In mammals, the transition from mitosis to meiosis facilitates the successful production of gametes. However, the regulatory mechanisms that control meiotic initiation remain unclear, particularly in the context of complex histone modifications. Herein, we show that KDM2A, acting as a lysine demethylase targeting H3K36me3 in male germ cells, plays an essential role in modulating meiotic entry and progression. Conditional deletion of Kdm2a in mouse pre-meiotic germ cells results in complete male sterility, with spermatogenesis ultimately arrested at the zygotene stage of meiosis. KDM2A deficiency disrupts H3K36me2/3 deposition in c-KIT+ germ cells, characterized by a reduction in H3K36me2 but a dramatic increase in H3K36me3. Furthermore, KDM2A recruits the transcription factor E2F1 and its co-factor HCFC1 to the promoters of key genes required for meiosis entry and progression, such as Stra8, Meiosin, Spo11, and Sycp1. Collectively, our study unveils an essential role for KDM2A in mediating H3K36me2/3 deposition and controlling the programmed gene expression necessary for the transition from mitosis to meiosis during spermatogenesis.
{"title":"Histone demethylase KDM2A recruits HCFC1 and E2F1 to orchestrate male germ cell meiotic entry and progression.","authors":"Shenglei Feng, Yiqian Gui, Shi Yin, Xinxin Xiong, Kuan Liu, Jinmei Li, Juan Dong, Xixiang Ma, Shunchang Zhou, Bingqian Zhang, Shiyu Yang, Fengli Wang, Xiaoli Wang, Xiaohua Jiang, Shuiqiao Yuan","doi":"10.1038/s44318-024-00203-4","DOIUrl":"10.1038/s44318-024-00203-4","url":null,"abstract":"<p><p>In mammals, the transition from mitosis to meiosis facilitates the successful production of gametes. However, the regulatory mechanisms that control meiotic initiation remain unclear, particularly in the context of complex histone modifications. Herein, we show that KDM2A, acting as a lysine demethylase targeting H3K36me3 in male germ cells, plays an essential role in modulating meiotic entry and progression. Conditional deletion of Kdm2a in mouse pre-meiotic germ cells results in complete male sterility, with spermatogenesis ultimately arrested at the zygotene stage of meiosis. KDM2A deficiency disrupts H3K36me2/3 deposition in c-KIT<sup>+</sup> germ cells, characterized by a reduction in H3K36me2 but a dramatic increase in H3K36me3. Furthermore, KDM2A recruits the transcription factor E2F1 and its co-factor HCFC1 to the promoters of key genes required for meiosis entry and progression, such as Stra8, Meiosin, Spo11, and Sycp1. Collectively, our study unveils an essential role for KDM2A in mediating H3K36me2/3 deposition and controlling the programmed gene expression necessary for the transition from mitosis to meiosis during spermatogenesis.</p>","PeriodicalId":50533,"journal":{"name":"EMBO Journal","volume":" ","pages":"4197-4227"},"PeriodicalIF":9.4,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11448500/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142005775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-01Epub Date: 2024-08-22DOI: 10.1038/s44318-024-00206-1
Man Xu, Jason J Hong, Xiyuan Zhang, Ming Sun, Xingyu Liu, Jeeyoun Kang, Hannah Stack, Wendy Fang, Haiyan Lei, Xavier Lacoste, Reona Okada, Raina Jung, Rosa Nguyen, Jack F Shern, Carol J Thiele, Zhihui Liu
Tumor cell heterogeneity defines therapy responsiveness in neuroblastoma (NB), a cancer derived from neural crest cells. NB consists of two primary subtypes: adrenergic and mesenchymal. Adrenergic traits predominate in NB tumors, while mesenchymal features becomes enriched post-chemotherapy or after relapse. The interconversion between these subtypes contributes to NB lineage plasticity, but the underlying mechanisms driving this phenotypic switching remain unclear. Here, we demonstrate that SWI/SNF chromatin remodeling complex ATPases are essential in establishing an mesenchymal gene-permissive chromatin state in adrenergic-type NB, facilitating lineage plasticity. Targeting SWI/SNF ATPases with SMARCA2/4 dual degraders effectively inhibits NB cell proliferation, invasion, and notably, cellular plasticity, thereby preventing chemotherapy resistance. Mechanistically, depletion of SWI/SNF ATPases compacts cis-regulatory elements, diminishes enhancer activity, and displaces core transcription factors (MYCN, HAND2, PHOX2B, and GATA3) from DNA, thereby suppressing transcriptional programs associated with plasticity. These findings underscore the pivotal role of SWI/SNF ATPases in driving intrinsic plasticity and therapy resistance in neuroblastoma, highlighting an epigenetic target for combinational treatments in this cancer.
肿瘤细胞的异质性决定了神经母细胞瘤(NB)的治疗反应性,这是一种源自神经嵴细胞的癌症。神经母细胞瘤包括两种主要亚型:肾上腺素能型和间质型。肾上腺素能特性在 NB 肿瘤中占主导地位,而间质特性则在化疗后或复发后变得丰富。这些亚型之间的相互转换有助于NB血统的可塑性,但驱动这种表型转换的潜在机制仍不清楚。在这里,我们证明了SWI/SNF染色质重塑复合体ATP酶在肾上腺素能型NB中建立间质基因允许的染色质状态、促进谱系可塑性方面的重要作用。用SMARCA2/4双降解器靶向SWI/SNF ATP酶可有效抑制NB细胞的增殖、侵袭,尤其是细胞的可塑性,从而防止化疗耐药。从机理上讲,耗尽SWI/SNF ATP酶会压缩顺式调节元件,降低增强子活性,并从DNA中移除核心转录因子(MYCN、HAND2、PHOX2B和GATA3),从而抑制与可塑性相关的转录程序。这些发现强调了SWI/SNF ATP酶在驱动神经母细胞瘤内在可塑性和耐药性方面的关键作用,突出了该癌症综合治疗的表观遗传学靶点。
{"title":"Targeting SWI/SNF ATPases reduces neuroblastoma cell plasticity.","authors":"Man Xu, Jason J Hong, Xiyuan Zhang, Ming Sun, Xingyu Liu, Jeeyoun Kang, Hannah Stack, Wendy Fang, Haiyan Lei, Xavier Lacoste, Reona Okada, Raina Jung, Rosa Nguyen, Jack F Shern, Carol J Thiele, Zhihui Liu","doi":"10.1038/s44318-024-00206-1","DOIUrl":"10.1038/s44318-024-00206-1","url":null,"abstract":"<p><p>Tumor cell heterogeneity defines therapy responsiveness in neuroblastoma (NB), a cancer derived from neural crest cells. NB consists of two primary subtypes: adrenergic and mesenchymal. Adrenergic traits predominate in NB tumors, while mesenchymal features becomes enriched post-chemotherapy or after relapse. The interconversion between these subtypes contributes to NB lineage plasticity, but the underlying mechanisms driving this phenotypic switching remain unclear. Here, we demonstrate that SWI/SNF chromatin remodeling complex ATPases are essential in establishing an mesenchymal gene-permissive chromatin state in adrenergic-type NB, facilitating lineage plasticity. Targeting SWI/SNF ATPases with SMARCA2/4 dual degraders effectively inhibits NB cell proliferation, invasion, and notably, cellular plasticity, thereby preventing chemotherapy resistance. Mechanistically, depletion of SWI/SNF ATPases compacts cis-regulatory elements, diminishes enhancer activity, and displaces core transcription factors (MYCN, HAND2, PHOX2B, and GATA3) from DNA, thereby suppressing transcriptional programs associated with plasticity. These findings underscore the pivotal role of SWI/SNF ATPases in driving intrinsic plasticity and therapy resistance in neuroblastoma, highlighting an epigenetic target for combinational treatments in this cancer.</p>","PeriodicalId":50533,"journal":{"name":"EMBO Journal","volume":" ","pages":"4522-4541"},"PeriodicalIF":9.4,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11480351/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142037607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-01DOI: 10.1038/s44318-024-00230-1
Joycelyn Tan, Sam Virtue, Dougall M Norris, Olivia J Conway, Ming Yang, Guillaume Bidault, Christopher Gribben, Fatima Lugtu, Ioannis Kamzolas, James R Krycer, Richard J Mills, Lu Liang, Conceição Pereira, Martin Dale, Amber S Shun-Shion, Harry Jm Baird, James A Horscroft, Alice P Sowton, Marcella Ma, Stefania Carobbio, Evangelia Petsalaki, Andrew J Murray, David C Gershlick, James A Nathan, James E Hudson, Ludovic Vallier, Kelsey H Fisher-Wellman, Christian Frezza, Antonio Vidal-Puig, Daniel J Fazakerley
{"title":"Author Correction: Limited oxygen in standard cell culture alters metabolism and function of differentiated cells.","authors":"Joycelyn Tan, Sam Virtue, Dougall M Norris, Olivia J Conway, Ming Yang, Guillaume Bidault, Christopher Gribben, Fatima Lugtu, Ioannis Kamzolas, James R Krycer, Richard J Mills, Lu Liang, Conceição Pereira, Martin Dale, Amber S Shun-Shion, Harry Jm Baird, James A Horscroft, Alice P Sowton, Marcella Ma, Stefania Carobbio, Evangelia Petsalaki, Andrew J Murray, David C Gershlick, James A Nathan, James E Hudson, Ludovic Vallier, Kelsey H Fisher-Wellman, Christian Frezza, Antonio Vidal-Puig, Daniel J Fazakerley","doi":"10.1038/s44318-024-00230-1","DOIUrl":"10.1038/s44318-024-00230-1","url":null,"abstract":"","PeriodicalId":50533,"journal":{"name":"EMBO Journal","volume":" ","pages":"4439"},"PeriodicalIF":9.4,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11445423/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142146760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-01DOI: 10.1038/s44318-024-00243-w
Arianna Mangiavacchi, Gabriele Morelli, Sjur Reppe, Alfonso Saera-Vila, Peng Liu, Benjamin Eggerschwiler, Huoming Zhang, Dalila Bensaddek, Elisa A Casanova, Carolina Medina Gomez, Vid Prijatelj, Francesco Della Valle, Nazerke Atinbayeva, Juan Carlos Izpisua Belmonte, Fernando Rivadeneira, Paolo Cinelli, Kaare Morten Gautvik, Valerio Orlando
{"title":"Author Correction: LINE-1 RNA triggers matrix formation in bone cells via a PKR-mediated inflammatory response.","authors":"Arianna Mangiavacchi, Gabriele Morelli, Sjur Reppe, Alfonso Saera-Vila, Peng Liu, Benjamin Eggerschwiler, Huoming Zhang, Dalila Bensaddek, Elisa A Casanova, Carolina Medina Gomez, Vid Prijatelj, Francesco Della Valle, Nazerke Atinbayeva, Juan Carlos Izpisua Belmonte, Fernando Rivadeneira, Paolo Cinelli, Kaare Morten Gautvik, Valerio Orlando","doi":"10.1038/s44318-024-00243-w","DOIUrl":"10.1038/s44318-024-00243-w","url":null,"abstract":"","PeriodicalId":50533,"journal":{"name":"EMBO Journal","volume":" ","pages":"4805-4806"},"PeriodicalIF":9.4,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11480486/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142300033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-01Epub Date: 2024-08-19DOI: 10.1038/s44318-024-00202-5
Thomas M Guérin, Christopher Barrington, Georgii Pobegalov, Maxim I Molodtsov, Frank Uhlmann
The ring-shaped cohesin complex topologically entraps two DNA molecules to establish sister chromatid cohesion. Cohesin also shapes the interphase chromatin landscape with wide-ranging implications for gene regulation, and cohesin is thought to achieve this by actively extruding DNA loops without topologically entrapping DNA. The 'loop extrusion' hypothesis finds motivation from in vitro observations-whether this process underlies in vivo chromatin loop formation remains untested. Here, using the budding yeast S. cerevisiae, we generate cohesin variants that have lost their ability to extrude DNA loops but retain their ability to topologically entrap DNA. Analysis of these variants suggests that in vivo chromatin loops form independently of loop extrusion. Instead, we find that transcription promotes loop formation, and acts as an extrinsic motor that expands these loops and defines their ultimate positions. Our results necessitate a re-evaluation of the loop extrusion hypothesis. We propose that cohesin, akin to sister chromatid cohesion establishment at replication forks, forms chromatin loops by DNA-DNA capture at places of transcription, thus unifying cohesin's two roles in chromosome segregation and interphase genome organisation.
环形的凝聚素复合物拓扑地夹住两个DNA分子,以建立姐妹染色单体的内聚力。人们认为,凝聚素是通过主动挤出DNA环而不拓扑夹持DNA来实现这一目的的。环挤压 "假说的动机来自体外观察,但这一过程是否是体内染色质环形成的基础仍有待验证。在这里,我们利用出芽酵母 S. cerevisiae,产生了失去挤出 DNA 环能力但保留拓扑学上夹带 DNA 能力的凝聚素变体。对这些变体的分析表明,体内染色质环的形成与环的挤出无关。相反,我们发现转录促进了环的形成,并充当了扩大这些环并确定其最终位置的外在马达。我们的研究结果要求对环路挤压假说进行重新评估。我们提出,粘合素类似于复制分叉处姐妹染色单体粘合的建立,通过DNA-DNA捕获在转录处形成染色质环,从而统一了粘合素在染色体分离和间期基因组组织中的两种作用。
{"title":"An extrinsic motor directs chromatin loop formation by cohesin.","authors":"Thomas M Guérin, Christopher Barrington, Georgii Pobegalov, Maxim I Molodtsov, Frank Uhlmann","doi":"10.1038/s44318-024-00202-5","DOIUrl":"10.1038/s44318-024-00202-5","url":null,"abstract":"<p><p>The ring-shaped cohesin complex topologically entraps two DNA molecules to establish sister chromatid cohesion. Cohesin also shapes the interphase chromatin landscape with wide-ranging implications for gene regulation, and cohesin is thought to achieve this by actively extruding DNA loops without topologically entrapping DNA. The 'loop extrusion' hypothesis finds motivation from in vitro observations-whether this process underlies in vivo chromatin loop formation remains untested. Here, using the budding yeast S. cerevisiae, we generate cohesin variants that have lost their ability to extrude DNA loops but retain their ability to topologically entrap DNA. Analysis of these variants suggests that in vivo chromatin loops form independently of loop extrusion. Instead, we find that transcription promotes loop formation, and acts as an extrinsic motor that expands these loops and defines their ultimate positions. Our results necessitate a re-evaluation of the loop extrusion hypothesis. We propose that cohesin, akin to sister chromatid cohesion establishment at replication forks, forms chromatin loops by DNA-DNA capture at places of transcription, thus unifying cohesin's two roles in chromosome segregation and interphase genome organisation.</p>","PeriodicalId":50533,"journal":{"name":"EMBO Journal","volume":" ","pages":"4173-4196"},"PeriodicalIF":9.4,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11445435/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142005773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-01Epub Date: 2024-08-19DOI: 10.1038/s44318-024-00198-y
Joshua Greig, George T Bates, Daowen I Yin, Kit Briant, Boris Simonetti, Peter J Cullen, Frances M Brodsky
The two clathrin isoforms, CHC17 and CHC22, mediate separate intracellular transport routes. CHC17 performs endocytosis and housekeeping membrane traffic in all cells. CHC22, expressed most highly in skeletal muscle, shuttles the glucose transporter GLUT4 from the ERGIC (endoplasmic-reticulum-to-Golgi intermediate compartment) directly to an intracellular GLUT4 storage compartment (GSC), from where GLUT4 can be mobilized to the plasma membrane by insulin. Here, molecular determinants distinguishing CHC22 from CHC17 trafficking are defined. We show that the C-terminal trimerization domain of CHC22 interacts with SNX5, which also binds the ERGIC tether p115. SNX5, and the functionally redundant SNX6, are required for CHC22 localization independently of their participation in the endosomal ESCPE-1 complex. In tandem, an isoform-specific patch in the CHC22 N-terminal domain separately mediates binding to p115. This dual mode of clathrin recruitment, involving interactions at both N- and C-termini of the heavy chain, is required for CHC22 targeting to ERGIC membranes to mediate the Golgi-bypass route for GLUT4 trafficking. Interference with either interaction inhibits GLUT4 targeting to the GSC, defining a bipartite mechanism regulating a key pathway in human glucose metabolism.
{"title":"CHC22 clathrin recruitment to the early secretory pathway requires two-site interaction with SNX5 and p115.","authors":"Joshua Greig, George T Bates, Daowen I Yin, Kit Briant, Boris Simonetti, Peter J Cullen, Frances M Brodsky","doi":"10.1038/s44318-024-00198-y","DOIUrl":"10.1038/s44318-024-00198-y","url":null,"abstract":"<p><p>The two clathrin isoforms, CHC17 and CHC22, mediate separate intracellular transport routes. CHC17 performs endocytosis and housekeeping membrane traffic in all cells. CHC22, expressed most highly in skeletal muscle, shuttles the glucose transporter GLUT4 from the ERGIC (endoplasmic-reticulum-to-Golgi intermediate compartment) directly to an intracellular GLUT4 storage compartment (GSC), from where GLUT4 can be mobilized to the plasma membrane by insulin. Here, molecular determinants distinguishing CHC22 from CHC17 trafficking are defined. We show that the C-terminal trimerization domain of CHC22 interacts with SNX5, which also binds the ERGIC tether p115. SNX5, and the functionally redundant SNX6, are required for CHC22 localization independently of their participation in the endosomal ESCPE-1 complex. In tandem, an isoform-specific patch in the CHC22 N-terminal domain separately mediates binding to p115. This dual mode of clathrin recruitment, involving interactions at both N- and C-termini of the heavy chain, is required for CHC22 targeting to ERGIC membranes to mediate the Golgi-bypass route for GLUT4 trafficking. Interference with either interaction inhibits GLUT4 targeting to the GSC, defining a bipartite mechanism regulating a key pathway in human glucose metabolism.</p>","PeriodicalId":50533,"journal":{"name":"EMBO Journal","volume":" ","pages":"4298-4323"},"PeriodicalIF":9.4,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11445476/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142005774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-01Epub Date: 2024-09-03DOI: 10.1038/s44318-024-00178-2
Manuel Iburg, Andrew P Anderson, Vivian T Wong, Erica D Anton, Art He, George J Lu
Gas vesicles (GVs) are gas-filled microbial organelles formed by unique 3-nm thick, amphipathic, force-bearing protein shells, which can withstand multiple atmospheric pressures and maintain a physically stable air bubble with megapascal surface tension. However, the molecular process of GV assembly remains elusive. To begin understanding this process, we have devised a high-throughput in vivo assay to determine the interactions of all 11 proteins in the pNL29 GV operon. Complete or partial deletions of the operon establish interdependent relationships among GV proteins during assembly. We also examine the tolerance of the GV assembly process to protein mutations and the cellular burdens caused by GV proteins. Clusters of GV protein interactions are revealed, proposing plausible protein complexes that are important for GV assembly. We anticipate our findings will set the stage for designing GVs that efficiently assemble in heterologous hosts during biomedical applications.
{"title":"Elucidating the assembly of gas vesicles by systematic protein-protein interaction analysis.","authors":"Manuel Iburg, Andrew P Anderson, Vivian T Wong, Erica D Anton, Art He, George J Lu","doi":"10.1038/s44318-024-00178-2","DOIUrl":"10.1038/s44318-024-00178-2","url":null,"abstract":"<p><p>Gas vesicles (GVs) are gas-filled microbial organelles formed by unique 3-nm thick, amphipathic, force-bearing protein shells, which can withstand multiple atmospheric pressures and maintain a physically stable air bubble with megapascal surface tension. However, the molecular process of GV assembly remains elusive. To begin understanding this process, we have devised a high-throughput in vivo assay to determine the interactions of all 11 proteins in the pNL29 GV operon. Complete or partial deletions of the operon establish interdependent relationships among GV proteins during assembly. We also examine the tolerance of the GV assembly process to protein mutations and the cellular burdens caused by GV proteins. Clusters of GV protein interactions are revealed, proposing plausible protein complexes that are important for GV assembly. We anticipate our findings will set the stage for designing GVs that efficiently assemble in heterologous hosts during biomedical applications.</p>","PeriodicalId":50533,"journal":{"name":"EMBO Journal","volume":" ","pages":"4156-4172"},"PeriodicalIF":9.4,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11445434/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142127228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-01Epub Date: 2024-08-14DOI: 10.1038/s44318-024-00195-1
Lucie Valentová, Tibor Füzik, Jiří Nováček, Zuzana Hlavenková, Jakub Pospíšil, Pavel Plevka
Bacteriophages are the most abundant biological entities on Earth, but our understanding of many aspects of their lifecycles is still incomplete. Here, we have structurally analysed the infection cycle of the siphophage Casadabanvirus JBD30. Using its baseplate, JBD30 attaches to Pseudomonas aeruginosa via the bacterial type IV pilus, whose subsequent retraction brings the phage to the bacterial cell surface. Cryo-electron microscopy structures of the baseplate-pilus complex show that the tripod of baseplate receptor-binding proteins attaches to the outer bacterial membrane. The tripod and baseplate then open to release three copies of the tape-measure protein, an event that is followed by DNA ejection. JBD30 major capsid proteins assemble into procapsids, which expand by 7% in diameter upon filling with phage dsDNA. The DNA-filled heads are finally joined with 180-nm-long tails, which bend easily because flexible loops mediate contacts between the successive discs of major tail proteins. It is likely that the structural features and replication mechanisms described here are conserved among siphophages that utilize the type IV pili for initial cell attachment.
噬菌体是地球上最丰富的生物实体,但我们对其生命周期许多方面的了解仍不全面。在这里,我们从结构上分析了虹吸噬菌体卡萨达班病毒 JBD30 的感染周期。JBD30 利用其基板,通过细菌的 IV 型柔毛附着到铜绿假单胞菌上,随后细菌的柔毛回缩将噬菌体带到细菌细胞表面。基板-纤毛器复合体的冷冻电镜结构显示,基板受体结合蛋白的三脚架附着在细菌外膜上。然后,三脚架和基底板打开,释放出三个拷贝的胶带测量蛋白,随后DNA喷射而出。JBD30 的主要噬菌体蛋白组装成原噬菌体,在充满噬菌体 dsDNA 后,原噬菌体直径扩大了 7%。充满 DNA 的头部最后与 180nm 长的尾部连接在一起,尾部很容易弯曲,因为柔性环介导了主要尾蛋白连续圆盘之间的接触。这里描述的结构特征和复制机制很可能在利用 IV 型纤毛器进行初始细胞附着的虹吸噬菌体中是一致的。
{"title":"Structure and replication of Pseudomonas aeruginosa phage JBD30.","authors":"Lucie Valentová, Tibor Füzik, Jiří Nováček, Zuzana Hlavenková, Jakub Pospíšil, Pavel Plevka","doi":"10.1038/s44318-024-00195-1","DOIUrl":"10.1038/s44318-024-00195-1","url":null,"abstract":"<p><p>Bacteriophages are the most abundant biological entities on Earth, but our understanding of many aspects of their lifecycles is still incomplete. Here, we have structurally analysed the infection cycle of the siphophage Casadabanvirus JBD30. Using its baseplate, JBD30 attaches to Pseudomonas aeruginosa via the bacterial type IV pilus, whose subsequent retraction brings the phage to the bacterial cell surface. Cryo-electron microscopy structures of the baseplate-pilus complex show that the tripod of baseplate receptor-binding proteins attaches to the outer bacterial membrane. The tripod and baseplate then open to release three copies of the tape-measure protein, an event that is followed by DNA ejection. JBD30 major capsid proteins assemble into procapsids, which expand by 7% in diameter upon filling with phage dsDNA. The DNA-filled heads are finally joined with 180-nm-long tails, which bend easily because flexible loops mediate contacts between the successive discs of major tail proteins. It is likely that the structural features and replication mechanisms described here are conserved among siphophages that utilize the type IV pili for initial cell attachment.</p>","PeriodicalId":50533,"journal":{"name":"EMBO Journal","volume":" ","pages":"4384-4405"},"PeriodicalIF":9.4,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11445458/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141983785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Meiosis is the developmental program that generates gametes. To produce healthy gametes, meiotic recombination creates reciprocal exchanges between each pair of homologous chromosomes that facilitate faithful chromosome segregation. Using fission yeast and biochemical, genetic, and cytological approaches, we have studied the role of CDK (cyclin-dependent kinase) in the control of Swi5-Sfr1, a Rad51-recombinase auxiliary factor involved in homolog invasion during recombination. We show that Sfr1 is a CDK target, and its phosphorylation downregulates Swi5-Sfr1 function in the meiotic prophase. Expression of a phospho-mimetic sfr1-7D mutant inhibits Rad51 binding, its robust chromosome loading, and subsequently decreases interhomolog recombination. On the other hand, the non-phosphorylatable sfr1-7A mutant alters Rad51 dynamics at late prophase, and exacerbates chromatin segregation defects and Rad51 retention observed in dbl2 deletion mutants when combined with them. We propose Sfr1 phospho-inhibition as a novel cell-cycle-dependent mechanism, which ensures timely resolution of recombination intermediates and successful chromosome distribution into the gametes. Furthermore, the N-terminal disordered part of Sfr1, an evolutionarily conserved feature, serves as a regulatory platform coordinating this phospho-regulation, protein localization and stability, with several CDK sites and regulatory sequences being conserved.
{"title":"CDK phosphorylation of Sfr1 downregulates Rad51 function in late-meiotic homolog invasions.","authors":"Inés Palacios-Blanco, Lucía Gómez, María Bort, Nina Mayerová, Silvia Bágeľová Poláková, Cristina Martín-Castellanos","doi":"10.1038/s44318-024-00205-2","DOIUrl":"10.1038/s44318-024-00205-2","url":null,"abstract":"<p><p>Meiosis is the developmental program that generates gametes. To produce healthy gametes, meiotic recombination creates reciprocal exchanges between each pair of homologous chromosomes that facilitate faithful chromosome segregation. Using fission yeast and biochemical, genetic, and cytological approaches, we have studied the role of CDK (cyclin-dependent kinase) in the control of Swi5-Sfr1, a Rad51-recombinase auxiliary factor involved in homolog invasion during recombination. We show that Sfr1 is a CDK target, and its phosphorylation downregulates Swi5-Sfr1 function in the meiotic prophase. Expression of a phospho-mimetic sfr1-7D mutant inhibits Rad51 binding, its robust chromosome loading, and subsequently decreases interhomolog recombination. On the other hand, the non-phosphorylatable sfr1-7A mutant alters Rad51 dynamics at late prophase, and exacerbates chromatin segregation defects and Rad51 retention observed in dbl2 deletion mutants when combined with them. We propose Sfr1 phospho-inhibition as a novel cell-cycle-dependent mechanism, which ensures timely resolution of recombination intermediates and successful chromosome distribution into the gametes. Furthermore, the N-terminal disordered part of Sfr1, an evolutionarily conserved feature, serves as a regulatory platform coordinating this phospho-regulation, protein localization and stability, with several CDK sites and regulatory sequences being conserved.</p>","PeriodicalId":50533,"journal":{"name":"EMBO Journal","volume":" ","pages":"4356-4383"},"PeriodicalIF":9.4,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11445502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142037606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-01Epub Date: 2024-08-29DOI: 10.1038/s44318-024-00210-5
Cristian David Peña Martinez, Mahdi Zeraati, Romain Rouet, Ohan Mazigi, Jake Y Henry, Brian Gloss, Jessica A Kretzmann, Cameron W Evans, Emanuela Ruggiero, Irene Zanin, Maja Marušič, Janez Plavec, Sara N Richter, Tracy M Bryan, Nicole M Smith, Marcel E Dinger, Sarah Kummerfeld, Daniel Christ
DNA i-motif structures are formed in the nuclei of human cells and are believed to provide critical genomic regulation. While the existence, abundance, and distribution of i-motif structures in human cells has been demonstrated and studied by immunofluorescent staining, and more recently NMR and CUT&Tag, the abundance and distribution of such structures in human genomic DNA have remained unclear. Here we utilise high-affinity i-motif immunoprecipitation followed by sequencing to map i-motifs in the purified genomic DNA of human MCF7, U2OS and HEK293T cells. Validated by biolayer interferometry and circular dichroism spectroscopy, our approach aimed to identify DNA sequences capable of i-motif formation on a genome-wide scale, revealing that such sequences are widely distributed throughout the human genome and are common in genes upregulated in G0/G1 cell cycle phases. Our findings provide experimental evidence for the widespread formation of i-motif structures in human genomic DNA and a foundational resource for future studies of their genomic, structural, and molecular roles.
DNA i-motif结构在人类细胞核中形成,被认为具有重要的基因组调控作用。虽然免疫荧光染色法以及最近的核磁共振和 CUT&Tag 技术已经证明并研究了 i-motif 结构在人类细胞中的存在、丰度和分布,但这种结构在人类基因组 DNA 中的丰度和分布仍不清楚。在这里,我们利用高亲和力 i-motif 免疫沉淀,然后进行测序,绘制了人类 MCF7、U2OS 和 HEK293T 细胞纯化基因组 DNA 中 i-motif 的图谱。通过生物层干涉测量法和圆二色性光谱法的验证,我们的方法旨在鉴定能够在全基因组范围内形成i-motif的DNA序列,结果发现此类序列广泛分布于人类基因组中,并且常见于在G0/G1细胞周期阶段上调的基因中。我们的发现为 i-motif 结构在人类基因组 DNA 中的广泛形成提供了实验证据,也为今后研究其基因组、结构和分子作用提供了基础资源。
{"title":"Human genomic DNA is widely interspersed with i-motif structures.","authors":"Cristian David Peña Martinez, Mahdi Zeraati, Romain Rouet, Ohan Mazigi, Jake Y Henry, Brian Gloss, Jessica A Kretzmann, Cameron W Evans, Emanuela Ruggiero, Irene Zanin, Maja Marušič, Janez Plavec, Sara N Richter, Tracy M Bryan, Nicole M Smith, Marcel E Dinger, Sarah Kummerfeld, Daniel Christ","doi":"10.1038/s44318-024-00210-5","DOIUrl":"10.1038/s44318-024-00210-5","url":null,"abstract":"<p><p>DNA i-motif structures are formed in the nuclei of human cells and are believed to provide critical genomic regulation. While the existence, abundance, and distribution of i-motif structures in human cells has been demonstrated and studied by immunofluorescent staining, and more recently NMR and CUT&Tag, the abundance and distribution of such structures in human genomic DNA have remained unclear. Here we utilise high-affinity i-motif immunoprecipitation followed by sequencing to map i-motifs in the purified genomic DNA of human MCF7, U2OS and HEK293T cells. Validated by biolayer interferometry and circular dichroism spectroscopy, our approach aimed to identify DNA sequences capable of i-motif formation on a genome-wide scale, revealing that such sequences are widely distributed throughout the human genome and are common in genes upregulated in G0/G1 cell cycle phases. Our findings provide experimental evidence for the widespread formation of i-motif structures in human genomic DNA and a foundational resource for future studies of their genomic, structural, and molecular roles.</p>","PeriodicalId":50533,"journal":{"name":"EMBO Journal","volume":" ","pages":"4786-4804"},"PeriodicalIF":9.4,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11480443/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142114396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}