Pub Date : 2025-04-10DOI: 10.1016/j.molcel.2025.02.030
Li-Nan Chen, Hui Zhou, Kun Xi, Shizhuo Cheng, Yongfeng Liu, Yifan Fu, Xiangyu Ma, Ping Xu, Su-Yu Ji, Wei-Wei Wang, Dan-Dan Shen, Huibing Zhang, Qingya Shen, Renjie Chai, Min Zhang, Lin Yang, Feng Han, Chunyou Mao, Xiujun Cai, Yan Zhang
Maintaining pH at cellular, tissular, and systemic levels is essential for human health. Proton-sensing GPCRs regulate physiological and pathological processes by sensing the extracellular acidity. However, the molecular mechanism of proton sensing and activation of these receptors remains elusive. Here, we present cryoelectron microscopy (cryo-EM) structures of human GPR4, a prototypical proton-sensing GPCR, in its inactive and active states. Our studies reveal that three extracellular histidine residues are crucial for proton sensing of human GPR4. The binding of protons induces substantial conformational changes in GPR4’s ECLs, particularly in ECL2, which transforms from a helix-loop to a β-turn-β configuration. This transformation leads to the rearrangements of H-bond network and hydrophobic packing, relayed by non-canonical motifs to accommodate G proteins. Furthermore, the antagonist NE52-QQ57 hinders human GPR4 activation by preventing hydrophobic stacking rearrangement. Our findings provide a molecular framework for understanding the activation mechanism of a human proton-sensing GPCR, aiding future drug discovery.
{"title":"Proton perception and activation of a proton-sensing GPCR","authors":"Li-Nan Chen, Hui Zhou, Kun Xi, Shizhuo Cheng, Yongfeng Liu, Yifan Fu, Xiangyu Ma, Ping Xu, Su-Yu Ji, Wei-Wei Wang, Dan-Dan Shen, Huibing Zhang, Qingya Shen, Renjie Chai, Min Zhang, Lin Yang, Feng Han, Chunyou Mao, Xiujun Cai, Yan Zhang","doi":"10.1016/j.molcel.2025.02.030","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.02.030","url":null,"abstract":"Maintaining pH at cellular, tissular, and systemic levels is essential for human health. Proton-sensing GPCRs regulate physiological and pathological processes by sensing the extracellular acidity. However, the molecular mechanism of proton sensing and activation of these receptors remains elusive. Here, we present cryoelectron microscopy (cryo-EM) structures of human GPR4, a prototypical proton-sensing GPCR, in its inactive and active states. Our studies reveal that three extracellular histidine residues are crucial for proton sensing of human GPR4. The binding of protons induces substantial conformational changes in GPR4’s ECLs, particularly in ECL2, which transforms from a helix-loop to a β-turn-β configuration. This transformation leads to the rearrangements of H-bond network and hydrophobic packing, relayed by non-canonical motifs to accommodate G proteins. Furthermore, the antagonist NE52-QQ57 hinders human GPR4 activation by preventing hydrophobic stacking rearrangement. Our findings provide a molecular framework for understanding the activation mechanism of a human proton-sensing GPCR, aiding future drug discovery.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"39 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143814000","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}
Proton sensing by G protein-coupled receptors (GPCRs) is crucial in many life activities. However, its underlying mechanism remains unclear. Here, we report 8 cryoelectron microscopy (cryo-EM) structures of human GPR4 and GPR68 at different pH values and in complex with Gs or Gq trimers or in apo state. Structural inspection, structure-based pKa calculations, and mutational and computational analyses revealed that protonation of two conserved extracellular histidines induced polar network formation and other conformational changes to tether 7-transmembrane (TM7) to second extracellular loop (ECL2), and these changes constitute the central mechanisms of proton-induced activation of GPR4 and GPR68. Unexpectedly, proton sensation by specific extracellular histidine determined biased G protein coupling of GPR4. Moreover, GPR68's additional pH-sensing H842.67 enhances its function in a more acidic optimal pH range. The propagation path connecting proton-sensing histidines to the toggle switch was characterized. Collectively, we provide structural insights into the proton sensing, activation, and downstream effector coupling mechanisms of proton-sensing GPCRs.
{"title":"Structural basis and biased signaling of proton sensation by GPCRs mediated by extracellular histidine rearrangement","authors":"Lulu Guo, Kongkai Zhu, Ya-Ni Zhong, Mingxin Gao, Junyan Liu, Zhimin Qi, Zili Liu, Naikang Rong, Minghui Zhang, Dongfang Li, Qiyue Zhang, Gongming Yang, Xinxin Zhang, Mingyue Zhang, Ning Ding, Yu-qi Ping, Zhao Yang, Peng Xiao, Ming Xia, Xiao Yu, Fan Yang","doi":"10.1016/j.molcel.2025.03.018","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.03.018","url":null,"abstract":"Proton sensing by G protein-coupled receptors (GPCRs) is crucial in many life activities. However, its underlying mechanism remains unclear. Here, we report 8 cryoelectron microscopy (cryo-EM) structures of human GPR4 and GPR68 at different pH values and in complex with Gs or Gq trimers or in apo state. Structural inspection, structure-based pKa calculations, and mutational and computational analyses revealed that protonation of two conserved extracellular histidines induced polar network formation and other conformational changes to tether 7-transmembrane (TM7) to second extracellular loop (ECL2), and these changes constitute the central mechanisms of proton-induced activation of GPR4 and GPR68. Unexpectedly, proton sensation by specific extracellular histidine determined biased G protein coupling of GPR4. Moreover, GPR68's additional pH-sensing H84<sup>2.67</sup> enhances its function in a more acidic optimal pH range. The propagation path connecting proton-sensing histidines to the toggle switch was characterized. Collectively, we provide structural insights into the proton sensing, activation, and downstream effector coupling mechanisms of proton-sensing GPCRs.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"37 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143813999","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}
Pub Date : 2025-04-09DOI: 10.1016/j.molcel.2025.03.015
Uris Ros, Veronica Martinez-Osorio, Pedro A. Valiente, Yasmin Abdelwahab, Milos Gojkovic, Raed Shalaby, Silvia Zanna, Julia Saggau, Laurens Wachsmuth, Harshal N. Nemade, Jonathan Zoeller, Hannah Lottermoser, Yu-Guang Chen, Mohamed Ibrahim, Konstantinos Kelepouras, Lazaros Vasilikos, Paula Bedoya, Rafael A. Espiritu, Stefan Müller, Veronika Altmannova, Ana J. García-Sáez
Necroptosis is an inflammatory form of regulated cell death implicated in a range of human pathologies, whose execution depends on the poorly understood pseudokinase mixed lineage kinase domain-like (MLKL). Here, we report that splicing-dependent insertion of a short amino acid sequence in the C-terminal α-helix (Hc) of MLKL abolishes cell killing activity and creates an anti-necroptotic isoform that counteracts cell death induced by the necroptosis-proficient protein in mice and humans. We show that interaction of Hc with a previously unrecognized hydrophobic groove is essential for necroptosis, which we exploited in a strategy to identify small molecules that inhibit MLKL and substantially ameliorate disease in murine models of necroptosis-driven dermatitis and abdominal aortic aneurysm. Thus, alternative splicing of microexons controls the ability of MLKL to undergo an intramolecular rearrangement essential for necroptosis with potential to guide the development of allosteric MLKL inhibitors for the treatment of human disease.
{"title":"MLKL activity requires a splicing-regulated, druggable intramolecular interaction","authors":"Uris Ros, Veronica Martinez-Osorio, Pedro A. Valiente, Yasmin Abdelwahab, Milos Gojkovic, Raed Shalaby, Silvia Zanna, Julia Saggau, Laurens Wachsmuth, Harshal N. Nemade, Jonathan Zoeller, Hannah Lottermoser, Yu-Guang Chen, Mohamed Ibrahim, Konstantinos Kelepouras, Lazaros Vasilikos, Paula Bedoya, Rafael A. Espiritu, Stefan Müller, Veronika Altmannova, Ana J. García-Sáez","doi":"10.1016/j.molcel.2025.03.015","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.03.015","url":null,"abstract":"Necroptosis is an inflammatory form of regulated cell death implicated in a range of human pathologies, whose execution depends on the poorly understood pseudokinase mixed lineage kinase domain-like (MLKL). Here, we report that splicing-dependent insertion of a short amino acid sequence in the C-terminal α-helix (Hc) of MLKL abolishes cell killing activity and creates an anti-necroptotic isoform that counteracts cell death induced by the necroptosis-proficient protein in mice and humans. We show that interaction of Hc with a previously unrecognized hydrophobic groove is essential for necroptosis, which we exploited in a strategy to identify small molecules that inhibit MLKL and substantially ameliorate disease in murine models of necroptosis-driven dermatitis and abdominal aortic aneurysm. Thus, alternative splicing of microexons controls the ability of MLKL to undergo an intramolecular rearrangement essential for necroptosis with potential to guide the development of allosteric MLKL inhibitors for the treatment of human disease.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"16 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143806108","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}
Pub Date : 2025-04-07DOI: 10.1016/j.molcel.2025.03.014
Narumon Thongdee, Miranda M. Alaniz, Ekaterina Samatova, Aoshu Zhong, Caroline Esnault, Hongen Zhang, Ryan K. Dale, Marina V. Rodnina, Gisela Storz
Most characterized interactions between bacterial small RNAs (sRNAs) and their target mRNAs occur near ribosome binding sites, resulting in changes in translation initiation or target mRNA decay. To understand the consequences of sRNA pairing internal to coding sequences detected by global RNA-RNA interactome approaches, we examined the impact of sRNA overexpression on seven target proteins. Overexpression of the sRNA led to decreased target protein levels for two pairs, but there were no differences for the others. By further examining ArcZ-ligA and ArcZ-hemK, we discovered that ArcZ pairing with the mRNAs leads to translation pausing and increased protein activity. A ligA point mutation that eliminates sRNA pairing resulted in increased sensitivity to DNA damage, revealing the physiological consequences of the regulation. Thus, regulatory RNA pairing in coding sequences can locally slow translation elongation, likely impacting co-translational protein folding and allowing improved incorporation of co-factors or more optimal folding under specific conditions.
{"title":"Modulation of protein activity by small RNA base pairing internal to coding sequences","authors":"Narumon Thongdee, Miranda M. Alaniz, Ekaterina Samatova, Aoshu Zhong, Caroline Esnault, Hongen Zhang, Ryan K. Dale, Marina V. Rodnina, Gisela Storz","doi":"10.1016/j.molcel.2025.03.014","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.03.014","url":null,"abstract":"Most characterized interactions between bacterial small RNAs (sRNAs) and their target mRNAs occur near ribosome binding sites, resulting in changes in translation initiation or target mRNA decay. To understand the consequences of sRNA pairing internal to coding sequences detected by global RNA-RNA interactome approaches, we examined the impact of sRNA overexpression on seven target proteins. Overexpression of the sRNA led to decreased target protein levels for two pairs, but there were no differences for the others. By further examining ArcZ-<em>ligA</em> and ArcZ-<em>hemK</em>, we discovered that ArcZ pairing with the mRNAs leads to translation pausing and increased protein activity. A <em>ligA</em> point mutation that eliminates sRNA pairing resulted in increased sensitivity to DNA damage, revealing the physiological consequences of the regulation. Thus, regulatory RNA pairing in coding sequences can locally slow translation elongation, likely impacting co-translational protein folding and allowing improved incorporation of co-factors or more optimal folding under specific conditions.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"1 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143789760","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}
Pub Date : 2025-04-04DOI: 10.1016/j.molcel.2025.03.013
Shagun Srivastava, Giridhar Sekar, Adedolapo Ojoawo, Anup Aggarwal, Elisabeth Ferreira, Emiko Uchikawa, Meek Yang, Christy R. Grace, Raja Dey, Yi-Lun Lin, Cristina D. Guibao, Seetharaman Jayaraman, Somnath Mukherjee, Anthony A. Kossiakoff, Bin Dong, Alexander Myasnikov, Tudor Moldoveanu
Apoptosis controls cell fate, ensuring tissue homeostasis and promoting disease when dysregulated. The rate-limiting step in apoptosis is mitochondrial poration by the effector B cell lymphoma 2 (BCL-2) family proteins BAK and BAX, which are activated by initiator BCL-2 homology 3 (BH3)-only proteins (e.g., BIM) and inhibited by guardian BCL-2 family proteins (e.g., MCL-1). We integrated structural, biochemical, and pharmacological approaches to characterize the human prosurvival MCL-1:BAK complex assembled from their BCL-2 globular core domains. We reveal a canonical interaction with BAK BH3 bound to the hydrophobic groove of MCL-1 and disordered and highly dynamic BAK regions outside the complex interface. We predict similar conformations of activated effectors in complex with other guardians or effectors. The MCL-1:BAK complex is a major cancer drug target. We show that MCL-1 inhibitors are inefficient in neutralizing the MCL-1:BAK complex, requiring high doses to initiate apoptosis. Our study underscores the need to design superior clinical candidate MCL-1 inhibitors.
{"title":"Structural basis of BAK sequestration by MCL-1 in apoptosis","authors":"Shagun Srivastava, Giridhar Sekar, Adedolapo Ojoawo, Anup Aggarwal, Elisabeth Ferreira, Emiko Uchikawa, Meek Yang, Christy R. Grace, Raja Dey, Yi-Lun Lin, Cristina D. Guibao, Seetharaman Jayaraman, Somnath Mukherjee, Anthony A. Kossiakoff, Bin Dong, Alexander Myasnikov, Tudor Moldoveanu","doi":"10.1016/j.molcel.2025.03.013","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.03.013","url":null,"abstract":"Apoptosis controls cell fate, ensuring tissue homeostasis and promoting disease when dysregulated. The rate-limiting step in apoptosis is mitochondrial poration by the effector B cell lymphoma 2 (BCL-2) family proteins BAK and BAX, which are activated by initiator BCL-2 homology 3 (BH3)-only proteins (e.g., BIM) and inhibited by guardian BCL-2 family proteins (e.g., MCL-1). We integrated structural, biochemical, and pharmacological approaches to characterize the human prosurvival MCL-1:BAK complex assembled from their BCL-2 globular core domains. We reveal a canonical interaction with BAK BH3 bound to the hydrophobic groove of MCL-1 and disordered and highly dynamic BAK regions outside the complex interface. We predict similar conformations of activated effectors in complex with other guardians or effectors. The MCL-1:BAK complex is a major cancer drug target. We show that MCL-1 inhibitors are inefficient in neutralizing the MCL-1:BAK complex, requiring high doses to initiate apoptosis. Our study underscores the need to design superior clinical candidate MCL-1 inhibitors.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"34 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143775922","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}
Pub Date : 2025-04-04DOI: 10.1016/j.molcel.2025.03.010
Lindsey V. Soles, Liang Liu, Xudong Zou, Yoseop Yoon, Shuangyu Li, Lusong Tian, Marielle Valdez, Angela M Yu, Hong Yin, Wei Li, Fangyuan Ding, Georg Seelig, Lei Li, Yongsheng Shi
The RNA exosome plays critical roles in eukaryotic RNA degradation, but how it specifically recognizes its targets remains unclear. The poly(A) tail exosome targeting (PAXT) connection is a nuclear adaptor that recruits the exosome to polyadenylated RNAs, especially transcripts polyadenylated at intronic poly(A) sites. Here, we show that PAXT-mediated RNA degradation is induced by the combination of a 5′ splice site (ss) and a poly(A) junction (PAJ) but not by either sequence alone. These sequences are bound by U1 small nuclear ribonucleoprotein particle (snRNP) and cleavage/polyadenylation factors, which, in turn, cooperatively recruit PAXT. As the 5′ ss-PAJ combination is typically absent on correctly processed RNAs, it functions as a “nuclear RNA degradation code” (NRDC). Importantly, disease-associated single nucleotide polymorphisms that create novel 5′ ss in 3′ untranslated regions can induce aberrant mRNA degradation via the NRDC mechanism. Together, our study identified the first NRDC, revealed its recognition mechanism, and characterized its role in human diseases.
{"title":"A nuclear RNA degradation code is recognized by PAXT for eukaryotic transcriptome surveillance","authors":"Lindsey V. Soles, Liang Liu, Xudong Zou, Yoseop Yoon, Shuangyu Li, Lusong Tian, Marielle Valdez, Angela M Yu, Hong Yin, Wei Li, Fangyuan Ding, Georg Seelig, Lei Li, Yongsheng Shi","doi":"10.1016/j.molcel.2025.03.010","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.03.010","url":null,"abstract":"The RNA exosome plays critical roles in eukaryotic RNA degradation, but how it specifically recognizes its targets remains unclear. The poly(A) tail exosome targeting (PAXT) connection is a nuclear adaptor that recruits the exosome to polyadenylated RNAs, especially transcripts polyadenylated at intronic poly(A) sites. Here, we show that PAXT-mediated RNA degradation is induced by the combination of a 5′ splice site (ss) and a poly(A) junction (PAJ) but not by either sequence alone. These sequences are bound by U1 small nuclear ribonucleoprotein particle (snRNP) and cleavage/polyadenylation factors, which, in turn, cooperatively recruit PAXT. As the 5′ ss-PAJ combination is typically absent on correctly processed RNAs, it functions as a “nuclear RNA degradation code” (NRDC). Importantly, disease-associated single nucleotide polymorphisms that create novel 5′ ss in 3′ untranslated regions can induce aberrant mRNA degradation via the NRDC mechanism. Together, our study identified the first NRDC, revealed its recognition mechanism, and characterized its role in human diseases.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"23 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143776162","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}
Pub Date : 2025-04-03DOI: 10.1016/j.molcel.2025.03.002
Yutao Zhao, Chuan He
In this issue, Huang et al.1 report the acetylation of METTL3 as a negative regulator of m6A deposition of chromatin-associated regulatory RNAs from enhancers and promoters. This acetylation is mediated by p300 and positively regulated by PAK2.
{"title":"Acetylation of METTL3: A negative regulator of m6A deposition on chromatin-associated regulatory RNAs","authors":"Yutao Zhao, Chuan He","doi":"10.1016/j.molcel.2025.03.002","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.03.002","url":null,"abstract":"In this issue, Huang et al.<span><span><sup>1</sup></span></span> report the acetylation of METTL3 as a negative regulator of m<sup>6</sup>A deposition of chromatin-associated regulatory RNAs from enhancers and promoters. This acetylation is mediated by p300 and positively regulated by PAK2.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"73 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143766806","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}
Pub Date : 2025-04-03DOI: 10.1016/j.molcel.2025.03.011
Elena Maspero, Simona Polo
In this issue of Molecular Cell, Kiss et al.1 introduce UbiREAD, a technology that deciphers ubiquitin chain-mediated degradation in living cells, revealing a hierarchy where K48 chains of at least three ubiquitins drive rapid proteasomal degradation and branched K48/K63 chains follow substrate-anchored rules.
{"title":"Deconstructing destruction: A rapid route to proteasomal fate","authors":"Elena Maspero, Simona Polo","doi":"10.1016/j.molcel.2025.03.011","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.03.011","url":null,"abstract":"In this issue of <em>Molecular Cell</em>, Kiss et al.<span><span><sup>1</sup></span></span> introduce UbiREAD, a technology that deciphers ubiquitin chain-mediated degradation in living cells, revealing a hierarchy where K48 chains of at least three ubiquitins drive rapid proteasomal degradation and branched K48/K63 chains follow substrate-anchored rules.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"107 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143766807","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}
Pub Date : 2025-04-03DOI: 10.1016/j.molcel.2025.03.008
Zhen Tang, Cong Xing, Antonina Araszkiewicz, Kun Yang, Wanwan Huai, Devon Jeltema, Nicole Dobbs, Yihe Zhang, Lu O. Sun, Nan Yan
Lysosomes are essential organelles for cellular homeostasis. Defective lysosomes are associated with diseases like lysosomal storage disorders (LSDs). How lysosomal defects are detected and lysosomal function restored remain incompletely understood. Here, we show that STING mediates a neuroinflammatory gene signature in three distinct LSD mouse models, Galctwi/twi, Ppt1−/−, and Cln7−/−. Transcriptomic analysis of Galctwi/twi mouse brain tissue revealed that STING also mediates the expression of lysosomal genes that are regulated by transcriptional factor EB (TFEB). Immunohistochemical and single-nucleus RNA-sequencing (snRNA-seq) analysis show that STING regulates lysosomal gene expression in microglia. Mechanistically, we show that STING activation leads to TFEB dephosphorylation, nuclear translocation, and expression of lysosomal genes. This process requires STING’s proton channel function, the V-ATPase-ATG5-ATG8 cascade, and is independent of immune signaling. Furthermore, we show that the STING-TFEB axis facilitates lysosomal repair. Together, our data identify STING-TFEB as a lysosomal quality control mechanism that responds to lysosomal dysfunction.
{"title":"STING mediates lysosomal quality control and recovery through its proton channel function and TFEB activation in lysosomal storage disorders","authors":"Zhen Tang, Cong Xing, Antonina Araszkiewicz, Kun Yang, Wanwan Huai, Devon Jeltema, Nicole Dobbs, Yihe Zhang, Lu O. Sun, Nan Yan","doi":"10.1016/j.molcel.2025.03.008","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.03.008","url":null,"abstract":"Lysosomes are essential organelles for cellular homeostasis. Defective lysosomes are associated with diseases like lysosomal storage disorders (LSDs). How lysosomal defects are detected and lysosomal function restored remain incompletely understood. Here, we show that STING mediates a neuroinflammatory gene signature in three distinct LSD mouse models, <em>Galc</em><sup><em>twi/twi</em></sup>, <em>Ppt1</em><sup>−/−</sup>, and <em>Cln7</em><sup>−/−</sup>. Transcriptomic analysis of <em>Galc</em><sup><em>twi/twi</em></sup> mouse brain tissue revealed that STING also mediates the expression of lysosomal genes that are regulated by transcriptional factor EB (TFEB). Immunohistochemical and single-nucleus RNA-sequencing (snRNA-seq) analysis show that STING regulates lysosomal gene expression in microglia. Mechanistically, we show that STING activation leads to TFEB dephosphorylation, nuclear translocation, and expression of lysosomal genes. This process requires STING’s proton channel function, the V-ATPase-ATG5-ATG8 cascade, and is independent of immune signaling. Furthermore, we show that the STING-TFEB axis facilitates lysosomal repair. Together, our data identify STING-TFEB as a lysosomal quality control mechanism that responds to lysosomal dysfunction.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"33 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143766803","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}
Pub Date : 2025-04-03DOI: 10.1016/j.molcel.2025.03.006
Jong-Sun Lee, Tu Dan, He Zhang, Yujing Cheng, Frederick Rehfeld, James Brugarolas, Joshua T. Mendell
Cancer cells frequently upregulate ribosome production to support tumorigenesis. While small nucleolar RNAs (snoRNAs) are critical for ribosome biogenesis, the roles of other classes of noncoding RNAs in this process remain largely unknown. Here, we performed CRISPR interference (CRISPRi) screens to identify essential long noncoding RNAs (lncRNAs) in renal cell carcinoma (RCC) cells. This revealed that an alternatively spliced isoform of lncRNA colorectal neoplasia differentially expressed (CRNDE) containing an ultraconserved element (UCE), referred to as CRNDEUCE, is required for RCC cell proliferation. CRNDEUCE localizes to the nucleolus and promotes 60S ribosomal subunit biogenesis. The UCE of CRNDE functions as an unprocessed C/D box snoRNA that directly interacts with ribosomal RNA precursors. This facilitates delivery of eukaryotic initiation factor 6 (eIF6), a key 60S biogenesis factor, which binds to CRNDEUCE through a sequence element adjacent to the UCE. These findings highlight the functional versatility of snoRNA sequences and expand the known mechanisms through which noncoding RNAs orchestrate ribosome biogenesis.
{"title":"An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation","authors":"Jong-Sun Lee, Tu Dan, He Zhang, Yujing Cheng, Frederick Rehfeld, James Brugarolas, Joshua T. Mendell","doi":"10.1016/j.molcel.2025.03.006","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.03.006","url":null,"abstract":"Cancer cells frequently upregulate ribosome production to support tumorigenesis. While small nucleolar RNAs (snoRNAs) are critical for ribosome biogenesis, the roles of other classes of noncoding RNAs in this process remain largely unknown. Here, we performed CRISPR interference (CRISPRi) screens to identify essential long noncoding RNAs (lncRNAs) in renal cell carcinoma (RCC) cells. This revealed that an alternatively spliced isoform of lncRNA colorectal neoplasia differentially expressed (<em>CRNDE</em>) containing an ultraconserved element (UCE), referred to as <em>CRNDE</em><sup>UCE</sup>, is required for RCC cell proliferation. <em>CRNDE</em><sup>UCE</sup> localizes to the nucleolus and promotes 60S ribosomal subunit biogenesis. The UCE of <em>CRNDE</em> functions as an unprocessed C/D box snoRNA that directly interacts with ribosomal RNA precursors. This facilitates delivery of eukaryotic initiation factor 6 (eIF6), a key 60S biogenesis factor, which binds to <em>CRNDE</em><sup>UCE</sup> through a sequence element adjacent to the UCE. These findings highlight the functional versatility of snoRNA sequences and expand the known mechanisms through which noncoding RNAs orchestrate ribosome biogenesis.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"33 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143766841","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}
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