EMBO JournalPub Date : 2025-08-01Epub Date: 2025-06-10DOI: 10.1038/s44318-025-00485-2
Linh Thuy Mai, Sharada Swaminathan, Trieu Hai Nguyen, Etienne Collette, Tania Charpentier, Liseth Carmona-Pérez, Hamza Loucif, Alain Lamarre, Krista M Heinonen, David Langlais, Jörg H Fritz, Simona Stäger
{"title":"Transcription factor IRF-5 regulates lipid metabolism and mitochondrial function in murine CD8<sup>+</sup> T-cells during viral infection.","authors":"Linh Thuy Mai, Sharada Swaminathan, Trieu Hai Nguyen, Etienne Collette, Tania Charpentier, Liseth Carmona-Pérez, Hamza Loucif, Alain Lamarre, Krista M Heinonen, David Langlais, Jörg H Fritz, Simona Stäger","doi":"10.1038/s44318-025-00485-2","DOIUrl":"10.1038/s44318-025-00485-2","url":null,"abstract":"<p><p>Exhaustion of CD8<sup>+</sup> T-cells leads to their reduced immune functionality and is controlled by numerous transcription factors. Here we show that the transcription factor IRF-5 helps to limit functional exhaustion of murine CD8<sup>+</sup> T-cells during the chronic stage of LCMV (CL13) viral infection. Our results suggest that T-cell inhibitory receptors and transcription factor TOX, which are implicated in dampening T-cell activation and promoting exhaustion, are upregulated in infected IRF-5-deficient CD8<sup>+</sup> T-cells. In addition, these cells display a reduced capacity to produce cytokines and lower survival rates than wild-type cells. Our findings indicate that these effects are mediated by defective lipid metabolism, increased lipid peroxidation, enhanced mitochondrial ROS production, and reduced levels of oxidative phosphorylation in the absence of IRF-5. These results identify IRF-5 as an important regulator of lipid metabolism and mitochondrial function that protects CD8<sup>+</sup> T-cells from functional exhaustion during the chronic stage of viral infection.</p>","PeriodicalId":50533,"journal":{"name":"EMBO Journal","volume":" ","pages":"4280-4300"},"PeriodicalIF":8.3,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144267804","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}
EMBO JournalPub Date : 2025-08-01DOI: 10.1038/s44318-025-00491-4
Rachel E Butler, Marion Schuller, Ritu Jaiswal, Jayanta Mukhopadhyay, Jim Barber, Suzie Hingley-Wilson, Emily Wasson, Alexessander Couto Alves, Ivan Ahel, Graham R Stewart
{"title":"Author Correction: Control of replication and gene expression by ADP-ribosylation of DNA in Mycobacterium tuberculosis.","authors":"Rachel E Butler, Marion Schuller, Ritu Jaiswal, Jayanta Mukhopadhyay, Jim Barber, Suzie Hingley-Wilson, Emily Wasson, Alexessander Couto Alves, Ivan Ahel, Graham R Stewart","doi":"10.1038/s44318-025-00491-4","DOIUrl":"10.1038/s44318-025-00491-4","url":null,"abstract":"","PeriodicalId":50533,"journal":{"name":"EMBO Journal","volume":" ","pages":"4406"},"PeriodicalIF":8.3,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144499066","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}
EMBO JournalPub Date : 2025-08-01DOI: 10.1038/s44318-025-00513-1
Peter J Ratcliffe, Thomas P Keeley
{"title":"Making sense of oxygen sensing.","authors":"Peter J Ratcliffe, Thomas P Keeley","doi":"10.1038/s44318-025-00513-1","DOIUrl":"https://doi.org/10.1038/s44318-025-00513-1","url":null,"abstract":"","PeriodicalId":50533,"journal":{"name":"EMBO Journal","volume":" ","pages":""},"PeriodicalIF":8.3,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144765765","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}
EMBO JournalPub Date : 2025-08-01Epub Date: 2025-06-12DOI: 10.1038/s44318-025-00483-4
Rukmini Mukherjee, Anshu Bhattacharya, Ines Tomaskovic, João Mello-Vieira, Melinda Elaine Brunstein, Marion Başoğlu, Tineke Veenendaal, Henry Bailey, Thomas Colby, Mohit Misra, Stefan Eimer, Judith Klumperman, Christian Münch, Ivan Matic, Ivan Dikic
{"title":"Phosphoribosyl ubiquitination of SNARE proteins regulates autophagy during Legionella infection.","authors":"Rukmini Mukherjee, Anshu Bhattacharya, Ines Tomaskovic, João Mello-Vieira, Melinda Elaine Brunstein, Marion Başoğlu, Tineke Veenendaal, Henry Bailey, Thomas Colby, Mohit Misra, Stefan Eimer, Judith Klumperman, Christian Münch, Ivan Matic, Ivan Dikic","doi":"10.1038/s44318-025-00483-4","DOIUrl":"10.1038/s44318-025-00483-4","url":null,"abstract":"<p><p>Legionella pneumophila is an intracellular pathogen that causes Legionnaires' disease. The bacteria release effector proteins, some of which remodel host autophagic-lysosomal pathways. One such effector is RavZ, which delipidates ATG8 proteins, making compromising autophagy in Legionella-infected cells. Here we show that SidE effectors also affect these pathways, by mediating phosphoribosyl-ubiquitination (PR-Ub) of the autophagic SNARE proteins STX17 and SNAP29. STX17 modification induces recruitment of STX17-positive membranes from the endoplasmic reticulum to Legionella-containing phagosomes, forming replicative vacuoles. Using proximity labeling, biochemistry and Legionella infection studies, we define a mechanism by which autophagy is hijacked by bacteria to recruit ER membranes to the bacterial vacuole, via a structure bearing autophagy markers but not fusing with lysosomes. Mass-spectrometric identification of PR-Ub sites and mutational studies show that phosphoribosyl-ubiquitination of STX17 alters its interaction with ATG14L, which causes ER membranes to be recruited to the bacterial vacuole in a PI3K-dependent manner. On the other hand, phosphoribosyl-ubiquitination of SNAP29 inhibits the formation of the autophagosomal SNARE complex (STX17-SNAP29-VAMP8) via steric hindrance, thus preventing the fusion of bacterial vacuoles with lysosomes.</p>","PeriodicalId":50533,"journal":{"name":"EMBO Journal","volume":" ","pages":"4252-4279"},"PeriodicalIF":8.3,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144287016","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}
EMBO JournalPub Date : 2025-08-01Epub Date: 2025-06-16DOI: 10.1038/s44318-025-00486-1
Tamara Flohr, Markus Räschle, Johannes M Herrmann
{"title":"Dysfunctional mitochondria trap proteins in the intermembrane space.","authors":"Tamara Flohr, Markus Räschle, Johannes M Herrmann","doi":"10.1038/s44318-025-00486-1","DOIUrl":"10.1038/s44318-025-00486-1","url":null,"abstract":"<p><p>The accumulation of mitochondrial precursor proteins in the cytosol due to mitochondrial dysfunction compromises cellular proteostasis and is a hallmark of diseases. Why non-imported precursors are toxic and how eukaryotic cells prevent their accumulation in the cytosol is still poorly understood. Using a proximity labeling-based assay to globally monitor the intramitochondrial location of proteins, we show that, upon mitochondrial dysfunction, many mitochondrial matrix proteins are sequestered in the intermembrane space (IMS); something we refer to as \"mitochondrial triage of precursor proteins\" (MitoTraP). MitoTraP is not simply the result of a general translocation block at the level of the inner membrane, but specifically directs a subgroup of matrix proteins into the IMS, many of which are constituents of the mitochondrial ribosome. Using the mitoribosomal protein Mrp17 (bS6m) as a model, we found that IMS sequestration prevents its mistargeting to the nucleus, potentially averting interference with assembly of cytosolic ribosomes. Thus, MitoTraP represents a novel, so far unknown mechanism of the eukaryotic quality control system that protects the cellular proteome against the toxic effects of non-imported mitochondrial precursor proteins.</p>","PeriodicalId":50533,"journal":{"name":"EMBO Journal","volume":" ","pages":"4352-4377"},"PeriodicalIF":8.3,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144310724","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}
EMBO JournalPub Date : 2025-07-29DOI: 10.1038/s44318-025-00517-x
Maike Reinders, Bojana Kravic, Pinki Gahlot, Sandra Koska, Johannes van den Boom, Nina Schulze, Sophie Levantovsky, Stefan Kleine, Markus Kaiser, Yogesh Kulathu, Christian Behrends, Hemmo Meyer
{"title":"ATXN3 regulates lysosome regeneration after damage by targeting K48-K63-branched ubiquitin chains.","authors":"Maike Reinders, Bojana Kravic, Pinki Gahlot, Sandra Koska, Johannes van den Boom, Nina Schulze, Sophie Levantovsky, Stefan Kleine, Markus Kaiser, Yogesh Kulathu, Christian Behrends, Hemmo Meyer","doi":"10.1038/s44318-025-00517-x","DOIUrl":"https://doi.org/10.1038/s44318-025-00517-x","url":null,"abstract":"<p><p>The cellular response to lysosomal damage involves fine-tuned mechanisms of membrane repair, lysosome regeneration and lysophagy, but how these different processes are coordinated is unclear. Here we show in human cells that the deubiquitinating enzyme ATXN3 helps restore integrity of the lysosomal system after damage by targeting K48-K63-branched ubiquitin chains on regenerating lysosomes. We find that ATXN3 is required for lysophagic flux after lysosomal damage but is not involved in the initial phagophore formation on terminally damaged lysosomes. Instead, ATXN3 is recruited to a distinct subset of lysosomes that are decorated with phosphatidylinositol-(4,5)-bisphosphate and that are not yet fully reacidified. There, ATXN3, along with its partner VCP/p97, targets and turns over K48-K63-branched ubiquitin conjugates. ATXN3 thus facilitates degradation of a fraction of LAMP2 via microautophagy to regenerate the lysosomal membrane and to thereby reestablish degradative capacity needed also for completion of lysophagy. Our findings identify a key role of ATXN3 in restoring lysosomal function after lysosomal membrane damage and uncover K48-K63-branched ubiquitin chain-regulated regeneration as a critical element of the lysosomal damage stress response.</p>","PeriodicalId":50533,"journal":{"name":"EMBO Journal","volume":" ","pages":""},"PeriodicalIF":8.3,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144745796","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}
{"title":"YTHDF3 recognizes DNA N6-methyladenine and recruits ALKBH1 for 6mA removal from genomic DNA.","authors":"Xin-Hui Chen, Zi-Lu Wang, Jincui Yang, Min Chen, Si-Yi Zhao, Kun-Xiong Guo, Xuelong Zheng, Zhengwei Zhao, Xiaoqiang Chen, Jing Li, Min-Min Zhang, Ling Ran, Huifang Zhu, Xiao-Feng Gu, Guang-Rong Yan","doi":"10.1038/s44318-025-00512-2","DOIUrl":"https://doi.org/10.1038/s44318-025-00512-2","url":null,"abstract":"<p><p>DNA N<sup>6</sup>-methyladenine (6mA) is an emerging epigenetic mark in the mammalian genome. ALKBH1 preferentially exhibits 6mA demethylase activity for single-stranded DNA (ssDNA) or bubbled/bulged DNA, but not for double-stranded DNA (dsDNA). Nevertheless, ALKBH1 significantly decreases the cellular 6mA level in genomic DNA, whose prevailing DNA conformation in living mammalian cells is dsDNA. Therefore, the demethylase activity of ALKBH1 toward 6mA in genomic DNA, especially dsDNA, remains largely debated. Here, we found that YTHDF3 increases the 6mA demethylase activity of ALKBH1 in genomic DNA with different conformations, including dsDNA. Compared with ALKBH1, YTHDF3 preferentially recognizes and binds to 6mA-modified DNA with different conformations. YTHDF3 recognizes 6mA in genomic DNA, and binds ALKBH1 to recruit it to sites near 6mA in genomic DNA, thereby facilitating the ALKBH1-mediated removal of 6mA in genomic dsDNA. In summary, YTHDF3 is a novel genomic DNA reader and guides ALKBH1 to remove 6mA in human genomic DNA.</p>","PeriodicalId":50533,"journal":{"name":"EMBO Journal","volume":" ","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144719015","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}
EMBO JournalPub Date : 2025-07-17DOI: 10.1038/s44318-025-00501-5
Jesse L Turner, Laura Hinojosa-Gonzalez, Takayo Sasaki, Satoshi Uchino, Athanasios Vouzas, Mariella S Soto, Abhijit Chakraborty, Karen E Alexander, Cheryl A Fitch, Amber N Brown, Ferhat Ay, David M Gilbert
{"title":"Master transcription-factor binding sites constitute the core of early replication control elements.","authors":"Jesse L Turner, Laura Hinojosa-Gonzalez, Takayo Sasaki, Satoshi Uchino, Athanasios Vouzas, Mariella S Soto, Abhijit Chakraborty, Karen E Alexander, Cheryl A Fitch, Amber N Brown, Ferhat Ay, David M Gilbert","doi":"10.1038/s44318-025-00501-5","DOIUrl":"10.1038/s44318-025-00501-5","url":null,"abstract":"<p><p>Eukaryotic genomes replicate in a defined temporal order called the replication timing (RT) program. RT is developmentally regulated with the potential to drive cell fate transitions, but mechanisms controlling RT remain elusive. We previously identified \"Early Replication Control Elements\" (ERCEs), cis-acting elements necessary for early RT, domain-wide transcription, 3D chromatin architecture and compartmentalization in mouse embryonic stem cells (mESCs), but deletions identifying ERCEs were large and encompassed many putative regulatory elements. Here, we show that ERCEs are compound elements, whose RT activity can largely be accounted for by multiple binding sites for diverse master transcription factors (subERCEs). While deletion of subERCEs had large effects on both transcription and replication timing, deleting transcription start sites eliminated nearly all transcription with only moderate effects on replication timing. Our results suggest a model in which subERCEs are a class of transcriptional enhancers that can also organize chromatin domains structurally to support early replication timing, potentially providing a feed-forward loop to drive robust epigenomic change during cell fate transitions.</p>","PeriodicalId":50533,"journal":{"name":"EMBO Journal","volume":" ","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144660958","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}
EMBO JournalPub Date : 2025-07-16DOI: 10.1038/s44318-025-00493-2
Gabriele Zaffagnini, Miquel Solé, Juan Manuel Duran, Nikolaos P Polyzos, Elvan Böke
{"title":"The proteostatic landscape of healthy human oocytes.","authors":"Gabriele Zaffagnini, Miquel Solé, Juan Manuel Duran, Nikolaos P Polyzos, Elvan Böke","doi":"10.1038/s44318-025-00493-2","DOIUrl":"https://doi.org/10.1038/s44318-025-00493-2","url":null,"abstract":"<p><p>Oocytes, female germ cells that develop into eggs, are among the longest-lived cells in the animal body. Recent studies on mouse oocytes highlight unique adaptations in protein homeostasis (proteostasis) within these cells. However, the mechanisms of proteostasis in human oocytes remain virtually unstudied. We present the first large-scale study of proteostatic activity in human oocytes using over 100 freshly donated oocytes from 21 healthy women aged 19-34 years. We analysed the activity and distribution of lysosomes, proteasomes, and mitochondria in both immature and mature oocytes. Notably, human oocytes exhibit nearly twofold lower proteolytic activity than surrounding somatic cells, with further decreases as oocytes mature. Oocyte maturation is also coupled with lysosomal exocytosis and a decrease in mitochondrial membrane potential. We propose that reduced organelle activity preserves key cellular components critical for early embryonic development during the prolonged maturation of human oocytes. Our findings highlight the distinctive biology of human oocytes and the need to investigate human-specific reproductive biology to address challenges in female fertility.</p>","PeriodicalId":50533,"journal":{"name":"EMBO Journal","volume":" ","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144651116","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}
EMBO JournalPub Date : 2025-07-08DOI: 10.1038/s44318-025-00498-x
Antoine Sicard, Meilin Tian, Zakaria Mostefai, Sophie Shi, Cécile Cardoso, Joseph Zamith, Isabelle McCort-Tranchepain, Cécile Charrier, Pierre Paoletti, Laetitia Mony
{"title":"Optochemical profiling of NMDAR molecular diversity at synaptic and extrasynaptic sites.","authors":"Antoine Sicard, Meilin Tian, Zakaria Mostefai, Sophie Shi, Cécile Cardoso, Joseph Zamith, Isabelle McCort-Tranchepain, Cécile Charrier, Pierre Paoletti, Laetitia Mony","doi":"10.1038/s44318-025-00498-x","DOIUrl":"https://doi.org/10.1038/s44318-025-00498-x","url":null,"abstract":"<p><p>Neurotransmitter receptors are critical for neuronal communication. They often form large multimeric complexes that differ in their subunit composition, distribution, and signaling properties. N-methyl-D-aspartate receptors (NMDARs), a class of glutamate-gated ion channels with essential roles in brain development and plasticity, co-exist as multiple subtypes, with GluN2A diheteromers, GluN2B diheteromers, and GluN2A/GluN2B triheteromers prevailing in the adult forebrain. Studying individual subtypes in native tissues with subunit stoichiometry resolution remains challenging, and the relative abundance and subcellular distribution of these subtypes remain controversial. Here we develop and use the photochemical tool Opto2B for specific and reversible modulation of GluN2B diheteromers, while leaving other receptor subtypes (in particular GluN2A/GluN2B triheteromers) unaffected. Using Opto2B, we characterize the differential contribution of GluN2B diheteromers to synaptic and extrasynaptic NMDAR pools during mouse development. Our results suggest that GluN2A receptors predominate in both pools in adult hippocampal CA1 pyramidal cells, with no preferential contribution of GluN2B diheteromers to extrasynaptic currents, challenging the common view that GluN2A and GluN2B NMDARs segregate in synaptic and extrasynaptic compartments, respectively. Our study addresses long-standing questions on extrasynaptic NMDARs and paves the way for interrogating NMDAR signaling diversity with unprecedented molecular and spatio-temporal resolution.</p>","PeriodicalId":50533,"journal":{"name":"EMBO Journal","volume":" ","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144592851","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}