Pub Date : 2024-10-23DOI: 10.1016/j.tibs.2024.10.003
Lin Chou, Carly J Houghton, Aaron Wacholder, Anne-Ruxandra Carvunis
Complexification of macrobiomolecules, such as homodimer to heterodimer transitions, are common during evolution. Is such complexification always adaptive? Using large-scale experiments and in-depth biochemical analyses, Després et al. recently demonstrated that an obligate heterodimer can evolve from a homodimer through neutral, nonadaptive events, and quantified key parameters required for such transitions.
{"title":"Constructive neutral evolution of homodimer to heterodimer transition.","authors":"Lin Chou, Carly J Houghton, Aaron Wacholder, Anne-Ruxandra Carvunis","doi":"10.1016/j.tibs.2024.10.003","DOIUrl":"https://doi.org/10.1016/j.tibs.2024.10.003","url":null,"abstract":"<p><p>Complexification of macrobiomolecules, such as homodimer to heterodimer transitions, are common during evolution. Is such complexification always adaptive? Using large-scale experiments and in-depth biochemical analyses, Després et al. recently demonstrated that an obligate heterodimer can evolve from a homodimer through neutral, nonadaptive events, and quantified key parameters required for such transitions.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492411","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}
Pub Date : 2024-10-22DOI: 10.1016/j.tibs.2024.09.003
Bauke Albada
The development of non-biological applications of DNA has not only resulted in delicately shaped DNA-based nano-objects with complex functions but also spawned their use for novel catalytic applications. From the multitude of applications of DNAzymes that operate on a relatively simple substrate, we have witnessed the emergence of multifunctional catalytically active DNA-based nanostructures for one of the most challenging tasks known to a chemist: the controlled and precise modification of a wild-type protein in its natural environment. By incorporating various elements associated with post-translational modification (PTM) writer enzymes into complex nanostructures, it is now possible to chemically modify a specific protein in cell lysates under the influence of an externally added trigger, clearly illustrating the promising future for this approach.
脱氧核糖核酸(DNA)非生物应用的发展不仅造就了形状精致、功能复杂的脱氧核糖核酸(DNA)纳米物体,还催生了它们在新型催化应用中的使用。从 DNA 酶在相对简单的底物上的大量应用中,我们看到了多功能催化活性 DNA 纳米结构的出现,这种结构可用于化学家已知的最具挑战性的任务之一:在自然环境中对野生型蛋白质进行可控和精确的修饰。通过在复杂的纳米结构中加入与翻译后修饰(PTM)作者酶相关的各种元素,现在有可能在外部添加触发器的影响下,对细胞裂解物中的特定蛋白质进行化学修饰,这清楚地表明了这种方法的美好前景。
{"title":"Functionalized DNA secondary structures and nanostructures for specific protein modifications.","authors":"Bauke Albada","doi":"10.1016/j.tibs.2024.09.003","DOIUrl":"https://doi.org/10.1016/j.tibs.2024.09.003","url":null,"abstract":"<p><p>The development of non-biological applications of DNA has not only resulted in delicately shaped DNA-based nano-objects with complex functions but also spawned their use for novel catalytic applications. From the multitude of applications of DNAzymes that operate on a relatively simple substrate, we have witnessed the emergence of multifunctional catalytically active DNA-based nanostructures for one of the most challenging tasks known to a chemist: the controlled and precise modification of a wild-type protein in its natural environment. By incorporating various elements associated with post-translational modification (PTM) writer enzymes into complex nanostructures, it is now possible to chemically modify a specific protein in cell lysates under the influence of an externally added trigger, clearly illustrating the promising future for this approach.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492412","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}
Pub Date : 2024-10-22DOI: 10.1016/j.tibs.2024.09.007
Philip Schmiege, Xiaochun Li
Wnt morphogens induce signaling via binding their extracellular receptors. Here, we discuss several recent structural studies showing how Wnts engage their receptors frizzled (FZD) and low-density lipoprotein receptor-related protein 5/6 (LRP5/6), how Cachd1 has been shown as an alternative initiator of Wnt signaling, and how lipidated Wnt may be produced and secreted from the cell.
{"title":"Clues into Wnt cell surface signalosomes and its biogenesis.","authors":"Philip Schmiege, Xiaochun Li","doi":"10.1016/j.tibs.2024.09.007","DOIUrl":"https://doi.org/10.1016/j.tibs.2024.09.007","url":null,"abstract":"<p><p>Wnt morphogens induce signaling via binding their extracellular receptors. Here, we discuss several recent structural studies showing how Wnts engage their receptors frizzled (FZD) and low-density lipoprotein receptor-related protein 5/6 (LRP5/6), how Cachd1 has been shown as an alternative initiator of Wnt signaling, and how lipidated Wnt may be produced and secreted from the cell.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492410","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}
Pub Date : 2024-10-16DOI: 10.1016/j.tibs.2024.10.001
Nicolas Lehrbach
The Nrf1/Nfe2L1 transcription factor is a master regulator of proteasome biogenesis. New work by Yoshida and colleagues reveals a surprising mechanism by which ubiquitination of N-glycosylated Nrf1 controls its function.
{"title":"Anything you can do, glycans do better: deglycosylation and noncanonical ubiquitination vie to rule the proteasome.","authors":"Nicolas Lehrbach","doi":"10.1016/j.tibs.2024.10.001","DOIUrl":"https://doi.org/10.1016/j.tibs.2024.10.001","url":null,"abstract":"<p><p>The Nrf1/Nfe2L1 transcription factor is a master regulator of proteasome biogenesis. New work by Yoshida and colleagues reveals a surprising mechanism by which ubiquitination of N-glycosylated Nrf1 controls its function.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142455176","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}
Pub Date : 2024-10-08DOI: 10.1016/j.tibs.2024.09.006
Kawthar F Alashoor, Jian You Wang, Salim Al-Babili
Strigolactones (SLs) perform versatile functions in plants. The different members of the α/β-hydrolase superfamily bind and hydrolyze SLs at varying rates to transduce their signal or maintain SL homeostasis. Recent work by Palayam et al. on SL-degrading carboxylesterases (CXEs) uncovers structural elements that determine the mechanism, efficiency of SL hydrolysis, and biological functions.
{"title":"The role of hydrolysis in perceiving and degrading the plant hormone strigolactones.","authors":"Kawthar F Alashoor, Jian You Wang, Salim Al-Babili","doi":"10.1016/j.tibs.2024.09.006","DOIUrl":"https://doi.org/10.1016/j.tibs.2024.09.006","url":null,"abstract":"<p><p>Strigolactones (SLs) perform versatile functions in plants. The different members of the α/β-hydrolase superfamily bind and hydrolyze SLs at varying rates to transduce their signal or maintain SL homeostasis. Recent work by Palayam et al. on SL-degrading carboxylesterases (CXEs) uncovers structural elements that determine the mechanism, efficiency of SL hydrolysis, and biological functions.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387124","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}
Pub Date : 2024-10-01DOI: 10.1016/j.tibs.2024.06.012
Sally M. Kephart , Nancy Hom , Kelly K. Lee
Protein-mediated membrane fusion is the dynamic process where specialized protein machinery undergoes dramatic conformational changes that drive two membrane bilayers together, leading to lipid mixing and opening of a fusion pore between previously separate membrane-bound compartments. Membrane fusion is an essential stage of enveloped virus entry that results in viral genome delivery into host cells. Recent studies applying cryo-electron microscopy techniques in a time-resolved fashion provide unprecedented glimpses into the interaction of viral fusion proteins and membranes, revealing fusion intermediate states from the initiation of fusion to release of the viral genome. In combination with complementary structural, biophysical, and computation modeling approaches, these advances are shedding new light on the mechanics and dynamics of protein-mediated membrane fusion.
{"title":"Visualizing intermediate stages of viral membrane fusion by cryo-electron tomography","authors":"Sally M. Kephart , Nancy Hom , Kelly K. Lee","doi":"10.1016/j.tibs.2024.06.012","DOIUrl":"10.1016/j.tibs.2024.06.012","url":null,"abstract":"<div><div>Protein-mediated membrane fusion is the dynamic process where specialized protein machinery undergoes dramatic conformational changes that drive two membrane bilayers together, leading to lipid mixing and opening of a fusion pore between previously separate membrane-bound compartments. Membrane fusion is an essential stage of enveloped virus entry that results in viral genome delivery into host cells. Recent studies applying cryo-electron microscopy techniques in a time-resolved fashion provide unprecedented glimpses into the interaction of viral fusion proteins and membranes, revealing fusion intermediate states from the initiation of fusion to release of the viral genome. In combination with complementary structural, biophysical, and computation modeling approaches, these advances are shedding new light on the mechanics and dynamics of protein-mediated membrane fusion.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"49 10","pages":"Pages 916-931"},"PeriodicalIF":11.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11455608/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141756459","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: 10.1016/j.tibs.2024.06.014
Yinfeng Guo (郭寅风) , Xin Zhang (张鑫)
Intracellular biomolecular condensates, which form via phase separation, display a highly organized ultrastructure and complex properties. Recent advances in optical imaging techniques, including super-resolution microscopy and innovative microscopic methods that leverage the intrinsic properties of the molecules observed, have transcended the limitations of conventional microscopies. These advances facilitate the exploration of condensates at finer scales and in greater detail. The deployment of these emerging but sophisticated imaging tools allows for precise observations of the multiphasic organization and physicochemical properties of these condensates, shedding light on their functions in cellular processes. In this review, we highlight recent progress in methodological innovations and their profound implications for understanding the organization and dynamics of intracellular biomolecular condensates.
{"title":"Unveiling intracellular phase separation: advances in optical imaging of biomolecular condensates","authors":"Yinfeng Guo (郭寅风) , Xin Zhang (张鑫)","doi":"10.1016/j.tibs.2024.06.014","DOIUrl":"10.1016/j.tibs.2024.06.014","url":null,"abstract":"<div><div>Intracellular biomolecular condensates, which form via phase separation, display a highly organized ultrastructure and complex properties. Recent advances in optical imaging techniques, including super-resolution microscopy and innovative microscopic methods that leverage the intrinsic properties of the molecules observed, have transcended the limitations of conventional microscopies. These advances facilitate the exploration of condensates at finer scales and in greater detail. The deployment of these emerging but sophisticated imaging tools allows for precise observations of the multiphasic organization and physicochemical properties of these condensates, shedding light on their functions in cellular processes. In this review, we highlight recent progress in methodological innovations and their profound implications for understanding the organization and dynamics of intracellular biomolecular condensates.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"49 10","pages":"Pages 901-915"},"PeriodicalIF":11.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141733209","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}
Pub Date : 2024-10-01DOI: 10.1016/S0968-0004(24)00212-3
{"title":"Advisory Board and Contents","authors":"","doi":"10.1016/S0968-0004(24)00212-3","DOIUrl":"10.1016/S0968-0004(24)00212-3","url":null,"abstract":"","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"49 10","pages":"Page i"},"PeriodicalIF":11.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142424433","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}
Pub Date : 2024-10-01DOI: 10.1016/j.tibs.2024.08.001
Emeline Recazens , Alexis A. Jourdain
Mitochondrial double-stranded RNA (dsRNA) can form spontaneously in mitochondria, blocking mitochondrial gene expression and triggering an immune response. A recent study by Kim, Tan, et al. identified a safeguard mechanism in which NOP2/Sun RNA methyltransferase 4 (NSUN4)-mediated RNA methylation (m5C) recruits the RNA degradation machinery to prevent dsRNA formation.
{"title":"Cytosine methylation flags mitochondrial RNA for degradation","authors":"Emeline Recazens , Alexis A. Jourdain","doi":"10.1016/j.tibs.2024.08.001","DOIUrl":"10.1016/j.tibs.2024.08.001","url":null,"abstract":"<div><div>Mitochondrial double-stranded RNA (dsRNA) can form spontaneously in mitochondria, blocking mitochondrial gene expression and triggering an immune response. A recent study by <span><span>Kim, Tan, <em>et al</em>.</span><svg><path></path></svg></span> identified a safeguard mechanism in which NOP2/Sun RNA methyltransferase 4 (NSUN4)-mediated RNA methylation (m<sup>5</sup>C) recruits the RNA degradation machinery to prevent dsRNA formation.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"49 10","pages":"Pages 843-845"},"PeriodicalIF":11.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142054525","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: 10.1016/S0968-0004(24)00215-9
{"title":"Subscription and Copyright Information","authors":"","doi":"10.1016/S0968-0004(24)00215-9","DOIUrl":"10.1016/S0968-0004(24)00215-9","url":null,"abstract":"","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"49 10","pages":"Page e1"},"PeriodicalIF":11.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142424434","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}