{"title":"拟南芥染色质重塑器 DEK3 与组蛋白和 DNA 相互作用的特征。","authors":"Rajivgandhi Sundaram, Surajit Gandhi, Claudia Jonak, Dileep Vasudevan","doi":"10.1016/j.biochi.2024.07.018","DOIUrl":null,"url":null,"abstract":"<p><p>Chromatin structure and dynamics regulate all DNA-templated processes, such as transcription, replication, and repair. Chromatin binding factors, chromatin architectural proteins, and nucleosome remodelers modulate chromatin structure and dynamics and, thereby, the various DNA-dependent processes. Arabidopsis thaliana DEK3, a member of the evolutionarily conserved DEK domain-containing chromatin architectural proteins, is an important factor for chromatin structure and function, involved in transcriptional programming to regulate flowering time and abiotic stress tolerance. AtDEK3 contains an uncharacterized N-terminal domain, a middle SAF domain (winged helix-like domain), and a C-terminal DEK domain, but their role in the interaction of AtDEK3 with histones and DNA remained poorly understood. Using biochemical and biophysical analyses, we provide a comprehensive in vitro characterization of the different AtDEK3 domains for their interaction with histone H3/H4 and DNA. AtDEK3 directly interacts with histone H3/H4 tetramers through its N-terminal domain and the C-terminal DEK domain in a 1:1 stoichiometry. Upon interaction with H3/H4, the unstructured N-terminal domain of AtDEK3 undergoes a conformational change and adopts an alpha-helical conformation. In addition, the in-solution envelope structures of the AtDEK3 domains and their complex with H3/H4 have been characterized. The SAF and DEK domains associate with double-stranded and four-way junction DNA. As DEK3 possesses a histone-interacting domain at the N- and the C-terminus and a DNA-binding domain in the middle and at the C-terminus, the protein might play a complex role as a chromatin remodeler.</p>","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Characterization of the Arabidopsis thaliana chromatin remodeler DEK3 for its interaction with histones and DNA.\",\"authors\":\"Rajivgandhi Sundaram, Surajit Gandhi, Claudia Jonak, Dileep Vasudevan\",\"doi\":\"10.1016/j.biochi.2024.07.018\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Chromatin structure and dynamics regulate all DNA-templated processes, such as transcription, replication, and repair. Chromatin binding factors, chromatin architectural proteins, and nucleosome remodelers modulate chromatin structure and dynamics and, thereby, the various DNA-dependent processes. Arabidopsis thaliana DEK3, a member of the evolutionarily conserved DEK domain-containing chromatin architectural proteins, is an important factor for chromatin structure and function, involved in transcriptional programming to regulate flowering time and abiotic stress tolerance. AtDEK3 contains an uncharacterized N-terminal domain, a middle SAF domain (winged helix-like domain), and a C-terminal DEK domain, but their role in the interaction of AtDEK3 with histones and DNA remained poorly understood. Using biochemical and biophysical analyses, we provide a comprehensive in vitro characterization of the different AtDEK3 domains for their interaction with histone H3/H4 and DNA. AtDEK3 directly interacts with histone H3/H4 tetramers through its N-terminal domain and the C-terminal DEK domain in a 1:1 stoichiometry. Upon interaction with H3/H4, the unstructured N-terminal domain of AtDEK3 undergoes a conformational change and adopts an alpha-helical conformation. In addition, the in-solution envelope structures of the AtDEK3 domains and their complex with H3/H4 have been characterized. The SAF and DEK domains associate with double-stranded and four-way junction DNA. As DEK3 possesses a histone-interacting domain at the N- and the C-terminus and a DNA-binding domain in the middle and at the C-terminus, the protein might play a complex role as a chromatin remodeler.</p>\",\"PeriodicalId\":93898,\"journal\":{\"name\":\"Biochimie\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-08-06\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Biochimie\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1016/j.biochi.2024.07.018\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Biochimie","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1016/j.biochi.2024.07.018","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
摘要
染色质结构和动态调控着所有以 DNA 为模板的过程,如转录、复制和修复。染色质结合因子、染色质结构蛋白和核小体重塑因子调节染色质结构和动态,从而调节各种 DNA 依赖过程。拟南芥 DEK3 是进化保守的含 DEK 结构域的染色质结构蛋白的一员,是染色质结构和功能的重要因子,参与转录编程以调控开花时间和非生物胁迫耐受性。AtDEK3含有一个未定性的N端结构域、一个中间的SAF结构域(翼螺旋样结构域)和一个C端DEK结构域,但它们在AtDEK3与组蛋白和DNA相互作用中的作用仍然鲜为人知。通过生化和生物物理分析,我们对 AtDEK3 不同结构域与组蛋白 H3/H4 和 DNA 的相互作用进行了全面的体外鉴定。AtDEK3 通过其 N 端结构域和 C 端 DEK 结构域以 1:1 的比例直接与组蛋白 H3/H4 四聚体相互作用。与 H3/H4 相互作用时,AtDEK3 的非结构化 N 端结构域会发生构象变化,并采用α-螺旋构象。此外,AtDEK3结构域的溶液包膜结构及其与H3/H4的复合物也得到了表征。SAF和DEK结构域与双链和四向连接DNA有联系。由于 DEK3 在 N 端和 C 端具有组蛋白相互作用结构域,在中间和 C 端具有 DNA 结合结构域,因此该蛋白可能扮演着染色质重塑者的复杂角色。
Characterization of the Arabidopsis thaliana chromatin remodeler DEK3 for its interaction with histones and DNA.
Chromatin structure and dynamics regulate all DNA-templated processes, such as transcription, replication, and repair. Chromatin binding factors, chromatin architectural proteins, and nucleosome remodelers modulate chromatin structure and dynamics and, thereby, the various DNA-dependent processes. Arabidopsis thaliana DEK3, a member of the evolutionarily conserved DEK domain-containing chromatin architectural proteins, is an important factor for chromatin structure and function, involved in transcriptional programming to regulate flowering time and abiotic stress tolerance. AtDEK3 contains an uncharacterized N-terminal domain, a middle SAF domain (winged helix-like domain), and a C-terminal DEK domain, but their role in the interaction of AtDEK3 with histones and DNA remained poorly understood. Using biochemical and biophysical analyses, we provide a comprehensive in vitro characterization of the different AtDEK3 domains for their interaction with histone H3/H4 and DNA. AtDEK3 directly interacts with histone H3/H4 tetramers through its N-terminal domain and the C-terminal DEK domain in a 1:1 stoichiometry. Upon interaction with H3/H4, the unstructured N-terminal domain of AtDEK3 undergoes a conformational change and adopts an alpha-helical conformation. In addition, the in-solution envelope structures of the AtDEK3 domains and their complex with H3/H4 have been characterized. The SAF and DEK domains associate with double-stranded and four-way junction DNA. As DEK3 possesses a histone-interacting domain at the N- and the C-terminus and a DNA-binding domain in the middle and at the C-terminus, the protein might play a complex role as a chromatin remodeler.