifluidic Continuous Culture Device (MCCD), inspired by microfluidics, that enables bacterial cultivation in nutrient mixtures at low micromolar concentrations with rapid renewal driven by fluid flow. Unlike microfluidic systems, the MCCD retains sufficient culture volume to support batch-scale ‘omic analyses. Using the MCCD, we cultured <jats:italic toggle=\"yes\">Escherichia coli</jats:italic> in a mixture of amino acids and nucleobases at three concentration ranges spanning a fivefold difference in growth rates. Surprisingly, at the lowest concentration range, cells exhibited proteomic signatures of iron limitation despite equal total ferrous iron across conditions. Uptake experiments with labeled iron–histidine and iron–cysteine complexes confirmed that amino acids facilitated ferrous iron acquisition. Under continuous flow, siderophores were washed out, rendering this pathway ineffective and revealing a previously unrecognized mechanism of iron acquisition via soluble ferrous iron–amino acid complexes. These findings highlight the importance of studying bacterial physiology at low nutrient concentrations and also suggest a broader role for other organic substrates capable of complexing iron as potential iron sources in environments with rapid renewal.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"85 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146160984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Feng Li, Abhijith Radhakrishnan, Sudhanshu Gautam, Gabriel Diaz, Ramalingam Venkat Kalyana Sundaram, Jeff Coleman, Hong Zheng, Kirill Grushin, Matthieu Chavent, James E. Rothman, Frederic Pincet
Munc13-1 is a key protein involved in priming synaptic vesicles for rapid release at the presynaptic plasma membrane. It was previously revealed that Munc13-1 cycles between at least two alternate conformations, an upright (open) molecular conformation organized as a trimer and a lateral (closed) conformation organized as a hexagon. Munc13 binds PI(4,5)P 2 , a plasma membrane phospholipid essential for vesicle docking and fusion. We report that Munc13 is recruited to PI(4,5)P 2 domains induced by a Syntaxin-1A juxta-membrane peptide in supported bilayers. Statistical analysis of the copy numbers of Munc13 within the domains suggests that Munc13 exists in clusters of three molecules, i.e., it assembles into trimers. The trimeric clusters disappear with engineered interface mutations disrupting the upright trimers in cryo-EM as well as reconstituted vesicle priming suggesting the trimers observed on bilayers are identical to the upright trimer structures. These upright trimers can also be identified by cryo-electron tomography on vesicles containing PI(4,5)P 2 and Syntaxin-1A. Clusters of 3 or more Munc13 trimers forming on PI(4,5)P 2 domains efficiently capture phosphatidylserine-containing small unilamellar vesicles via their C 2 C domains, as shown by the effect of mutations that disrupt synaptic vesicle binding in synapses. We propose a two-step model for vesicle priming: i) synaptic vesicles are captured by clusters of upright trimers of Munc13 that self-assemble within PI(4,5)P 2 enriched domains; ii) these trimers transition into lateral hexamers when vesicles have bound and the transition would be promoted when the closed conformation of Munc13 is stabilized by diacylglycerol binding, resulting from Ca 2+ -dependent hydrolysis of PI(4,5)P 2 .
{"title":"Synaptic transmission: Munc13 assembles onto PI(4,5)P 2 -rich domains into trimers that cooperate to capture vesicles","authors":"Feng Li, Abhijith Radhakrishnan, Sudhanshu Gautam, Gabriel Diaz, Ramalingam Venkat Kalyana Sundaram, Jeff Coleman, Hong Zheng, Kirill Grushin, Matthieu Chavent, James E. Rothman, Frederic Pincet","doi":"10.1073/pnas.2523347123","DOIUrl":"https://doi.org/10.1073/pnas.2523347123","url":null,"abstract":"Munc13-1 is a key protein involved in priming synaptic vesicles for rapid release at the presynaptic plasma membrane. It was previously revealed that Munc13-1 cycles between at least two alternate conformations, an upright (open) molecular conformation organized as a trimer and a lateral (closed) conformation organized as a hexagon. Munc13 binds PI(4,5)P <jats:sub>2</jats:sub> , a plasma membrane phospholipid essential for vesicle docking and fusion. We report that Munc13 is recruited to PI(4,5)P <jats:sub>2</jats:sub> domains induced by a Syntaxin-1A juxta-membrane peptide in supported bilayers. Statistical analysis of the copy numbers of Munc13 within the domains suggests that Munc13 exists in clusters of three molecules, i.e., it assembles into trimers. The trimeric clusters disappear with engineered interface mutations disrupting the upright trimers in cryo-EM as well as reconstituted vesicle priming suggesting the trimers observed on bilayers are identical to the upright trimer structures. These upright trimers can also be identified by cryo-electron tomography on vesicles containing PI(4,5)P <jats:sub>2</jats:sub> and Syntaxin-1A. Clusters of 3 or more Munc13 trimers forming on PI(4,5)P <jats:sub>2</jats:sub> domains efficiently capture phosphatidylserine-containing small unilamellar vesicles via their C <jats:sub>2</jats:sub> C domains, as shown by the effect of mutations that disrupt synaptic vesicle binding in synapses. We propose a two-step model for vesicle priming: i) synaptic vesicles are captured by clusters of upright trimers of Munc13 that self-assemble within PI(4,5)P <jats:sub>2</jats:sub> enriched domains; ii) these trimers transition into lateral hexamers when vesicles have bound and the transition would be promoted when the closed conformation of Munc13 is stabilized by diacylglycerol binding, resulting from Ca <jats:sup>2+</jats:sup> -dependent hydrolysis of PI(4,5)P <jats:sub>2</jats:sub> .","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"11 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146160955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Zhiwei Li, Yinghong Xu, Wanheng Lu, Xinglong Pan, Langyuan Wu, Wei Li Ong, Netanel Shpigel, Gang Chen, Ghim Wei Ho
Doping to control carrier (electron or hole) transport is foundational to modulate the properties of semiconductors, enabling the development of homojunctions and heterojunctions for integrated electronics. Unlike semiconductors with unipolar charge-carrier dominance, both cations and anions in electrolytes are mobile, which is undesirable for many applications. Here, we report a universal strategy to dope electrolytes such that the ion transport can be unipolar by incorporating electroactive polymers within hydrogels that interact discriminately with one type of ion via redox and binding mechanisms, leaving the counterions mobile. This transforms the system into an active, selective conductor that directs ion flow with high precision. We demonstrate the generality of this strategy using a wide range of electroactive polymers and ions. Particularly, we use emeraldine base and leucoemeraldine base, derived from polyaniline to create both n-type and p-type conductors with high ion selectivity. This electrolyte doping strategy has significant implications beyond the developed thermoelectrochemical devices with boosted performance, with potential applications in supercapacitors, batteries, and electrochemical sensors.
{"title":"Ion transport control in electrolytes via electrochemical doping","authors":"Zhiwei Li, Yinghong Xu, Wanheng Lu, Xinglong Pan, Langyuan Wu, Wei Li Ong, Netanel Shpigel, Gang Chen, Ghim Wei Ho","doi":"10.1073/pnas.2532302123","DOIUrl":"https://doi.org/10.1073/pnas.2532302123","url":null,"abstract":"Doping to control carrier (electron or hole) transport is foundational to modulate the properties of semiconductors, enabling the development of homojunctions and heterojunctions for integrated electronics. Unlike semiconductors with unipolar charge-carrier dominance, both cations and anions in electrolytes are mobile, which is undesirable for many applications. Here, we report a universal strategy to dope electrolytes such that the ion transport can be unipolar by incorporating electroactive polymers within hydrogels that interact discriminately with one type of ion via redox and binding mechanisms, leaving the counterions mobile. This transforms the system into an active, selective conductor that directs ion flow with high precision. We demonstrate the generality of this strategy using a wide range of electroactive polymers and ions. Particularly, we use emeraldine base and leucoemeraldine base, derived from polyaniline to create both n-type and p-type conductors with high ion selectivity. This electrolyte doping strategy has significant implications beyond the developed thermoelectrochemical devices with boosted performance, with potential applications in supercapacitors, batteries, and electrochemical sensors.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"101 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146160981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Liming Lian, Bora Jang, Sebastian G. Huayamares, Avraham Shakked, Kara Gentry, Ryan Zenhausern, Afsane Radmand, Elisa Schrader Echeverri, Vaunita C. Parihar, Ricardo C. Guerrero-Ferreira, Randi Calkins, Daryll Vanover, Philip J. Santangelo, Hyejin Kim, James E. Dahlman
Granulocyte–macrophage colony-stimulating factor (GM-CSF) deficiency drives autoimmune pulmonary alveolar proteinosis (aPAP), a disease characterized by impaired macrophage-mediated clearance of pulmonary surfactants. Clinical data suggest that inhaled recombinant GM-CSF reduces symptoms in aPAP patients, providing a rationale for mRNA-based GM-CSF replacement therapies. However, these require effective mRNA delivery after nebulization. Here, we report the iterative in vivo design of a lipid nanoparticle, named nebulized lung delivery 2 (NLD2), that efficiently delivers mRNA after nebulization. NLD2 carrying GM-CSF mRNA transfected alveolar macrophages in vivo, leading to interleukin-10 pathway activation and subsequent surfactant lipoprotein clearance. In a preclinical disease model of aPAP, GM-CSF mRNA delivery reduced surfactant protein thickness more than recombinant GM-CSF. These data support continued exploration of nebulized lipid nanoparticle therapies for aPAP.
{"title":"Lipid nanoparticle GM-CSF replacement for autoimmune pulmonary alveolar proteinosis","authors":"Liming Lian, Bora Jang, Sebastian G. Huayamares, Avraham Shakked, Kara Gentry, Ryan Zenhausern, Afsane Radmand, Elisa Schrader Echeverri, Vaunita C. Parihar, Ricardo C. Guerrero-Ferreira, Randi Calkins, Daryll Vanover, Philip J. Santangelo, Hyejin Kim, James E. Dahlman","doi":"10.1073/pnas.2511483123","DOIUrl":"https://doi.org/10.1073/pnas.2511483123","url":null,"abstract":"Granulocyte–macrophage colony-stimulating factor (GM-CSF) deficiency drives autoimmune pulmonary alveolar proteinosis (aPAP), a disease characterized by impaired macrophage-mediated clearance of pulmonary surfactants. Clinical data suggest that inhaled recombinant GM-CSF reduces symptoms in aPAP patients, providing a rationale for mRNA-based GM-CSF replacement therapies. However, these require effective mRNA delivery after nebulization. Here, we report the iterative in vivo design of a lipid nanoparticle, named nebulized lung delivery 2 (NLD2), that efficiently delivers mRNA after nebulization. NLD2 carrying GM-CSF mRNA transfected alveolar macrophages in vivo, leading to interleukin-10 pathway activation and subsequent surfactant lipoprotein clearance. In a preclinical disease model of aPAP, GM-CSF mRNA delivery reduced surfactant protein thickness more than recombinant GM-CSF. These data support continued exploration of nebulized lipid nanoparticle therapies for aPAP.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"11 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146160991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sarah Hamada, Jack Beadle, Alice Koenig, Basile Sugranes, John Ferdinand, Chien-Chia Chen, Virginie Mathias, Maeva Eloudzeri, Thomas Barba, Helena Paidassi, Carole Saison, Valérie Dubois, Emmanuel Morelon, Thierry Walzer, Antoine Marcais, Maud Rabeyrin, Marion Rabant, Patrick Bruneval, Maud Racapé, Jean Paul Duong Van Huyen, Menna R. Clatworthy, Candice Roufosse, Olivier Thaunat
The inability of graft endothelial cells to deliver HLA-I-dependent inhibitory signals to recipient natural killer (NK) cells (missing self, MS), drives donor-specific antibody-independent microvascular inflammation (MVI), leading to graft failure. This study aimed to elucidate the signaling pathways involved in MS-associated NK cell activation and explore therapeutic strategies. Analyses of kidney graft biopsies identified calcium signaling pathways and mTOR as a key regulator of MS-induced NK cell activation. Two experimental models were developed to mimic the pathological condition: in vitro cocultures of human NK cells with allogeneic microvascular endothelial cells and a murine heart transplantation model. These models showed that while calcineurin inhibitor (CNI) alone had a limited impact, combining CNI with mTOR inhibitors (mTORinh) synergistically reduced NK cell activation and endothelial damage. In a pilot clinical study involving 50 renal transplant recipients with MS-associated NK cell–mediated microvascular inflammation, patients who tolerated mTORinh introduced on top of CNI at diagnosis demonstrated reduced MVI lesions and improved graft survival compared to a historical cohort left on CNI and mycophenolate mofetil. This translational study identifies mTOR inhibition as a pivotal adjunct to CNI in mitigating MS-associated NK cell–mediated inflammation, potentially improving long-term graft outcomes.
{"title":"Dual inhibition of mTOR and calcineurin pathways mitigates missing self–induced NK cell–mediated microvascular rejection","authors":"Sarah Hamada, Jack Beadle, Alice Koenig, Basile Sugranes, John Ferdinand, Chien-Chia Chen, Virginie Mathias, Maeva Eloudzeri, Thomas Barba, Helena Paidassi, Carole Saison, Valérie Dubois, Emmanuel Morelon, Thierry Walzer, Antoine Marcais, Maud Rabeyrin, Marion Rabant, Patrick Bruneval, Maud Racapé, Jean Paul Duong Van Huyen, Menna R. Clatworthy, Candice Roufosse, Olivier Thaunat","doi":"10.1073/pnas.2516594123","DOIUrl":"https://doi.org/10.1073/pnas.2516594123","url":null,"abstract":"The inability of graft endothelial cells to deliver HLA-I-dependent inhibitory signals to recipient natural killer (NK) cells (missing self, MS), drives donor-specific antibody-independent microvascular inflammation (MVI), leading to graft failure. This study aimed to elucidate the signaling pathways involved in MS-associated NK cell activation and explore therapeutic strategies. Analyses of kidney graft biopsies identified calcium signaling pathways and mTOR as a key regulator of MS-induced NK cell activation. Two experimental models were developed to mimic the pathological condition: in vitro cocultures of human NK cells with allogeneic microvascular endothelial cells and a murine heart transplantation model. These models showed that while calcineurin inhibitor (CNI) alone had a limited impact, combining CNI with mTOR inhibitors (mTORinh) synergistically reduced NK cell activation and endothelial damage. In a pilot clinical study involving 50 renal transplant recipients with MS-associated NK cell–mediated microvascular inflammation, patients who tolerated mTORinh introduced on top of CNI at diagnosis demonstrated reduced MVI lesions and improved graft survival compared to a historical cohort left on CNI and mycophenolate mofetil. This translational study identifies mTOR inhibition as a pivotal adjunct to CNI in mitigating MS-associated NK cell–mediated inflammation, potentially improving long-term graft outcomes.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"4 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146160993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yulong Duan, Suraya Kazi, Dongqing Lin, Longzhu Liu, Magnus P. Jonsson
Plasmonic resonances in nanostructured conducting polymers provide a compelling route to actively tunable nanophotonics and metasurfaces, owing to their ability to be dynamically modulated through electrochemical doping. Although their lower mobility limits resonance quality compared to noble metal plasmonics, we experimentally demonstrate that the resonances of conducting polymer nanoantennas can effectively couple to epsilon-near-zero (ENZ) mode of an underlying thin indium tin oxide layer, in a manner analogous to noble metal plasmon–ENZ interactions. We show that the coupling strength can be modulated reversibly via electrical bias or chemical redox control, enabling dynamic tuning of electromagnetic field enhancement in the ENZ layer with a modulation depth exceeding 90%. These findings establish conducting polymer nanoantennas as a versatile platform for reconfigurable ENZ-based photonic systems, paving the way for nanophotonic devices with tunable linear and nonlinear optical functionalities.
{"title":"Electrotunable coupling between an epsilon-near-zero thin film and conducting polymer nanoantennas","authors":"Yulong Duan, Suraya Kazi, Dongqing Lin, Longzhu Liu, Magnus P. Jonsson","doi":"10.1073/pnas.2517549123","DOIUrl":"https://doi.org/10.1073/pnas.2517549123","url":null,"abstract":"Plasmonic resonances in nanostructured conducting polymers provide a compelling route to actively tunable nanophotonics and metasurfaces, owing to their ability to be dynamically modulated through electrochemical doping. Although their lower mobility limits resonance quality compared to noble metal plasmonics, we experimentally demonstrate that the resonances of conducting polymer nanoantennas can effectively couple to epsilon-near-zero (ENZ) mode of an underlying thin indium tin oxide layer, in a manner analogous to noble metal plasmon–ENZ interactions. We show that the coupling strength can be modulated reversibly via electrical bias or chemical redox control, enabling dynamic tuning of electromagnetic field enhancement in the ENZ layer with a modulation depth exceeding 90%. These findings establish conducting polymer nanoantennas as a versatile platform for reconfigurable ENZ-based photonic systems, paving the way for nanophotonic devices with tunable linear and nonlinear optical functionalities.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"113 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146161083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sung Chul Park, Livia D. S. Oster, Jacob Golan, Jillian Myers, Anne Pringle, Milton T. Drott, Nancy P. Keller
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are secondary metabolites produced by bacteria, plants, animals, and fungi. Canonical fungal RiPP precursors possess a leader sequence cleaved during maturation. The first RiPPs described in fungi were the MSDIN-derived peptides responsible for the toxicity of lethal Amanita mushrooms. In this study, we upend the conventional understanding of fungal RiPPs, discovering a subclass that has diversified and lacks a leader sequence, an empirical example of leaderless RiPPs in fungi. We use a combinatorial analysis of NMR and MS/MS with an updated bioinformatic pipeline to pair MSDIN genes to leaderless peptides in Amanita phalloides , a European species spreading in California. Leaderless MSDIN transcripts are expressed several orders of magnitude more than most canonical MSDINs, with significantly higher expression in invasive populations. Our results redefine the understanding of fungal RiPP architectures and suggest differential regulation of non-canonical RiPPs may contribute to the invasion biology of the world’s deadliest mushroom.
{"title":"Leaderless RiPPs expand the repertoire of fungal secondary metabolites","authors":"Sung Chul Park, Livia D. S. Oster, Jacob Golan, Jillian Myers, Anne Pringle, Milton T. Drott, Nancy P. Keller","doi":"10.1073/pnas.2529748123","DOIUrl":"https://doi.org/10.1073/pnas.2529748123","url":null,"abstract":"Ribosomally synthesized and post-translationally modified peptides (RiPPs) are secondary metabolites produced by bacteria, plants, animals, and fungi. Canonical fungal RiPP precursors possess a leader sequence cleaved during maturation. The first RiPPs described in fungi were the MSDIN-derived peptides responsible for the toxicity of lethal <jats:italic toggle=\"yes\">Amanita</jats:italic> mushrooms. In this study, we upend the conventional understanding of fungal RiPPs, discovering a subclass that has diversified and lacks a leader sequence, an empirical example of leaderless RiPPs in fungi. We use a combinatorial analysis of NMR and MS/MS with an updated bioinformatic pipeline to pair MSDIN genes to leaderless peptides in <jats:italic toggle=\"yes\">Amanita phalloides</jats:italic> , a European species spreading in California. Leaderless MSDIN transcripts are expressed several orders of magnitude more than most canonical MSDINs, with significantly higher expression in invasive populations. Our results redefine the understanding of fungal RiPP architectures and suggest differential regulation of non-canonical RiPPs may contribute to the invasion biology of the world’s deadliest mushroom.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"33 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146160982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are a fertile ground for uncovering new enzymatic chemistry and structural complexity. Here, we describe minviopeptin, an unusual ADP-ribosylated triceptide accessed through heterologous expression of a cryptic biosynthetic gene cluster. Structural and functional analyses reveal a combination of crosslinking, ADP-ribosylation, and oxidative peptide cleavage, underscoring the capacity of RiPP pathways to generate densely functionalized molecular scaffolds. By revealing ADP-ribosylation as a previously unrecognized RiPP modification and exposing reactivity within radical SAM and nonheme iron enzymes, this work broadens the landscape of RiPP biosynthetic chemistries and offers opportunities for natural product diversification and peptide engineering.
{"title":"A ribosomally synthesized and posttranslationally modified peptide with ADP-ribosylation","authors":"Sijia Guo, Suze Ma, Lulu Song, Jun Wang, Tonghai Liu, Wupeng Yan, Wei Zhang, Zixin Deng, Wei Ding, Qi Zhang","doi":"10.1073/pnas.2527653123","DOIUrl":"https://doi.org/10.1073/pnas.2527653123","url":null,"abstract":"Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are a fertile ground for uncovering new enzymatic chemistry and structural complexity. Here, we describe minviopeptin, an unusual ADP-ribosylated triceptide accessed through heterologous expression of a cryptic biosynthetic gene cluster. Structural and functional analyses reveal a combination of crosslinking, ADP-ribosylation, and oxidative peptide cleavage, underscoring the capacity of RiPP pathways to generate densely functionalized molecular scaffolds. By revealing ADP-ribosylation as a previously unrecognized RiPP modification and exposing reactivity within radical SAM and nonheme iron enzymes, this work broadens the landscape of RiPP biosynthetic chemistries and offers opportunities for natural product diversification and peptide engineering.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"242 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146160980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Changyuan Wang, Denis F. Faerberg, Yuka Sekine, Takeaki Ozawa, John J. Tyson, Robert A. Marmion, Stanislav Y. Shvartsman
System identification approaches are commonly used in engineering to infer simple yet predictive models of complex systems from their responses to time-dependent perturbations. Here, we apply this strategy at the whole organism scale, establishing a predictive model of commitment to metamorphosis in Drosophila . At this critical point in animal development, the larva stops feeding and proceeds to take on the adult form. The neuroendocrine circuits governing commitment to metamorphosis assess the growth and patterning programs, eventually triggering the production of systemic hormones that terminate growth and initiate metamorphosis. Previous studies of these circuits relied on relatively static genetic perturbations and starvation experiments. Here, we take advantage of optogenetic approaches in Drosophila to flexibly perturb a key signaling node within the endocrine gland in otherwise undisturbed larvae. We used this approach to infer parameters in a compact mathematical model and demonstrate that it makes accurate predictions of larval commitment to metamorphosis. Our work paves the way for quantitative studies of other juvenile-to-adult transitions, including mammalian puberty, which relies on strikingly similar mechanisms.
{"title":"Optogenetic control of transition to metamorphosis","authors":"Changyuan Wang, Denis F. Faerberg, Yuka Sekine, Takeaki Ozawa, John J. Tyson, Robert A. Marmion, Stanislav Y. Shvartsman","doi":"10.1073/pnas.2524141123","DOIUrl":"https://doi.org/10.1073/pnas.2524141123","url":null,"abstract":"System identification approaches are commonly used in engineering to infer simple yet predictive models of complex systems from their responses to time-dependent perturbations. Here, we apply this strategy at the whole organism scale, establishing a predictive model of commitment to metamorphosis in <jats:italic toggle=\"yes\">Drosophila</jats:italic> . At this critical point in animal development, the larva stops feeding and proceeds to take on the adult form. The neuroendocrine circuits governing commitment to metamorphosis assess the growth and patterning programs, eventually triggering the production of systemic hormones that terminate growth and initiate metamorphosis. Previous studies of these circuits relied on relatively static genetic perturbations and starvation experiments. Here, we take advantage of optogenetic approaches in <jats:italic toggle=\"yes\">Drosophila</jats:italic> to flexibly perturb a key signaling node within the endocrine gland in otherwise undisturbed larvae. We used this approach to infer parameters in a compact mathematical model and demonstrate that it makes accurate predictions of larval commitment to metamorphosis. Our work paves the way for quantitative studies of other juvenile-to-adult transitions, including mammalian puberty, which relies on strikingly similar mechanisms.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"91 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146160978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-10Epub Date: 2025-02-10DOI: 10.1073/iti0626123
{"title":"In This Issue.","authors":"","doi":"10.1073/iti0626123","DOIUrl":"https://doi.org/10.1073/iti0626123","url":null,"abstract":"","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 6","pages":"eiti0626123"},"PeriodicalIF":9.1,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146150527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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