The file drawer problem—often operationalized in terms of statistically significant results being published and statistically insignificant not being published—is widely documented in the social sciences. We extend Franco’s et al. [ Science 345 , 1502–1505(2014)] seminal study of the file drawer problem in survey experiments submitted to the Time-sharing Experiments for the Social Sciences (TESS) data collection program. We examine projects begun after Franco et al. The updated period coincides with the contemporary open science movement. We find evidence of the problem, stemming from scholars opting to not write up insignificant results. However, that tendency is substantially smaller than it was in the prior decade. This suggests increased recognition of the importance of null results, even if the problem remains in the domain of survey experiments.
{"title":"The file drawer problem in social science survey experiments","authors":"Philip Moniz, James N. Druckman, Jeremy Freese","doi":"10.1073/pnas.2426937122","DOIUrl":"https://doi.org/10.1073/pnas.2426937122","url":null,"abstract":"The file drawer problem—often operationalized in terms of statistically significant results being published and statistically insignificant not being published—is widely documented in the social sciences. We extend Franco’s et al. [ <jats:italic>Science</jats:italic> 345 , 1502–1505(2014)] seminal study of the file drawer problem in survey experiments submitted to the Time-sharing Experiments for the Social Sciences (TESS) data collection program. We examine projects begun after Franco et al. The updated period coincides with the contemporary open science movement. We find evidence of the problem, stemming from scholars opting to not write up insignificant results. However, that tendency is substantially smaller than it was in the prior decade. This suggests increased recognition of the importance of null results, even if the problem remains in the domain of survey experiments.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"92 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661220","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}
Jian Zhou, Richard Huang, Nicolaie Moldovan, Liliana Stan, Jianguo Wen, Dafei Jin, David R. Nelson, Andrej Košmrlj, David A. Czaplewski, Daniel López
Thermally induced ripples are intrinsic features of nanometer-thick films, atomically thin materials, and cell membranes, significantly affecting their elastic properties. Despite decades of theoretical studies on the mechanics of suspended thermalized sheets, controversy still exists over the impact of these ripples, with conflicting predictions about whether elasticity is scale-dependent or scale-independent. Experimental progress has been hindered so far by the inability to have a platform capable of fully isolating and characterizing the effects of ripples. This knowledge gap limits the fundamental understanding of thin materials and their practical applications. Here, we show that thermal-like static ripples shape thin films into a class of metamaterials with scale-dependent, customizable elasticity. Utilizing a scalable semiconductor manufacturing process, we engineered nanometer-thick films with precisely controlled frozen random ripples, resembling snapshots of thermally fluctuating membranes. Resonant frequency measurements of rippled cantilevers reveal that random ripples effectively renormalize and enhance the average bending rigidity and sample-to-sample variations in a scale-dependent manner, consistent with recent theoretical estimations. The predictive power of the theoretical model, combined with the scalability of the fabrication process, was further exploited to create kirigami architectures with tailored bending rigidity and mechanical metamaterials with delayed buckling instability.
{"title":"Rippled metamaterials with scale-dependent tailorable elasticity","authors":"Jian Zhou, Richard Huang, Nicolaie Moldovan, Liliana Stan, Jianguo Wen, Dafei Jin, David R. Nelson, Andrej Košmrlj, David A. Czaplewski, Daniel López","doi":"10.1073/pnas.2425200122","DOIUrl":"https://doi.org/10.1073/pnas.2425200122","url":null,"abstract":"Thermally induced ripples are intrinsic features of nanometer-thick films, atomically thin materials, and cell membranes, significantly affecting their elastic properties. Despite decades of theoretical studies on the mechanics of suspended thermalized sheets, controversy still exists over the impact of these ripples, with conflicting predictions about whether elasticity is scale-dependent or scale-independent. Experimental progress has been hindered so far by the inability to have a platform capable of fully isolating and characterizing the effects of ripples. This knowledge gap limits the fundamental understanding of thin materials and their practical applications. Here, we show that thermal-like static ripples shape thin films into a class of metamaterials with scale-dependent, customizable elasticity. Utilizing a scalable semiconductor manufacturing process, we engineered nanometer-thick films with precisely controlled frozen random ripples, resembling snapshots of thermally fluctuating membranes. Resonant frequency measurements of rippled cantilevers reveal that random ripples effectively renormalize and enhance the average bending rigidity and sample-to-sample variations in a scale-dependent manner, consistent with recent theoretical estimations. The predictive power of the theoretical model, combined with the scalability of the fabrication process, was further exploited to create kirigami architectures with tailored bending rigidity and mechanical metamaterials with delayed buckling instability.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"201 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661479","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}
Sajina Dhungel, Michael Xiao, Rajesh Rajaian Pushpabai, Chintan K. Kikani
PAS domains are ubiquitous sensory modules that transduce environmental signals into cellular responses through tandem PAS folds and PAS-associated C-terminal (PAC) motifs. While this conserved architecture underpins their regulatory roles, here we uncover a structural divergence in the metazoan PAS domain–regulated kinase (PASK). By integrating evolutionary-scale domain mapping with deep learning-based structural models, we identified two PAS domains in PASK, namely PAS-B and PAS-C, in addition to the previously known PAS-A domain. Unlike canonical PAS domains, the PAS fold and PAC motif in the PAS-C domain are spatially segregated by an unstructured linker, yet a functional PAS module is assembled through intramolecular interactions. We demonstrate that this assembly is nutrient responsive and serves to remodel the quaternary structure of PASK that positions the PAS-A domain near the kinase activation loop. This nutrient-sensitive spatial arrangement stabilizes the activation loop, enabling catalytic activation of PASK. These findings revealed an alternative mode of regulatory control in PAS sensory proteins, where the structural assembly of PAS domains links environmental sensing to enzymatic activity. By demonstrating that PAS domains integrate signals through dynamic structural rearrangements, this study broadens the understanding of their functional and regulatory roles and highlights potential opportunities for targeting PAS domain–mediated pathways in therapeutic applications.
{"title":"Structural assembly of the PAS domain drives the catalytic activation of metazoan PASK","authors":"Sajina Dhungel, Michael Xiao, Rajesh Rajaian Pushpabai, Chintan K. Kikani","doi":"10.1073/pnas.2409685122","DOIUrl":"https://doi.org/10.1073/pnas.2409685122","url":null,"abstract":"PAS domains are ubiquitous sensory modules that transduce environmental signals into cellular responses through tandem PAS folds and PAS-associated C-terminal (PAC) motifs. While this conserved architecture underpins their regulatory roles, here we uncover a structural divergence in the metazoan PAS domain–regulated kinase (PASK). By integrating evolutionary-scale domain mapping with deep learning-based structural models, we identified two PAS domains in PASK, namely PAS-B and PAS-C, in addition to the previously known PAS-A domain. Unlike canonical PAS domains, the PAS fold and PAC motif in the PAS-C domain are spatially segregated by an unstructured linker, yet a functional PAS module is assembled through intramolecular interactions. We demonstrate that this assembly is nutrient responsive and serves to remodel the quaternary structure of PASK that positions the PAS-A domain near the kinase activation loop. This nutrient-sensitive spatial arrangement stabilizes the activation loop, enabling catalytic activation of PASK. These findings revealed an alternative mode of regulatory control in PAS sensory proteins, where the structural assembly of PAS domains links environmental sensing to enzymatic activity. By demonstrating that PAS domains integrate signals through dynamic structural rearrangements, this study broadens the understanding of their functional and regulatory roles and highlights potential opportunities for targeting PAS domain–mediated pathways in therapeutic applications.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"214 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661478","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}
Yuichiro Suzuki, Stephanie Amaya, Paula Gonzalez, Daniela Becerril, Surisadai Aquit, Maya Davis, Madeline Hoesel, Elizabeth Chou, Hesper Khong, Kathryn Zaia, Heidi S. Park, H. Frederik Nijhout, Brian Tjaden
How organisms evolve under extreme environmental changes is a critical question in the face of global climate change. Genetic accommodation is an evolutionary process by which natural selection acts on novel phenotypes generated through repeated encounters with extreme environments. In this study, polyphenic and monophenic strains of the black mutant tobacco hornworm, Manduca sexta , were evolved via genetic accommodation of heat stress-induced phenotypes, and the molecular differences between the two strains were explored. Transcriptomic analyses showed that epigenetic and hormonal differences underlie the differences between the two strains and their distinct responses to temperature. DNA methylation had diverged between the two strains potentially mediating genetic assimilation. Juvenile hormone (JH) signaling in the polyphenic strain was temperature sensitive, whereas in the monophenic strain, JH signaling remained low at all temperatures. Although 20-hydroxyecdysone titers were elevated under heat shock conditions in both strains, the strains did not differ in the titers. Tyrosine hydroxylase was also found to differ between the two strains at different temperatures, and its expression could be modulated by topical application of a JH analog. Finally, heat shock of unselected black mutants demonstrated that the expression of the JH-response gene, Krüppel-homolog 1 ( Kr-h1 ), increased within the first 30 min of heat shock, suggesting that JH levels respond readily to thermal stress. Our study highlights the critical role that hormones and epigenetics play during genetic accommodation and potentially in the evolution of populations in the face of climate change.
{"title":"Molecular mechanisms underlying the evolution of a color polyphenism by genetic accommodation in the tobacco hornworm, Manduca sexta","authors":"Yuichiro Suzuki, Stephanie Amaya, Paula Gonzalez, Daniela Becerril, Surisadai Aquit, Maya Davis, Madeline Hoesel, Elizabeth Chou, Hesper Khong, Kathryn Zaia, Heidi S. Park, H. Frederik Nijhout, Brian Tjaden","doi":"10.1073/pnas.2425004122","DOIUrl":"https://doi.org/10.1073/pnas.2425004122","url":null,"abstract":"How organisms evolve under extreme environmental changes is a critical question in the face of global climate change. Genetic accommodation is an evolutionary process by which natural selection acts on novel phenotypes generated through repeated encounters with extreme environments. In this study, polyphenic and monophenic strains of the <jats:italic>black</jats:italic> mutant tobacco hornworm, <jats:italic>Manduca sexta</jats:italic> , were evolved via genetic accommodation of heat stress-induced phenotypes, and the molecular differences between the two strains were explored. Transcriptomic analyses showed that epigenetic and hormonal differences underlie the differences between the two strains and their distinct responses to temperature. DNA methylation had diverged between the two strains potentially mediating genetic assimilation. Juvenile hormone (JH) signaling in the polyphenic strain was temperature sensitive, whereas in the monophenic strain, JH signaling remained low at all temperatures. Although 20-hydroxyecdysone titers were elevated under heat shock conditions in both strains, the strains did not differ in the titers. Tyrosine hydroxylase was also found to differ between the two strains at different temperatures, and its expression could be modulated by topical application of a JH analog. Finally, heat shock of unselected <jats:italic>black</jats:italic> mutants demonstrated that the expression of the JH-response gene, <jats:italic>Krüppel-homolog 1</jats:italic> ( <jats:italic>Kr-h1</jats:italic> ), increased within the first 30 min of heat shock, suggesting that JH levels respond readily to thermal stress. Our study highlights the critical role that hormones and epigenetics play during genetic accommodation and potentially in the evolution of populations in the face of climate change.","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":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661135","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}
Josseline Ramos-Figueroa, Haoqian Liang, Wilfred A. van der Donk
The continuing discovery of new peptide-aminoacyl-tRNA ligases (PEARLs) has unveiled a diverse array of enzymes with the unique potential to append amino acids to the C terminus of substrate peptides in an aminoacyl-tRNA-dependent manner. To date, PEARLs have been reported that can conjugate Cys, Ala, Trp, Gly, Leu, Asn, and Thr residues, but the basis of peptide substrate and aminoacyl-tRNA recognition is not known. Cell-free expression (CFE) has emerged as a powerful tool to rapidly assay activity of substrate variants, and we used the technique in this study to investigate the peptide substrate specificity of the PEARL <jats:inline-formula> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" overflow="scroll"> <mml:msubsup> <mml:mrow> <mml:mi mathvariant="normal">B</mml:mi> <mml:mi mathvariant="normal">h</mml:mi> <mml:mi mathvariant="normal">a</mml:mi> <mml:mi mathvariant="normal">B</mml:mi> </mml:mrow> <mml:mrow> <mml:mi mathvariant="normal">C</mml:mi> </mml:mrow> <mml:mrow> <mml:mi mathvariant="normal">T</mml:mi> <mml:mi mathvariant="normal">r</mml:mi> <mml:mi mathvariant="normal">p</mml:mi> </mml:mrow> </mml:msubsup> </mml:math> </jats:inline-formula> . This enzyme that adds Trp was discovered previously during genome mining for ribosomally synthesized and posttranslational modified peptides (RiPPs). The enzyme is remarkably tolerant of changes to the C-terminal amino acid of the peptide substrate, and truncation and replacement experiments suggest a minimal sequence requirement. An AlphaFold3 model provided insights into binding interactions of the substrate peptide BhaA-Ala to <jats:inline-formula> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" overflow="scroll"> <mml:msubsup> <mml:mrow> <mml:mi mathvariant="normal">B</mml:mi> <mml:mi mathvariant="normal">h</mml:mi> <mml:mi mathvariant="normal">a</mml:mi> <mml:mi mathvariant="normal">B</mml:mi> </mml:mrow> <mml:mrow> <mml:mi mathvariant="normal">C</mml:mi> </mml:mrow> <mml:mrow> <mml:mi mathvariant="normal">T</mml:mi> <mml:mi mathvariant="normal">r</mml:mi> <mml:mi mathvariant="normal">p</mml:mi> </mml:mrow> </mml:msubsup> </mml:math> </jats:inline-formula> and also generated predictions for tRNA, ATP, and Mg <jats:sup>2+</jats:sup> binding modes that were tested by site-directed mutagenesis. The data suggest that several highly conserved residues in PEARLs recognize the 3′-CCA sequence present in all tRNAs. The minimal sequence required for Trp incorporation by <jats:inline-formula> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" overflow="scroll"> <mml:msubsup> <mml:mrow> <mml:mi mathvariant="normal">B</mml:mi> <mml:mi mathvariant="normal">h</mml:mi> <mml:mi mathvariant="normal">a</mml:mi> <mml:mi mathvariant="normal">B</mml:mi> </mml:mrow> <mml:mrow> <mml:mi mathvariant="normal">C</mml:mi> </mml:mrow> <mml:mrow> <mml:mi mathvariant="normal">T</mml:mi> <mml:mi mathvariant="normal">r</mml:mi> <mml:mi mathvariant="
{"title":"Substrate recognition by a peptide-aminoacyl-tRNA ligase","authors":"Josseline Ramos-Figueroa, Haoqian Liang, Wilfred A. van der Donk","doi":"10.1073/pnas.2423858122","DOIUrl":"https://doi.org/10.1073/pnas.2423858122","url":null,"abstract":"The continuing discovery of new peptide-aminoacyl-tRNA ligases (PEARLs) has unveiled a diverse array of enzymes with the unique potential to append amino acids to the C terminus of substrate peptides in an aminoacyl-tRNA-dependent manner. To date, PEARLs have been reported that can conjugate Cys, Ala, Trp, Gly, Leu, Asn, and Thr residues, but the basis of peptide substrate and aminoacyl-tRNA recognition is not known. Cell-free expression (CFE) has emerged as a powerful tool to rapidly assay activity of substrate variants, and we used the technique in this study to investigate the peptide substrate specificity of the PEARL <jats:inline-formula> <mml:math xmlns:mml=\"http://www.w3.org/1998/Math/MathML\" display=\"inline\" overflow=\"scroll\"> <mml:msubsup> <mml:mrow> <mml:mi mathvariant=\"normal\">B</mml:mi> <mml:mi mathvariant=\"normal\">h</mml:mi> <mml:mi mathvariant=\"normal\">a</mml:mi> <mml:mi mathvariant=\"normal\">B</mml:mi> </mml:mrow> <mml:mrow> <mml:mi mathvariant=\"normal\">C</mml:mi> </mml:mrow> <mml:mrow> <mml:mi mathvariant=\"normal\">T</mml:mi> <mml:mi mathvariant=\"normal\">r</mml:mi> <mml:mi mathvariant=\"normal\">p</mml:mi> </mml:mrow> </mml:msubsup> </mml:math> </jats:inline-formula> . This enzyme that adds Trp was discovered previously during genome mining for ribosomally synthesized and posttranslational modified peptides (RiPPs). The enzyme is remarkably tolerant of changes to the C-terminal amino acid of the peptide substrate, and truncation and replacement experiments suggest a minimal sequence requirement. An AlphaFold3 model provided insights into binding interactions of the substrate peptide BhaA-Ala to <jats:inline-formula> <mml:math xmlns:mml=\"http://www.w3.org/1998/Math/MathML\" display=\"inline\" overflow=\"scroll\"> <mml:msubsup> <mml:mrow> <mml:mi mathvariant=\"normal\">B</mml:mi> <mml:mi mathvariant=\"normal\">h</mml:mi> <mml:mi mathvariant=\"normal\">a</mml:mi> <mml:mi mathvariant=\"normal\">B</mml:mi> </mml:mrow> <mml:mrow> <mml:mi mathvariant=\"normal\">C</mml:mi> </mml:mrow> <mml:mrow> <mml:mi mathvariant=\"normal\">T</mml:mi> <mml:mi mathvariant=\"normal\">r</mml:mi> <mml:mi mathvariant=\"normal\">p</mml:mi> </mml:mrow> </mml:msubsup> </mml:math> </jats:inline-formula> and also generated predictions for tRNA, ATP, and Mg <jats:sup>2+</jats:sup> binding modes that were tested by site-directed mutagenesis. The data suggest that several highly conserved residues in PEARLs recognize the 3′-CCA sequence present in all tRNAs. The minimal sequence required for Trp incorporation by <jats:inline-formula> <mml:math xmlns:mml=\"http://www.w3.org/1998/Math/MathML\" display=\"inline\" overflow=\"scroll\"> <mml:msubsup> <mml:mrow> <mml:mi mathvariant=\"normal\">B</mml:mi> <mml:mi mathvariant=\"normal\">h</mml:mi> <mml:mi mathvariant=\"normal\">a</mml:mi> <mml:mi mathvariant=\"normal\">B</mml:mi> </mml:mrow> <mml:mrow> <mml:mi mathvariant=\"normal\">C</mml:mi> </mml:mrow> <mml:mrow> <mml:mi mathvariant=\"normal\">T</mml:mi> <mml:mi mathvariant=\"normal\">r</mml:mi> <mml:mi mathvariant=\"","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"47 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661473","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}
Sexual dimorphism in immune responses is well documented, but the underlying mechanisms remain incompletely understood. Here, we identified a subset of corticotropin-releasing hormone (CRH) neurons that express androgen receptors (ARs) as key mediators of sex differences in restraint-induced immunosuppression. Mechanistically, androgens directly activate AR-positive CRH neurons, enhancing the hypothalamic–pituitary–adrenal axis activation. This results in elevated corticosterone levels in response to restraint stress, leading to increased immune cell apoptosis and immune organ atrophy in male mice. Conditional knockout of ARs in CRH neurons eliminated this sexual dimorphism, highlighting ARs in CRH neurons as pivotal regulators of sex-specific immune responses to stress.
{"title":"Androgen receptors in corticotropin-releasing hormone neurons mediate the sexual dimorphism in restraint-induced thymic atrophy","authors":"Yutong Meng, Yaning Li, Huating Gu, Ziyao Chen, Xiaoyang Cui, Xiaodong Wang","doi":"10.1073/pnas.2426107122","DOIUrl":"https://doi.org/10.1073/pnas.2426107122","url":null,"abstract":"Sexual dimorphism in immune responses is well documented, but the underlying mechanisms remain incompletely understood. Here, we identified a subset of corticotropin-releasing hormone (CRH) neurons that express androgen receptors (ARs) as key mediators of sex differences in restraint-induced immunosuppression. Mechanistically, androgens directly activate AR-positive CRH neurons, enhancing the hypothalamic–pituitary–adrenal axis activation. This results in elevated corticosterone levels in response to restraint stress, leading to increased immune cell apoptosis and immune organ atrophy in male mice. Conditional knockout of ARs in CRH neurons eliminated this sexual dimorphism, highlighting ARs in CRH neurons as pivotal regulators of sex-specific immune responses to stress.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"40 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661475","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}
Ryosuke Yamamoto, Yui Sahashi, Rieko Shimo-Kon, Miho Sakato-Antoku, Miyuka Suzuki, Leo Luo, Hideaki Tanaka, Takashi Ishikawa, Toshiki Yagi, Stephen M. King, Genji Kurisu, Takahide Kon
Motile cilia are organelles found on many eukaryotic cells that play critical roles in development and fertility. Human CFAP298 has been implicated in the transport/assembly of ciliary dyneins, and defects in this protein cause primary ciliary dyskinesia. However, neither the exact function nor the structure of CFAP298 have been elucidated. Here, we took advantage of Chlamydomonas , a ciliated alga, to study the structure and function of FBB18, an ortholog of CFAP298. Multiple ciliary dyneins were greatly reduced in cilia of Chlamydomonas fbb18 mutants. In addition, we found that both the stability of ciliary dynein heavy chains (HCs) and the association between HCs and intermediate/light chains (IC/LCs) are greatly reduced in fbb18 cytoplasm, strongly suggesting that FBB18 functions in the cytoplasmic assembly (the so-called “preassembly”) of dynein complexes from HC/IC/LCs. Furthermore, X-ray crystallography revealed that FBB18 forms a bilobed structure with globular domains at both ends of the molecule, connected by an α-helical bundle. Unexpectedly, one globular domain shows high similarity to ubiquitin, a small protein critical for the modification of a variety of protein complexes, and this ubiquitin-like domain is indispensable for the molecular function of FBB18. Our results demonstrate that FBB18, a specialized member of the ubiquitin-like protein family, plays a critical role in dynein preassembly, most likely by mediating diverse interactions between dynein HCs, molecular chaperone(s), and other preassembly factor(s) using the ubiquitin-like domain as well as other regions, and by facilitating the proper folding of dynein HCs.
{"title":"Chlamydomonas FBB18 is a ubiquitin-like protein essential for the cytoplasmic preassembly of various ciliary dyneins","authors":"Ryosuke Yamamoto, Yui Sahashi, Rieko Shimo-Kon, Miho Sakato-Antoku, Miyuka Suzuki, Leo Luo, Hideaki Tanaka, Takashi Ishikawa, Toshiki Yagi, Stephen M. King, Genji Kurisu, Takahide Kon","doi":"10.1073/pnas.2423948122","DOIUrl":"https://doi.org/10.1073/pnas.2423948122","url":null,"abstract":"Motile cilia are organelles found on many eukaryotic cells that play critical roles in development and fertility. Human CFAP298 has been implicated in the transport/assembly of ciliary dyneins, and defects in this protein cause primary ciliary dyskinesia. However, neither the exact function nor the structure of CFAP298 have been elucidated. Here, we took advantage of <jats:italic>Chlamydomonas</jats:italic> , a ciliated alga, to study the structure and function of FBB18, an ortholog of CFAP298. Multiple ciliary dyneins were greatly reduced in cilia of <jats:italic>Chlamydomonas fbb18</jats:italic> mutants. In addition, we found that both the stability of ciliary dynein heavy chains (HCs) and the association between HCs and intermediate/light chains (IC/LCs) are greatly reduced in <jats:italic>fbb18</jats:italic> cytoplasm, strongly suggesting that FBB18 functions in the cytoplasmic assembly (the so-called “preassembly”) of dynein complexes from HC/IC/LCs. Furthermore, X-ray crystallography revealed that FBB18 forms a bilobed structure with globular domains at both ends of the molecule, connected by an α-helical bundle. Unexpectedly, one globular domain shows high similarity to ubiquitin, a small protein critical for the modification of a variety of protein complexes, and this ubiquitin-like domain is indispensable for the molecular function of FBB18. Our results demonstrate that FBB18, a specialized member of the ubiquitin-like protein family, plays a critical role in dynein preassembly, most likely by mediating diverse interactions between dynein HCs, molecular chaperone(s), and other preassembly factor(s) using the ubiquitin-like domain as well as other regions, and by facilitating the proper folding of dynein HCs.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"88 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661474","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}
Tian-Chen Zhu, Zhang-Ping He, Shu-Ting Li, Lin Zheng, Xue-Yi Zheng, Xia-Lu Lan, Chun-Hua Qu, Run-Cong Nie, Chao Gu, Li-Ning Huang, Xiao-Xia Cai, Zhi-Cheng Xiang, Dan Xie, Mu-Yan Cai
Poly-ADP-ribose polymerase (PARP) inhibitors are vital therapeutic agents that exploit synthetic lethality, particularly effective in tumors with homologous recombination (HR) defects. However, broadening their clinical utility remains a significant challenge. In this study, we conducted a high-throughput kinase inhibitor screen to identify potential targets exhibiting synthetical lethality with PARP inhibitors. Our results show that thousand and one amino acid protein kinase 1 (TAOK1) plays a pivotal role in the DNA damage response by phosphorylating ubiquitin specific peptidase 7 (USP7), thereby promoting its enzymatic activity and preventing the ubiquitylation and subsequent degradation of RAD51, a crucial protein in the filament formation of HR repair. Notably, genetic depletion or pharmacological inhibition of TAOK1, as well as blocking peptide targeting the USP7 phosphorylation site, impaired USP7 function, leading to RAD51 degradation, disruption of HR repair, and increased tumor cell and sensitivity to PARP inhibition. This study highlights TAOK1 as a critical regulator of HR repair pathway in human cancer cells and presents a therapeutic strategy overcoming resistance to PARPi inhibitors. These findings support the potential clinical application of combining PARP inhibitors with TAOK1 inhibition or peptide treatment to improve therapeutic outcomes.
{"title":"TAOK1 promotes filament formation in HR repair through phosphorylating USP7","authors":"Tian-Chen Zhu, Zhang-Ping He, Shu-Ting Li, Lin Zheng, Xue-Yi Zheng, Xia-Lu Lan, Chun-Hua Qu, Run-Cong Nie, Chao Gu, Li-Ning Huang, Xiao-Xia Cai, Zhi-Cheng Xiang, Dan Xie, Mu-Yan Cai","doi":"10.1073/pnas.2422262122","DOIUrl":"https://doi.org/10.1073/pnas.2422262122","url":null,"abstract":"Poly-ADP-ribose polymerase (PARP) inhibitors are vital therapeutic agents that exploit synthetic lethality, particularly effective in tumors with homologous recombination (HR) defects. However, broadening their clinical utility remains a significant challenge. In this study, we conducted a high-throughput kinase inhibitor screen to identify potential targets exhibiting synthetical lethality with PARP inhibitors. Our results show that thousand and one amino acid protein kinase 1 (TAOK1) plays a pivotal role in the DNA damage response by phosphorylating ubiquitin specific peptidase 7 (USP7), thereby promoting its enzymatic activity and preventing the ubiquitylation and subsequent degradation of RAD51, a crucial protein in the filament formation of HR repair. Notably, genetic depletion or pharmacological inhibition of TAOK1, as well as blocking peptide targeting the USP7 phosphorylation site, impaired USP7 function, leading to RAD51 degradation, disruption of HR repair, and increased tumor cell and sensitivity to PARP inhibition. This study highlights TAOK1 as a critical regulator of HR repair pathway in human cancer cells and presents a therapeutic strategy overcoming resistance to PARPi inhibitors. These findings support the potential clinical application of combining PARP inhibitors with TAOK1 inhibition or peptide treatment to improve therapeutic outcomes.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"19 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661476","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}
Stefanie Muroya, Krishnendu Chatterjee, Thomas A. Henzinger
Quantum hardware is inherently fragile and noisy. We find that the accuracy of traditional quantum error correction algorithms can be improved depending on the hardware. Given different hardware specifications, we automatically synthesize hardware-optimal algorithms for parity correction, qubit resetting, and GHZ (Greenberger–Horne–Zeilinger) state preparation. Using stochastic techniques from computer science, our method presents a computational tool to compute exact accuracy guarantees and synthesize optimal algorithms that are often different from traditional ones. We also show that improvements can be gained with respect to the Qiskit transpiler as we compute the hardware-optimal qubit mapping for the GHZ state-preparation problem.
{"title":"Hardware-optimal quantum algorithms","authors":"Stefanie Muroya, Krishnendu Chatterjee, Thomas A. Henzinger","doi":"10.1073/pnas.2419273122","DOIUrl":"https://doi.org/10.1073/pnas.2419273122","url":null,"abstract":"Quantum hardware is inherently fragile and noisy. We find that the accuracy of traditional quantum error correction algorithms can be improved depending on the hardware. Given different hardware specifications, we automatically synthesize hardware-optimal algorithms for parity correction, qubit resetting, and GHZ (Greenberger–Horne–Zeilinger) state preparation. Using stochastic techniques from computer science, our method presents a computational tool to compute exact accuracy guarantees and synthesize optimal algorithms that are often different from traditional ones. We also show that improvements can be gained with respect to the Qiskit transpiler as we compute the hardware-optimal qubit mapping for the GHZ state-preparation problem.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"88 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661221","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}
Xue Qiao, Alan Houghton, James Reed, Burkhard Steuernagel, Jiahe Zhang, Charlotte Owen, Aymeric Leveau, Anastasia Orme, Thomas Louveau, Rachel Melton, Brande B. H. Wulff, Anne Osbourn
Plants produce diverse specialized metabolites with important ecological functions. It has recently become apparent that the genes for many of these pathways are not dispersed in plant genomes, but rather are arranged like beads on a string in biosynthetic gene clusters (BGCs). Pathways encoded by BGCs are as a rule dedicated linear pathways that do not form parts of wider metabolic networks. In contrast, the genes for the biosynthesis of widely distributed more ancestral metabolites such as carotenoids and anthocyanins are not clustered. Little is known about how these more recently evolved clustered pathways interact with general plant metabolism. We recently characterized a 12-gene BGC for the biosynthesis of the antimicrobial defense compound avenacin A-1, a triterpene glycoside produced by oats. Avenacin A-1 is acylated with the fluorophore N -methyl anthranilate and confers bright blue fluorescence of oat root tips under ultraviolet light. Here, we exploit a suite of >100 avenacin-deficient mutants identified by screening for reduced root fluorescence to identify genes required for the function of this paradigm BGC. Using a combination of mutant chemotyping, biochemical and molecular analysis, and genome resequencing, we identify two nonclustered genes ( Sad4 and Pal2 ) encoding enzymes that synthesize the donors required for avenacin glycosylation and acylation (recruited from the phenylpropanoid and tryptophan pathways). Our finding of these Cluster Auxiliary Enzymes (CAEs) provides insights into the interplay between general plant metabolism and a newly evolved lineage-specific BGC.
{"title":"Comprehensive mutant chemotyping reveals embedding of a lineage-specific biosynthetic gene cluster in wider plant metabolism","authors":"Xue Qiao, Alan Houghton, James Reed, Burkhard Steuernagel, Jiahe Zhang, Charlotte Owen, Aymeric Leveau, Anastasia Orme, Thomas Louveau, Rachel Melton, Brande B. H. Wulff, Anne Osbourn","doi":"10.1073/pnas.2417588122","DOIUrl":"https://doi.org/10.1073/pnas.2417588122","url":null,"abstract":"Plants produce diverse specialized metabolites with important ecological functions. It has recently become apparent that the genes for many of these pathways are not dispersed in plant genomes, but rather are arranged like beads on a string in biosynthetic gene clusters (BGCs). Pathways encoded by BGCs are as a rule dedicated linear pathways that do not form parts of wider metabolic networks. In contrast, the genes for the biosynthesis of widely distributed more ancestral metabolites such as carotenoids and anthocyanins are not clustered. Little is known about how these more recently evolved clustered pathways interact with general plant metabolism. We recently characterized a 12-gene BGC for the biosynthesis of the antimicrobial defense compound avenacin A-1, a triterpene glycoside produced by oats. Avenacin A-1 is acylated with the fluorophore <jats:italic>N</jats:italic> -methyl anthranilate and confers bright blue fluorescence of oat root tips under ultraviolet light. Here, we exploit a suite of >100 avenacin-deficient mutants identified by screening for reduced root fluorescence to identify genes required for the function of this paradigm BGC. Using a combination of mutant chemotyping, biochemical and molecular analysis, and genome resequencing, we identify two nonclustered genes ( <jats:italic>Sad4</jats:italic> and <jats:italic>Pal2</jats:italic> ) encoding enzymes that synthesize the donors required for avenacin glycosylation and acylation (recruited from the phenylpropanoid and tryptophan pathways). Our finding of these Cluster Auxiliary Enzymes (CAEs) provides insights into the interplay between general plant metabolism and a newly evolved lineage-specific BGC.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"1 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661471","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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