Baraj Doray, Benjamin C Jennings, Xi Yang, Lin Liu, Varsha Venkatarangan, Stuart Kornfeld, Ming Li
{"title":"LYSET facilitates integration of both the N- and C-terminal transmembrane helices/cytoplasmic domains of GlcNAc-1-phosphotransferase.","authors":"Baraj Doray, Benjamin C Jennings, Xi Yang, Lin Liu, Varsha Venkatarangan, Stuart Kornfeld, Ming Li","doi":"10.1091/mbc.E24-08-0349","DOIUrl":"10.1091/mbc.E24-08-0349","url":null,"abstract":"<p><p>LYSET is a recently identified Golgi transmembrane (TM) protein, and inactivating mutations in the <i>LYSET</i> gene phenocopy mucolipidosis II (MLII), the lysosomal storage disease caused by loss of function of GlcNAc-1-phosphotransferase αβ (GNPTαβ), which tags lysosomal hydrolases with the mannose 6-phosphate (M6P) tag for delivery to lysosomes. It is conceivable that LYSET facilitates integration of both hydrophilic TM helices (TMHs) of GNPTαβ and retain the latter in the Golgi, although this has only been directly demonstrated for the N-terminal TMH wherein a membrane-stabilized GNPTαβ variant restores lysosomal function in cells lacking LYSET. Here we show that the C-terminal TMH of GNPTαβ also contributes to LYSET-mediated Golgi retention. In addition, disease-causing patient mutations in the N-terminal TMH of GNPTαβ, which increase the hydrophilicity of the helix, are partly rescued by overexpression of LYSET. Finally, we show that a membrane-stabilized GNPTαβ variant, despite overcoming the requirement for LYSET, still requires COPI-mediated recycling via the N-terminal cytosolic domain (CD) for GNPTαβ retention and function in the Golgi.</p>","PeriodicalId":18735,"journal":{"name":"Molecular Biology of the Cell","volume":" ","pages":"br12"},"PeriodicalIF":3.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143409198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Orchestration of SARS-CoV-2 Nsp4 and host cell ESCRT proteins induces morphological changes of the endoplasmic reticulum.","authors":"Allison Kifer, Franciso Pina, Nicholas Codallos, Anita Hermann, Lauren Ziegler, Maho Niwa","doi":"10.1091/mbc.E24-12-0542","DOIUrl":"10.1091/mbc.E24-12-0542","url":null,"abstract":"<p><p>Upon entry into the host cell, the nonstructural proteins 3, 4, and 6 (Nsp3, Nsp 4, and Nsp6) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) facilitate the formation of double-membrane vesicles (DMVs) through extensive rearrangement of the host cell endoplasmic reticulum (ER) to replicate the viral genome and translate viral proteins. To dissect the functional roles of each Nsp and the molecular mechanisms underlying the ER changes, we exploited both yeast <i>Saccharomyces cerevisiae</i> and human cell experimental systems. Our results demonstrate that Nsp4 alone is sufficient to induce ER structural changes. Nsp4 expression led to robust activation of both the unfolded protein response (UPR) and the ER surveillance (ERSU) cell cycle checkpoint, resulting in cortical ER inheritance block and septin ring mislocalization. Interestingly, these ER morphological changes occurred independently of the canonical UPR and ERSU components but were mediated by the endosomal sorting complex for transport (ESCRT) proteins Vps4 and Vps24 in yeast. Similarly, ER structural changes occurred in human cells upon Nsp4 expression, providing a basis for a minimal experimental system for testing the involvement of human ESCRT proteins and ultimately advancing our understanding of DMV formation.</p>","PeriodicalId":18735,"journal":{"name":"Molecular Biology of the Cell","volume":" ","pages":"ar40"},"PeriodicalIF":3.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143409199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Francesco Scavone, Sharon Lian, Eeva-Liisa Eskelinen, Robert E Cohen, Tingting Yao
{"title":"Trafficking of K63-polyubiquitin-modified membrane proteins in a macroautophagy-independent pathway is linked to ATG9A.","authors":"Francesco Scavone, Sharon Lian, Eeva-Liisa Eskelinen, Robert E Cohen, Tingting Yao","doi":"10.1091/mbc.E24-12-0535","DOIUrl":"10.1091/mbc.E24-12-0535","url":null,"abstract":"<p><p>Cytoplasmic K63-linked polyubiquitin signals have well-established roles in endocytosis and selective autophagy. However, how these signals help to direct different cargos to different intracellular trafficking routes is unclear. Here we report that, when the K63-polyubiquitin signal is blocked by intracellular expression of a high-affinity sensor (named Vx3), many proteins originating from the plasma membrane are found trapped in clusters of small vesicles that colocalize with ATG9A, a transmembrane protein that plays an essential role in autophagy. Importantly, whereas ATG9A is required for cluster formation, other core autophagy machinery as well as selective autophagy cargo receptors are not required. Although the cargos are sequestered in the vesicular clusters in an ATG9-dependent manner, additional signals are needed to induce LC3 conjugation. Upon removal of the Vx3 block, K63-polyubiquitylated cargos are rapidly delivered to lysosomes. These observations suggest that ATG9A plays an unexpected role in the trafficking of K63-polyubiquitin-modified membrane proteins.</p>","PeriodicalId":18735,"journal":{"name":"Molecular Biology of the Cell","volume":" ","pages":"ar42"},"PeriodicalIF":3.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rachel A Howard-Till, Sam Li, Usha Pallabi Kar, Christopher N Fuentes, Amy S Fabritius, Mark Winey
{"title":"A ternary complex of MIPs in the A-tubule of basal bodies and axonemes depends on RIB22 and the EF-hand domain of RIB72A in <i>Tetrahymena</i> cilia.","authors":"Rachel A Howard-Till, Sam Li, Usha Pallabi Kar, Christopher N Fuentes, Amy S Fabritius, Mark Winey","doi":"10.1091/mbc.E24-12-0557","DOIUrl":"10.1091/mbc.E24-12-0557","url":null,"abstract":"<p><p>The lumens of the highly stable microtubules that make up the core of basal bodies, cilia, and flagella are coated with a network of proteins known as MIPs, or microtubule inner proteins. MIPs are hypothesized to enhance the rigidity and stability of these microtubules, but how they assemble and contribute to cilia function is poorly understood. Here we describe a ciliate specific MIP, RIB22, in <i>Tetrahymena thermophila</i>. RIB22 is a calmodulin-like protein found in the A-tubule of doublet and triplet microtubules in cilia and basal bodies. Its localization is dependent on the conserved MIP RIB72. Here we use cryogenic electron tomography (cryoET) to examine RIB22 and its interacting partners in axonemes and basal bodies. RIB22 forms a ternary complex with the C-terminal EF-hand domain of RIB72A and another MIP, FAM166A. <i>Tetrahymena</i> strains lacking RIB22 or the EF-hand domain of RIB72A showed impaired cilia function. CryoET on axonemes from these strains demonstrated an interdependence of the three proteins for stabilization within the structure. Deletion of the RIB72A EF-hand domain resulted in the apparent loss of multiple MIPs in the region. These findings emphasize the intricacy of the MIP network and the importance of understanding MIPs' functions during cilium assembly and regulation.</p>","PeriodicalId":18735,"journal":{"name":"Molecular Biology of the Cell","volume":" ","pages":"br13"},"PeriodicalIF":3.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143409196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"β3 accelerates microtubule plus end maturation through a divergent lateral interface.","authors":"Lisa M Wood, Jeffrey K Moore","doi":"10.1091/mbc.E24-08-0354","DOIUrl":"10.1091/mbc.E24-08-0354","url":null,"abstract":"<p><p>β-tubulin isotypes exhibit similar sequences but different activities, suggesting that limited sequence divergence is functionally important. We investigated this hypothesis for TUBB3/β3, a β-tubulin linked to aggressive cancers and chemoresistance in humans. We created mutant yeast strains with β-tubulin alleles that mimic variant residues in β3 and find that residues at the lateral interface are sufficient to alter microtubule dynamics and response to microtubule targeting agents. In HeLa cells, β3 overexpression decreases the lifetime of microtubule growth, and this requires residues at the lateral interface. These microtubules exhibit a shorter region of EB binding at the plus end, suggesting faster lattice maturation, and resist stabilization by paclitaxel. Resistance requires the H1-S2 and H2-S3 regions at the lateral interface of β3. Our results identify the mechanistic origins of the unique activity of β3 tubulin and suggest that tubulin isotype expression may tune the rate of lattice maturation at growing microtubule plus ends in cells.</p>","PeriodicalId":18735,"journal":{"name":"Molecular Biology of the Cell","volume":" ","pages":"ar36"},"PeriodicalIF":3.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142984157","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Mutually independent and cilia-independent assembly of IFT-A and IFT-B complexes at mother centriole.","authors":"Koshi Tasaki, Yuuki Satoda, Shuhei Chiba, Hye-Won Shin, Yohei Katoh, Kazuhisa Nakayama","doi":"10.1091/mbc.E24-11-0509","DOIUrl":"10.1091/mbc.E24-11-0509","url":null,"abstract":"<p><p>The intraflagellar transport (IFT) machinery, containing the IFT-A and IFT-B complexes and powered by dynein-2 and kinesin-2 motors, is crucial for bidirectional trafficking of ciliary proteins and their import/export across the transition zone (TZ). Stepwise assembly of anterograde IFT trains was proposed previously; that is, the IFT-B complex first forms a TZ-tethered scaffold with sequential incorporation of IFT-A, dynein-2, and finally kinesin-2. However, IFT-A and IFT-B complexes also demonstrate distinct localization to the basal body/mother centriole. We show that IFT-A, IFT-B, and dynein-2 complexes are recruited to the mother centriole independently of ciliogenesis. Furthermore, mother centriole recruitment of IFT-A and IFT-B can occur in the absence of IFT-B and IFT-A, respectively, and dynein-2 recruitment is independent of IFT-A and IFT-B. Expansion microscopy revealed that the IFT-A/IFT-B pool at the basal body is distinct from that at the TZ. We conclude that IFT-A and IFT-B are recruited to the mother centriole in a mutually independent and ciliogenesis-independent manner before IFT train assembly.</p>","PeriodicalId":18735,"journal":{"name":"Molecular Biology of the Cell","volume":" ","pages":"ar48"},"PeriodicalIF":3.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143527873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rajshikhar Gupta, Paulina Schärer, Yawen Liao, Bibhas Roy, Roger M Benoit, G V Shivashankar
{"title":"Regulation of p65 nuclear localization and chromatin states by compressive force.","authors":"Rajshikhar Gupta, Paulina Schärer, Yawen Liao, Bibhas Roy, Roger M Benoit, G V Shivashankar","doi":"10.1091/mbc.E23-11-0431","DOIUrl":"10.1091/mbc.E23-11-0431","url":null,"abstract":"<p><p>The tumor microenvironment (TME) is a dynamic ecosystem, that evolves with the developing tumor to support its growth and metastasis. A key aspect of TME evolution is the recruitment of stromal fibroblasts, carried out via the release of various tumor signals including tumor necrosis factor (TNFα). These tumor signals in turn alter the mechanical properties of the TME as the tumor grows. Because of the important role of stromal cells in supporting tumor progression, new therapies aim to target stromal fibroblasts. However, these therapies have been unsuccessful in part due to the limited understanding of cross-talk between chemical and altered mechanical signaling within stromal fibroblasts. To investigate this, we designed a coculture assay with YFP-TNFα releasing spheroids embedded within collagen gels alongside fibroblasts to mimic the stromal response within the TME. This resulted in the nuclear translocation of p65 in the stromal fibroblasts which was further intensified by the addition of compressive stress. The combination of mechanical and chemical signals led to cytoskeletal disruption and induced a distinct chromatin state in the stromal fibroblasts. These results highlight the important cross-talk between cytokine signaling and mechanical forces on stromal cells within the TME and facilitate the development of a better spheroid model for therapeutic interventions.</p>","PeriodicalId":18735,"journal":{"name":"Molecular Biology of the Cell","volume":" ","pages":"ar37"},"PeriodicalIF":3.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143255835","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Miho Sakato-Antoku, Nikisha Patel, Mayu Inaba, Qinhui Rao, Jun Yang, Ramila S Patel-King, Kazuo Inaba, Jeremy L Balsbaugh, Stephen M King
{"title":"Phyloproteomics reveals conserved patterns of axonemal dynein methylation across the motile ciliated eukaryotes.","authors":"Miho Sakato-Antoku, Nikisha Patel, Mayu Inaba, Qinhui Rao, Jun Yang, Ramila S Patel-King, Kazuo Inaba, Jeremy L Balsbaugh, Stephen M King","doi":"10.1091/mbc.E25-02-0055","DOIUrl":"10.1091/mbc.E25-02-0055","url":null,"abstract":"<p><p>Axonemal dynein assembly occurs in the cytoplasm and numerous cytosolic factors are specifically required for this process. Recently, one factor (DNAAF3/PF22) was identified as a methyltransferase. Examination of <i>Chlamydomonas</i> dyneins found they are methylated at substoichiometric levels on multiple sites, including Lys and Arg residues in several of the nucleotide-binding domains and on the microtubule-binding region. Given the highly conserved nature of axonemal dyneins, one key question is whether methylation happens only in dyneins from the chlorophyte algae, or whether these modifications occur more broadly throughout the motile ciliated eukaryotes. Here we take a phyloproteomic approach and examine dynein methylation in a wide range of eukaryotic organisms bearing motile cilia. We find unambiguous evidence for methylation of axonemal dyneins in alveolates, chlorophytes, trypanosomes, and a broad range of metazoans. Intriguingly, we were unable to identify a single instance of methylation on <i>Drosophila melanogaster</i> sperm dyneins even though dipterans express a Dnaaf3 orthologue, or in spermatozoids of the fern <i>Ceratopteris</i>, which assembles inner arms but lacks both outer arm dyneins and DNAAF3. Thus, methylation of axonemal dyneins has been broadly conserved in most eukaryotic groups and has the potential to variably modify the function of these motors.</p>","PeriodicalId":18735,"journal":{"name":"Molecular Biology of the Cell","volume":" ","pages":"ar49"},"PeriodicalIF":3.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Joseph A Danos, Merve Addemir, Lily McGettigan, Daniel W Summers
{"title":"Nerve growth factor signaling tunes axon maintenance protein abundance and kinetics of Wallerian degeneration.","authors":"Joseph A Danos, Merve Addemir, Lily McGettigan, Daniel W Summers","doi":"10.1091/mbc.E25-01-0005","DOIUrl":"10.1091/mbc.E25-01-0005","url":null,"abstract":"<p><p>Neurotrophic factors are critical for establishing functional connectivity in the nervous system and sustaining neuronal survival through adulthood. As the first neurotrophic factor purified, nerve growth factor (NGF) is extensively studied for its prolific role in axon outgrowth, pruning, and survival. Applying NGF to diseased neuronal tissue is an exciting therapeutic option and understanding how NGF regulates local axon susceptibility to pathological degeneration is critical for exploiting its full potential. Our study identifies surprising connections between NGF signaling and proteostasis of axon maintenance factors. NGF deprivation increases Nmnat2 and Stmn2 protein levels in axon segments with a corresponding delay in Wallerian degeneration. Conversely, acute NGF stimulation reduces local abundance of these axon maintenance factors and accelerates Wallerian degeneration. Pharmacological studies implicate phospholipase C as the key effector in tropomyosin-related kinase A (TrkA) activation, which drives degradation of palmitoylated Stmn2. While seemingly opposed to neuroprotective activities well-documented for NGF, downregulating Nmnat2 and Stmn2 favors axonal outgrowth over transient hypersusceptibility to Sarm1-dependent degeneration. This new facet of NGF biology has important implications for axonal remodeling during development and sustained integrity through adulthood.</p>","PeriodicalId":18735,"journal":{"name":"Molecular Biology of the Cell","volume":" ","pages":"ar46"},"PeriodicalIF":3.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Szymon Juszkiewicz, Sew-Yeu Peak-Chew, Ramanujan S Hegde
{"title":"Mechanism of chaperone recruitment and retention on mitochondrial precursors.","authors":"Szymon Juszkiewicz, Sew-Yeu Peak-Chew, Ramanujan S Hegde","doi":"10.1091/mbc.E25-01-0035","DOIUrl":"10.1091/mbc.E25-01-0035","url":null,"abstract":"<p><p>Nearly all mitochondrial proteins are imported into mitochondria from the cytosol. How nascent mitochondrial precursors acquire and sustain import competence in the cytosol under normal and stress conditions is incompletely understood. Here, we show that under normal conditions, the Hsc70 and Hsp90 systems interact with and redundantly minimize precursor degradation. During acute import stress, Hsp90 buffers precursor degradation, preserving proteins in an import-competent state until stress resolution. Unexpectedly, buffering by Hsp90 relies critically on a mitochondrial targeting signal (MTS), the absence of which greatly decreases precursor-Hsp90 interaction. Site-specific photo-cross-linking and biochemical reconstitution showed how the MTS directly engages co-chaperones of Hsc70 (St13 and Stip1) and Hsp90 (p23 and Cdc37) to facilitate chaperone retention on the mature domain. Thus, the MTS has a previously unappreciated role in regulating chaperone dynamics on mitochondrial precursors to buffer their degradation and maintain import competence, functions that may facilitate restoration of mitochondrial homeostasis after acute import stress.</p>","PeriodicalId":18735,"journal":{"name":"Molecular Biology of the Cell","volume":" ","pages":"ar39"},"PeriodicalIF":3.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7617541/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143059248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}