Proximity labeling catalyzed by promiscuous enzymes,such as APEX2,has emerged as a powerful approach to characterize multiprotein complexes and protein-protein interactions.However,current methods depend on the expres...Proximity labeling catalyzed by promiscuous enzymes,such as APEX2,has emerged as a powerful approach to characterize multiprotein complexes and protein-protein interactions.However,current methods depend on the expression of exogenous fusion proteins and cannot be applied to identify proteins surrounding post-translationally modified proteins.To address this limitation,we developed a new method to label proximal proteins of interest by antibody-mediated protein A-ascorbate peroxidase 2(pA-APEX2) labeling(AMAPEX).In this method,a modified protein is bound in situ by a specific antibody,which then tethers a pA-APEX2 fusion protein.Activation of APEX2 labels the nearby proteins with biotin;the biotinylated proteins are then purified using streptavidin beads and identified by mass spectrometry.We demonstrated the utility of this approach by profiling the proximal proteins of histone modifications including H3 K27 me3,H3 K9 me3,H3 K4 me3,H4 K5 ac,and H4 K12 ac,as well as verifying the co-localization of these identified proteins with bait proteins by published ChIP-seq analysis and nucleosome immunoprecipitation.Overall,AMAPEX is an efficient method to identify proteins that are proximal to modified histones.展开更多
Dehydration of serine/threonine residues necessitates the activity of a dehydratase enzyme(domain)during the biosynthesis of RiPP.Recently,it was reported that dehydration in the thioviridamide pathway relies on a dis...Dehydration of serine/threonine residues necessitates the activity of a dehydratase enzyme(domain)during the biosynthesis of RiPP.Recently,it was reported that dehydration in the thioviridamide pathway relies on a distinct dehydratase complex that showcases the activities of a phosphotransferase TvaC for serine/threonine phosphorylation and a lyase TvaD for subsequent phosphate elimination.Herein,we report that dehydration reactions in the pathway of lantibiotic cacaoidin involves a similar dehydratase complex,CaoK/CaoY.Remarkably,this dehydratase complex exhibits flexible enzymatic activity and tolerates significant variations in its substrate peptide sequence.By binding with the leader peptide(LP)sequence of precursor peptide CaoA,the dehydration reactions proceed in a directional manner from the C-terminus of the core peptide(CP)to the N-terminus,and C-terminally truncated variants of CP are acceptable.We show that fusing CaoK to CaoY in a 1:1 molar ratio enables the resulting enzyme CaoYK to exert enhanced dehydration activity.CaoK binds with the LP to improve its own solubility and to ensure the phosphate transfer activity,while CaoY functions in a manner independently of LP.This work advances our understanding of the dehydration process during cacaoidin formation,and provides useful enzymes and methods for the studies of the rapidly emerging RiPPs.展开更多
Complex peptide natural products exhibit diverse biological functions and a wide range of physico-chemical properties.As a result,many peptides have entered the clinics for various applications.Two main routes for the...Complex peptide natural products exhibit diverse biological functions and a wide range of physico-chemical properties.As a result,many peptides have entered the clinics for various applications.Two main routes for the biosynthesis of complex peptides have evolved in nature:ribosomally synthesized and post-translationally modified peptide(RiPP)biosynthetic pathways and non-ribosomal peptide synthetases(NRPSs).Insights into both bioorthogonal peptide biosynthetic strategies led to the establishment of universal principles for each of the two routes.These universal rules can be leveraged for the targeted identification of novel peptide biosynthetic blueprints in genome sequences and used for the rational engineering of biosynthetic pathways to produce non-natural peptides.In this review,we contrast the key principles of both biosynthetic routes and compare the different biochemical strategies to install the most frequently encountered peptide modifications.In addition,the influence of the fundamentally different biosynthetic principles on past,current and future engineering ap-proaches is illustrated.Despite the different biosynthetic principles of both peptide biosynthetic routes,the arsenal of characterized peptide modifications encountered in RiPP and NRPS systems is largely overlapping.The continuous expansion of the biocatalytic toolbox of peptide modifying enzymes for both routes paves the way towards the production of complex tailor-made peptides and opens up the possibility to produce NRPS-derived peptides using the ribosomal route and vice versa.展开更多
Ubiquitin-fold modifier 1（UFM1） is one of the newly-identified ubiquitin-like proteins.Similar to ubiquitin,UFM1 is conjugated to its target proteins by a three-step enzymatic reaction.The UFM1-activating enzyme,ubi...Ubiquitin-fold modifier 1（UFM1） is one of the newly-identified ubiquitin-like proteins.Similar to ubiquitin,UFM1 is conjugated to its target proteins by a three-step enzymatic reaction.The UFM1-activating enzyme,ubiquitin-like modifier-activating enzyme 5（UBA5）,serves as the E1 to activate UFM1;UFM1-conjugating enzyme 1（UFC1） acts as the E2 to transfer the activated UFM1 to the active site of the E2;and the UFM1-specific ligase 1（UFL1） acts as the E3 to recognize its substrate,transfer,and ligate the UFM1 from E2 to the substrate.This process is called ufmylation.UFM1 chains can be cleaved from its target proteins by UFM1-specific proteases（Uf SPs）,suggesting that the ufmylation modification is reversible.UFM1 cascade is conserved among nearly all of the eukaryotic organisms,but not in yeast,and associated with several cellular activities including the endoplasmic reticulum stress response and hematopoiesis.Furthermore,the UFM1 cascade is closely related to a series of human diseases.In this review,we summarize the molecular details of this reversible modification process,the recent progress of its functional studies,as well as its implication in tumorigenesis and potential therapeutic targets for cancer.展开更多
全球化时代是一个翻译的时代,翻译研究无论是内容、方法还是视角都经历了深刻的变化。Edwin Gentzler于2017年出版了专著Translation and Rewriting in the Age of Post-Translation Studies,呼吁扩大翻译研究的界限,探索翻译前的文化...全球化时代是一个翻译的时代,翻译研究无论是内容、方法还是视角都经历了深刻的变化。Edwin Gentzler于2017年出版了专著Translation and Rewriting in the Age of Post-Translation Studies,呼吁扩大翻译研究的界限,探索翻译前的文化环境、单语文本内的翻译因素和翻译后的影响,聚焦语际和符际的改编与重写,关注边缘领域的翻译现象,从而由翻译研究转向后翻译研究。展开更多
基金supported by the National Key R&D Program of China(Grant No.2019YFA0903803)the Major Program of National Natural Science Foundation of China(Grant No.32090031)+10 种基金the General Program of National Natural Science Foundation of China(Grant Nos.31971354 and 32070610)the National Natural Science Foundation of China for Young Scholars(Grant No.32000580)the Guangdong Province Fund for Distinguished Young Scholars,China(Grant No.2021B1515020109)the Key Project from Natural Science Foundation of Guangdong Province,China(Grant No.2020B1515120034)the Guangdong Provincial Key Laboratory of Synthetic Genomics,China(Grant No.2019B030301006)the Shenzhen Key Laboratory of Synthetic Genomics,China(Grant No.ZDSYS201802061806209)the Project from Shenzhen Science and Technology Innovation Committee,China(Grant No.JCYJ20170818164014753)the Mayo Clinic Cancer Center Eagles Cancer Fund awarded to ZWthe Mayo Clinic Cancer Center Hematologic Malignancies Program awarded to ZWthe Mayo Clinic division of Hematology awarded to ZWthe Mayo Clinic Center for Biomedical Discovery awarded to SMO,United States。
文摘Proximity labeling catalyzed by promiscuous enzymes,such as APEX2,has emerged as a powerful approach to characterize multiprotein complexes and protein-protein interactions.However,current methods depend on the expression of exogenous fusion proteins and cannot be applied to identify proteins surrounding post-translationally modified proteins.To address this limitation,we developed a new method to label proximal proteins of interest by antibody-mediated protein A-ascorbate peroxidase 2(pA-APEX2) labeling(AMAPEX).In this method,a modified protein is bound in situ by a specific antibody,which then tethers a pA-APEX2 fusion protein.Activation of APEX2 labels the nearby proteins with biotin;the biotinylated proteins are then purified using streptavidin beads and identified by mass spectrometry.We demonstrated the utility of this approach by profiling the proximal proteins of histone modifications including H3 K27 me3,H3 K9 me3,H3 K4 me3,H4 K5 ac,and H4 K12 ac,as well as verifying the co-localization of these identified proteins with bait proteins by published ChIP-seq analysis and nucleosome immunoprecipitation.Overall,AMAPEX is an efficient method to identify proteins that are proximal to modified histones.
基金supported in part by grants from the National Key Research and Development Program of China(2022YFC2303100 for L.P and W.L)the National Natural Science Foundation of China(32030002 and 22193070 for W.L)+1 种基金the Science and Technology Commission of Shanghai Municipality(20XD1425200 for L.P)the CAS Youth Interdisciplinary Team(JCTD-2022-10 for L.P).
文摘Dehydration of serine/threonine residues necessitates the activity of a dehydratase enzyme(domain)during the biosynthesis of RiPP.Recently,it was reported that dehydration in the thioviridamide pathway relies on a distinct dehydratase complex that showcases the activities of a phosphotransferase TvaC for serine/threonine phosphorylation and a lyase TvaD for subsequent phosphate elimination.Herein,we report that dehydration reactions in the pathway of lantibiotic cacaoidin involves a similar dehydratase complex,CaoK/CaoY.Remarkably,this dehydratase complex exhibits flexible enzymatic activity and tolerates significant variations in its substrate peptide sequence.By binding with the leader peptide(LP)sequence of precursor peptide CaoA,the dehydration reactions proceed in a directional manner from the C-terminus of the core peptide(CP)to the N-terminus,and C-terminally truncated variants of CP are acceptable.We show that fusing CaoK to CaoY in a 1:1 molar ratio enables the resulting enzyme CaoYK to exert enhanced dehydration activity.CaoK binds with the LP to improve its own solubility and to ensure the phosphate transfer activity,while CaoY functions in a manner independently of LP.This work advances our understanding of the dehydration process during cacaoidin formation,and provides useful enzymes and methods for the studies of the rapidly emerging RiPPs.
基金the LOEWE Center for Translational Biodiversity Genomics(LOEWE-TBG).
文摘Complex peptide natural products exhibit diverse biological functions and a wide range of physico-chemical properties.As a result,many peptides have entered the clinics for various applications.Two main routes for the biosynthesis of complex peptides have evolved in nature:ribosomally synthesized and post-translationally modified peptide(RiPP)biosynthetic pathways and non-ribosomal peptide synthetases(NRPSs).Insights into both bioorthogonal peptide biosynthetic strategies led to the establishment of universal principles for each of the two routes.These universal rules can be leveraged for the targeted identification of novel peptide biosynthetic blueprints in genome sequences and used for the rational engineering of biosynthetic pathways to produce non-natural peptides.In this review,we contrast the key principles of both biosynthetic routes and compare the different biochemical strategies to install the most frequently encountered peptide modifications.In addition,the influence of the fundamentally different biosynthetic principles on past,current and future engineering ap-proaches is illustrated.Despite the different biosynthetic principles of both peptide biosynthetic routes,the arsenal of characterized peptide modifications encountered in RiPP and NRPS systems is largely overlapping.The continuous expansion of the biocatalytic toolbox of peptide modifying enzymes for both routes paves the way towards the production of complex tailor-made peptides and opens up the possibility to produce NRPS-derived peptides using the ribosomal route and vice versa.
基金supported by the National Natural Science Foundation of China (NSFCGrant Nos.31530016 and 31461143012)+2 种基金the National Basic Research Program of China (973 ProgramGrant Nos.2013CB911002 and 2015CB910601)the Scientific Research Base Development Program of the Beijing Municipal Commission of Education,China to XX
文摘Ubiquitin-fold modifier 1（UFM1） is one of the newly-identified ubiquitin-like proteins.Similar to ubiquitin,UFM1 is conjugated to its target proteins by a three-step enzymatic reaction.The UFM1-activating enzyme,ubiquitin-like modifier-activating enzyme 5（UBA5）,serves as the E1 to activate UFM1;UFM1-conjugating enzyme 1（UFC1） acts as the E2 to transfer the activated UFM1 to the active site of the E2;and the UFM1-specific ligase 1（UFL1） acts as the E3 to recognize its substrate,transfer,and ligate the UFM1 from E2 to the substrate.This process is called ufmylation.UFM1 chains can be cleaved from its target proteins by UFM1-specific proteases（Uf SPs）,suggesting that the ufmylation modification is reversible.UFM1 cascade is conserved among nearly all of the eukaryotic organisms,but not in yeast,and associated with several cellular activities including the endoplasmic reticulum stress response and hematopoiesis.Furthermore,the UFM1 cascade is closely related to a series of human diseases.In this review,we summarize the molecular details of this reversible modification process,the recent progress of its functional studies,as well as its implication in tumorigenesis and potential therapeutic targets for cancer.
文摘全球化时代是一个翻译的时代,翻译研究无论是内容、方法还是视角都经历了深刻的变化。Edwin Gentzler于2017年出版了专著Translation and Rewriting in the Age of Post-Translation Studies,呼吁扩大翻译研究的界限,探索翻译前的文化环境、单语文本内的翻译因素和翻译后的影响,聚焦语际和符际的改编与重写,关注边缘领域的翻译现象,从而由翻译研究转向后翻译研究。
