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Melatonin-mediated cGAS-STING signal in senescent macrophages promote TNBC chemotherapy resistance and drive the SASP.
IF 4 2区 生物学
Journal of Biological Chemistry Pub Date : 2025-03-22 DOI: 10.1016/j.jbc.2025.108438
Xiaoqiang Zhang, Minyu Zhuang, Hongfei Zhang, Yanhui Zhu, Junzhe Yang, Xian Wu, Xiafei Yu, Jing Tao, Xiaoan Liu
{"title":"Melatonin-mediated cGAS-STING signal in senescent macrophages promote TNBC chemotherapy resistance and drive the SASP.","authors":"Xiaoqiang Zhang, Minyu Zhuang, Hongfei Zhang, Yanhui Zhu, Junzhe Yang, Xian Wu, Xiafei Yu, Jing Tao, Xiaoan Liu","doi":"10.1016/j.jbc.2025.108438","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.108438","url":null,"abstract":"<p><p>The build-up of senescent cells in tissues is a key indicator of aging, associated with negative prognosis and therapy resistance. Despite immune dysfunction related to aging, also known as immunosenescence, is recognized as a factor in this process, the exact mechanisms are still unclear. In this study, we reported that melatonin deficiency accelerated macrophage senescence in triple-negative breast cancer (TNBC), whereas, melatonin could defend macrophages against senescence through the Nfatc1-Trim26-cgas-Sting pathway. Mechanistically, melatonin enhanced the nuclear translocation of Nfatc1 and elevated Trim26 transcription levels. Trim26, functioning as an E3 ligase, ubiquitinates cgas, thereby inhibiting the activation of the cgas-Sing pathway and consequently preventing cell senescence. Conversely, melatonin deficiency induced cgas-Sting pathway activation to promote macrophage aging. Our results show that melatonin inhibited macrophage senescence and improved chemotherapy responsiveness, with further enhancement when combined with the cgas inhibitor (G150). Overall, our findings indicated that melatonin protects macrophages from immunosenescence, suggesting its therapeutic potential for enhancing chemotherapy response.</p>","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":" ","pages":"108438"},"PeriodicalIF":4.0,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143700526","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mapping the structural heterogeneity of Pup ligase PafA using H/D exchange mass spectrometry.
IF 4 2区 生物学
Journal of Biological Chemistry Pub Date : 2025-03-21 DOI: 10.1016/j.jbc.2025.108437
Alicia Plourde, Jacquelyn C Ogata-Bean, Siavash Vahidi
{"title":"Mapping the structural heterogeneity of Pup ligase PafA using H/D exchange mass spectrometry.","authors":"Alicia Plourde, Jacquelyn C Ogata-Bean, Siavash Vahidi","doi":"10.1016/j.jbc.2025.108437","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.108437","url":null,"abstract":"<p><p>The Pup-proteasome system (PPS) is a unique bacterial proteolytic pathway found in some bacterial species, including in Mycobacterium tuberculosis, that plays a vital role in maintaining proteome integrity and survival during infection. Pupylation is the process of tagging substrates with Pup for degradation and is catalyzed by PafA, the sole Pup ligase in bacteria. However, how PafA interacts with diverse targets and its oligomeric state remain poorly understood. Although X-ray crystal structures have characterized PafA as a domain-swapped dimer, it is widely regarded as functionally active in its monomeric form. It remains to be established whether PafA dimerizes in solution, and how dimerization influences its function. In this study, we employed hydrogen-deuterium exchange mass spectrometry (HDX-MS) alongside complementary biophysical techniques to explore the oligomeric states and conformational dynamics of PafA. We show that recombinantly-produced PafA exists in a monomeric and a domain-swapped dimeric state in solution. Although nucleotide binding stabilizes PafA<sub>dimer</sub>, it primarily adopts a catalytically inactive conformation. Our HDX-MS highlighted regions throughout the N- and C-terminal domains that facilitate the PafA dimerization process. HDX-MS also revealed nucleotide binding induces global conformational changes on PafA<sub>monomer</sub>, underscoring the structural plasticity of this promiscuous enzyme. Our findings enhance our understanding of the structural and conformational heterogeneity of PafA and demonstrate how nucleotide binding and dimerization may influence its function.</p>","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":" ","pages":"108437"},"PeriodicalIF":4.0,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Pseudomonas aeruginosa PhuS proximal ligand His-209 triggers a conformational switch in function from DNA binding to heme transfer.
IF 4 2区 生物学
Journal of Biological Chemistry Pub Date : 2025-03-21 DOI: 10.1016/j.jbc.2025.108440
Nicholas Montes, Tyree Wilson, Samuel A Krug, Susana Mouriño, Maureen A Kane, Daniel Deredge, Angela Wilks
{"title":"The Pseudomonas aeruginosa PhuS proximal ligand His-209 triggers a conformational switch in function from DNA binding to heme transfer.","authors":"Nicholas Montes, Tyree Wilson, Samuel A Krug, Susana Mouriño, Maureen A Kane, Daniel Deredge, Angela Wilks","doi":"10.1016/j.jbc.2025.108440","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.108440","url":null,"abstract":"<p><p>Pseudomonas aeruginosa can acquire iron from heme via the heme assimilation system (Has) and Pseudomonas heme uptake (Phu) systems. Heme uptake is regulated at the metabolic level by the cytoplasmic protein PhuS, that controls heme flux through a heme oxygenase HemO, releasing iron and biliverdin IXβ and IXδ. We have shown PhuS regulates extracellular heme flux, and in its apo-form transcriptionally regulates the iron and heme-dependent sRNAs PrrF/PrrH. This mutual exclusivity of function is driven by conformational rearrangement of PhuS on heme binding. Herein we show through a combination of EMSA and fluorescence anisotropy that mutation of the His-209 proximal ligand allows both apo- and holo-PhuS H209A to bind to the prrF1 promoter with significantly lower affinity when compared to PAO1 WT. HDX-MS revealed the apo- and holo-PhuS H209A structures are closer to each other than their WT counterparts and sample a conformational landscape between the apo- and holo-PhuS WT conformations, that is neither optimal for heme transfer nor DNA-binding. Furthermore, qPCR and Western blot analysis of the phuSH209A allelic strain compared to PAO1 WT revealed an uncoupling of the PhuS-HemO dependent regulation of heme flux into the cell that abrogates the heme dependent regulation of the PrrF/PrrH sRNAs. The data supports a model where heme coordination through His-209 drives the conformational switch that determines mutual exclusivity in function of apo- and holo-PhuS. This dual function of PhuS is central to integrating extracellular heme utilization into the PrrF/PrrH sRNA regulatory network critical for P. aeruginosa adaptation within the host.</p>","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":" ","pages":"108440"},"PeriodicalIF":4.0,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
PKM2 regulates osteoclastogenesis by affecting osteoclast precursor cell fusion via downregulation of OC-STAMP and DC-STAMP.
IF 4 2区 生物学
Journal of Biological Chemistry Pub Date : 2025-03-21 DOI: 10.1016/j.jbc.2025.108439
Cong Cai, Jiawei Jiang, Song Li, Chenghao Gao, Hongxu Pu, Libo Zhao, Jun Xiao
{"title":"PKM2 regulates osteoclastogenesis by affecting osteoclast precursor cell fusion via downregulation of OC-STAMP and DC-STAMP.","authors":"Cong Cai, Jiawei Jiang, Song Li, Chenghao Gao, Hongxu Pu, Libo Zhao, Jun Xiao","doi":"10.1016/j.jbc.2025.108439","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.108439","url":null,"abstract":"<p><p>Osteoporosis is a common bone disease that has become a serious public health problem with the aging of population. Osteoclasts are the only cells in body that can resorb bone, whose dysfunction is closely related to osteoporosis. Pyruvate kinase M2 (PKM2) is one of the essential rate-limiting enzymes in the process of glycolysis. This study aimed to elucidate the role of PKM2 in osteoclastogenesis and bone resorption. Bone marrow-derived macrophages (BMMs) were transfected with adenovirus to knock down the expression of PKM2 gene or treated with the PKM2 activators DASA-58 and TEPP-46. Osteoclast formation was detected by TRAP staining, osteoclast-specific gene and protein expression was detected by RT-qPCR and Western blotting, and the effect of DASA-58 on osteoclast gene expression at the transcriptional level was examined by RNA-seq. The results showed that knockdown of PKM2 by adenoviral transfection or treatment with PKM2 activators DASA-58 and TEPP-46 inhibited osteoclast differentiation and suppressed the expression of osteoclast-associated genes in BMMs. Furthermore, PKM2 activators DASA-58 and TEPP-46 could inhibit several signaling pathways in osteoclasts; knockdown of PKM2 or treatment with PKM2 activators DASA-58 and TEPP-46 both affected osteoclast precursor cell fusion by inhibiting the expression of osteoclast stimulatory transmembrane protein (OC-STAMP) and dendritic cell-specific transmembrane protein (DC-STAMP). Therefore, PKM2 is closely related to osteoclast differentiation and formation, and the development of new therapeutic strategies targeting the PKM2 gene in osteoclasts may be feasible for the prevention and treatment of osteoporosis.</p>","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":" ","pages":"108439"},"PeriodicalIF":4.0,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
H2S remodels mitochondrial ultrastructure and destabilizes respiratory supercomplexes.
IF 4 2区 生物学
Journal of Biological Chemistry Pub Date : 2025-03-20 DOI: 10.1016/j.jbc.2025.108433
David A Hanna, Brandon Chen, Yatrik M Shah, Oleh Khalimonchuk, Brian Cunniff, Ruma Banerjee
{"title":"H<sub>2</sub>S remodels mitochondrial ultrastructure and destabilizes respiratory supercomplexes.","authors":"David A Hanna, Brandon Chen, Yatrik M Shah, Oleh Khalimonchuk, Brian Cunniff, Ruma Banerjee","doi":"10.1016/j.jbc.2025.108433","DOIUrl":"10.1016/j.jbc.2025.108433","url":null,"abstract":"<p><p>Mitochondrial form and function are intimately interconnected, responding to cellular stresses and changes in energy demand. Hydrogen sulfide, a product of amino acid metabolism, has dual roles as an electron transport chain substrate and complex IV (CIV) inhibitor, leading to a reductive shift, which has pleiotropic metabolic consequences. Luminal sulfide concentration in colon is high due to microbial activity, and in this study, we demonstrate that chronic sulfide exposure of colonocyte-derived cells leads to lower Mic60 and Mic19 expression that is correlated with a profound loss of cristae and lower mitochondrial networking. Sulfide-induced depolarization of the inner mitochondrial membrane activates Oma1-dependent cleavage of Opa1 and is associated with a profound loss of CI and CIV activities associated with respirasomes. Our study reveals a potential role for sulfide as an endogenous modulator of mitochondrial dynamics and suggests that this regulation is corrupted in hereditary or acquired diseases associated with elevated sulfide.</p>","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":" ","pages":"108433"},"PeriodicalIF":4.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structure and membrane interactions of Arabidopsis thaliana DGD2, a glycosyltransferase in the chloroplast membrane.
IF 4 2区 生物学
Journal of Biological Chemistry Pub Date : 2025-03-20 DOI: 10.1016/j.jbc.2025.108431
Emma Scaletti Hutchinson, Markel Martínez-Carranza, Biao Fu, Lena Mäler, Pål Stenmark
{"title":"Structure and membrane interactions of Arabidopsis thaliana DGD2, a glycosyltransferase in the chloroplast membrane.","authors":"Emma Scaletti Hutchinson, Markel Martínez-Carranza, Biao Fu, Lena Mäler, Pål Stenmark","doi":"10.1016/j.jbc.2025.108431","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.108431","url":null,"abstract":"<p><p>Galactolipids are characteristic lipids of the photosynthesis membranes of higher plants and cyanobacteria. Due to their close relationship to the stability of the photosystem protein complexes, the biogenesis of galactolipids has been intensively studied on the genetic and molecular levels. There are two major types of galactolipids in chloroplastic membranes: monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG). Under phosphate-limiting conditions, the amount of DGDG increases dramatically to allow for phosphate salvage from phospholipids. In Arabidopsis thaliana, the membrane-associated glycosyltransferase Digalactosyldiacylglycerol synthase 2 (atDGD2) is highly responsive to phosphate starvation and is significantly upregulated during such conditions. The lipid galactosylation reactions are also fundamentally interesting as they require a catalyst that is capable of bringing a hydrophilic and lipophilic substrate together at the solution-membrane phase border. Here we present the X-ray crystal structure of atDGD2, which is the first reported DGDG synthase structure. AtDGD2 is most structurally similar to functionally unrelated GT-B enzymes. Interestingly, in spite of significant donor substrate binding differences we identified four amino acids (Gly22, His151, Lys243 and Glu321, atDGD2 numbering) which were entirely conserved between the structurally similar enzymes. We also investigated the membrane interaction kinetics and membrane anchoring mechanism of atDGD2. This demonstrated that atDGD2 is membrane-bound, but also showed that membrane binding is highly dynamic. Furthermore, our structural information in context of previous biophysical studies highlights regions of the enzyme exhibiting a high degree of structural plasticity, which we propose to be important for allowing atDGD2 to quickly adapt its activity based on the membrane lipid environment.</p>","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":" ","pages":"108431"},"PeriodicalIF":4.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structural and functional analysis of Pseudomonas aeruginosa PelA provides insight into the modification of the Pel exopolysaccharide.
IF 4 2区 生物学
Journal of Biological Chemistry Pub Date : 2025-03-20 DOI: 10.1016/j.jbc.2025.108432
Jaime C Van Loon, François Le Mauff, Mario A Vargas, Stephanie Gilbert, Roland Pfoh, Zachary A Morrison, Erum Razvi, Mark Nitz, Donald C Sheppard, P Lynne Howell
{"title":"Structural and functional analysis of Pseudomonas aeruginosa PelA provides insight into the modification of the Pel exopolysaccharide.","authors":"Jaime C Van Loon, François Le Mauff, Mario A Vargas, Stephanie Gilbert, Roland Pfoh, Zachary A Morrison, Erum Razvi, Mark Nitz, Donald C Sheppard, P Lynne Howell","doi":"10.1016/j.jbc.2025.108432","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.108432","url":null,"abstract":"<p><p>A major biofilm matrix determinant of Pseudomonas aeruginosa is the partially deacetylated α-1,4 linked N-acetylgalactosamine polymer, Pel. After synthesis and transport of the GalNAc polysaccharide across the inner membrane, PelA partially deacetylates and hydrolyzes Pel before its export out of the cell via PelB. While the Pel modification and export proteins are known to interact in the periplasm, it is unclear how the interaction of PelA and PelB coordinates these processes. To determine how PelA modifies the polymer, we determined its structure to 2.1 Å and found a unique arrangement of four distinct domains. We have shown previously that the hydrolase domain exhibits endo-α-1,4-N-acetylgalactosaminidase activity. Characterization of the deacetylase domain revealed that PelA is the founding member of a new carbohydrate esterase family, CE#. Further, we found that the PelAB interaction enhances the deacetylation of N-acetylgalactosamine oligosaccharides. Using the PelA structure in conjunction with AlphaFold2 modelling of the PelAB complex, we propose a model wherein PelB guides Pel to the deacetylase domain of PelA and subsequently to the porin domain of PelB for export. Perturbation or loss of the PelAB interaction would result in less efficient deacetylation and potentially increase Pel hydrolysis. In PelA homologues across many phyla, the predicted structure and active sites are conserved, suggesting a common modification mechanism in Gram-negative bacterial species containing a functional pel operon.</p>","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":" ","pages":"108432"},"PeriodicalIF":4.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Hippo pathway effector YAP inhibits NF-κB signaling and ccRCC growth by opposing ZHX2.
IF 4 2区 生物学
Journal of Biological Chemistry Pub Date : 2025-03-20 DOI: 10.1016/j.jbc.2025.108430
Xu Li, Yong Suk Cho, Yuhong Han, Mengmeng Zhou, Yuchen Liu, Yingzi Yang, Shu Zhuo, Jin Jiang
{"title":"The Hippo pathway effector YAP inhibits NF-κB signaling and ccRCC growth by opposing ZHX2.","authors":"Xu Li, Yong Suk Cho, Yuhong Han, Mengmeng Zhou, Yuchen Liu, Yingzi Yang, Shu Zhuo, Jin Jiang","doi":"10.1016/j.jbc.2025.108430","DOIUrl":"10.1016/j.jbc.2025.108430","url":null,"abstract":"<p><p>The prevailing view in the cancer field is that Hippo signaling pathway functions as a tumor suppressor pathway by blocking the oncogenic potential of the pathway effectors Yes1 associated transcriptional regulator (YAP)/transcriptional coactivator with PDZ-binding motif (TAZ). However, YAP can also function as a context-dependent tumor suppressor in several types of cancer including clear cell renal cell carcinomas (ccRCC). We find that, in additional to inhibiting hypoxia-inducible factor 2α (HIF2α), a major oncogenic driver in Von Hippel-Lindau (VHL)-/- ccRCC, YAP also blocks nuclear factor κB (NF-κB) signaling in ccRCC to inhibit cancer cell growth under conditions where HIF2α is dispensable. Mechanistically, YAP inhibits the expression of Zinc fingers and homeoboxes 2 (ZHX2), a VHL substrate and critical co-factor of NF-κB in ccRCC. Furthermore, YAP competes with ZHX2 for binding to the NF-κB subunit p65. Consequently, elevated nuclear YAP blocks the cooperativity between ZHX2 and the NF-κB subunit p65, leading to diminished NF-κB target gene expression. Pharmacological inhibition of Hippo kinase blocked NF-κB transcriptional program and suppressed ccRCC cancer cell growth, which can be rescued by overexpression of ZHX2 or p65. Our study uncovers a crosstalk between the Hippo and NF-κB/ZHX2 pathways and its involvement in ccRCC growth inhibition, suggesting that targeting the Hippo pathway may provide a therapeutical opportunity for ccRCC treatment.</p>","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":" ","pages":"108430"},"PeriodicalIF":4.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Dissecting RNA selectivity mediated by tandem RNA-binding domains.
IF 4 2区 生物学
Journal of Biological Chemistry Pub Date : 2025-03-20 DOI: 10.1016/j.jbc.2025.108435
Sarah E Harris, Yue Hu, Kaitlin Bridges, Francisco F Cavazos, Justin G Martyr, Bryan B Guzmán, Jernej Murn, Maria M Aleman, Daniel Dominguez
{"title":"Dissecting RNA selectivity mediated by tandem RNA-binding domains.","authors":"Sarah E Harris, Yue Hu, Kaitlin Bridges, Francisco F Cavazos, Justin G Martyr, Bryan B Guzmán, Jernej Murn, Maria M Aleman, Daniel Dominguez","doi":"10.1016/j.jbc.2025.108435","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.108435","url":null,"abstract":"<p><p>RNA-protein interactions are pivotal to proper gene regulation. Many RNA-binding proteins possess multiple RNA-binding domains; however, how these domains interplay to select and regulate RNA targets remains poorly understood. Here, we investigate three multi-domain proteins, Musashi-1, Musashi-2, and unkempt, which share a high degree of RNA specificity, a common feature across RNA-binding proteins. We used massively parallel in vitro assays with unprecedented depth with random or naturally-derived RNA sequences and find that individual domains within a protein can have differing affinities, specificities, and motif spacing preferences. We conducted large scale competition assays between these proteins and determined how individual protein specificities and affinities influence competitive binding. Integration of binding and regulation in cells with in vitro specificities showed that target selection involves a combination of the protein intrinsic specificities described here, but cellular context is critical to drive these proteins to motifs in specific transcript regions. Finally, evolutionarily conserved RNA regions displayed evidence of binding multiple RBPs in cultured cells, and these RNA regions represent the highest affinity targets. This work emphasizes the importance of in vitro and in cultured cells studies to fully profile RNA-binding proteins and highlights the complex modes of RNA-protein interactions and the contributing factors in target selection.</p>","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":" ","pages":"108435"},"PeriodicalIF":4.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Epitomic Profiling and Functional Characteristics of Pemphigus Vulgaris Autoantibody Binding to Keratinocyte M3 Muscarinic Acetylcholine Receptor.
IF 4 2区 生物学
Journal of Biological Chemistry Pub Date : 2025-03-20 DOI: 10.1016/j.jbc.2025.108434
Jorge Mauricio Reyes-Ruiz, Alex Chernyavsky, Sergei A Grando, Charles Glabe
{"title":"Epitomic Profiling and Functional Characteristics of Pemphigus Vulgaris Autoantibody Binding to Keratinocyte M3 Muscarinic Acetylcholine Receptor.","authors":"Jorge Mauricio Reyes-Ruiz, Alex Chernyavsky, Sergei A Grando, Charles Glabe","doi":"10.1016/j.jbc.2025.108434","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.108434","url":null,"abstract":"<p><p>Patients with pemphigus vulgaris (PV) develop IgG autoantibodies (AuAbs) binding to keratinocyte desmogleins (Dsg), acetylcholine (ACh) receptors, mitochondrial proteins, and some other self-antigens. In this study, we identified linear and discontinuous peptide tetrameric epitope segments (ES) of M3 muscarinic ACh receptor (M3AR) targeted by different anti-M3AR AuAbs. As positive controls, we identified Dsg1 and Dsg3 ES targeted by PV sera. Healthy individuals also possessed natural antibodies targeting M3AR, Dsg1 and Dsg3 epitopes that were different from those targeted by AuAbs produced by PV patients. The two targeted M3AR pentameric ES encompass the 10 amino acids-long epitope LSEPTITFGT included the tetramer TFGT containing Thr235 which is a part of the ACh-binding pocket. Previously, it has been demonstrated that the anti-M3AR AuAb produces an agonist-like effect on downstream signaling, but its long-term effect is receptor desensitization. In this study, we compared the functional consequences of binding anti-M3AR AuAbs that target the ACh-binding pocket with that of AuAbs that target M3AR outside of its ACh-binding pocket. While the former AuAbs induced a very high elevation of phospholipase C, inositol triphosphate and diacylglycerol, which represents an agonist-like effect, the latter AuAbs produced a much weaker signaling response. These results indicate that PV patients develop two types of anti-M3AR AuAbs. One type attaches to orthosteric, ie, ACh-binding, site and elicits a strong signaling response comparable to that induced by a full pharmacologic agonist, whereas another type binds to an allosteric site and elicits submaximal signaling response comparable to that induced by a partial (allosteric) agonist.</p>","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":" ","pages":"108434"},"PeriodicalIF":4.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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