Nature chemical biology最新文献_第2页

Control of DNA demethylation by superoxide anion in plant stem cells 超氧阴离子对植物干细胞 DNA 去甲基化的控制

IF 14.8 1区生物学

Nature chemical biology Pub Date : 2024-09-12 DOI: 10.1038/s41589-024-01737-8

Shiwen Wang, Min Liu, Dongping Hu, Zhicheng Dong, Zhong Zhao

引用次数: 0

Customizable gene sensing and response without altering endogenous coding sequences 无需改变内源编码序列即可定制基因感应和响应

IF 14.8 1区生物学

Nature chemical biology Pub Date : 2024-09-12 DOI: 10.1038/s41589-024-01733-y

Fabio Caliendo, Elvira Vitu, Junmin Wang, Shuo-Hsiu Kuo, Hayden Sandt, Casper Nørskov Enghuus, Jesse Tordoff, Neslly Estrada, James J. Collins, Ron Weiss

{"title":"Customizable gene sensing and response without altering endogenous coding sequences","authors":"Fabio Caliendo, Elvira Vitu, Junmin Wang, Shuo-Hsiu Kuo, Hayden Sandt, Casper Nørskov Enghuus, Jesse Tordoff, Neslly Estrada, James J. Collins, Ron Weiss","doi":"10.1038/s41589-024-01733-y","DOIUrl":"https://doi.org/10.1038/s41589-024-01733-y","url":null,"abstract":"Synthetic biology aims to modify cellular behaviors by implementing genetic circuits that respond to changes in cell state. Integrating genetic biosensors into endogenous gene coding sequences using clustered regularly interspaced short palindromic repeats and Cas9 enables interrogation of gene expression dynamics in the appropriate chromosomal context. However, embedding a biosensor into a gene coding sequence may unpredictably alter endogenous gene regulation. To address this challenge, we developed an approach to integrate genetic biosensors into endogenous genes without modifying their coding sequence by inserting into their terminator region single-guide RNAs that activate downstream circuits. Sensor dosage responses can be fine-tuned and predicted through a mathematical model. We engineered a cell stress sensor and actuator in CHO-K1 cells that conditionally activates antiapoptotic protein BCL-2 through a downstream circuit, thereby increasing cell survival under stress conditions. Our gene sensor and actuator platform has potential use for a wide range of applications that include biomanufacturing, cell fate control and cell-based therapeutics.<figure></figure>","PeriodicalId":18832,"journal":{"name":"Nature chemical biology","volume":null,"pages":null},"PeriodicalIF":14.8,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142170880","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}

引用次数: 0

Enriching productive mutational paths accelerates enzyme evolution 丰富富有成效的突变途径可加速酶的进化

IF 14.8 1区生物学

Nature chemical biology Pub Date : 2024-09-11 DOI: 10.1038/s41589-024-01712-3

David Patsch, Thomas Schwander, Moritz Voss, Daniela Schaub, Sean Hüppi, Michael Eichenberger, Peter Stockinger, Lisa Schelbert, Sandro Giger, Francesca Peccati, Gonzalo Jiménez-Osés, Mojmír Mutný, Andreas Krause, Uwe T. Bornscheuer, Donald Hilvert, Rebecca M. Buller

{"title":"Enriching productive mutational paths accelerates enzyme evolution","authors":"David Patsch, Thomas Schwander, Moritz Voss, Daniela Schaub, Sean Hüppi, Michael Eichenberger, Peter Stockinger, Lisa Schelbert, Sandro Giger, Francesca Peccati, Gonzalo Jiménez-Osés, Mojmír Mutný, Andreas Krause, Uwe T. Bornscheuer, Donald Hilvert, Rebecca M. Buller","doi":"10.1038/s41589-024-01712-3","DOIUrl":"https://doi.org/10.1038/s41589-024-01712-3","url":null,"abstract":"Darwinian evolution has given rise to all the enzymes that enable life on Earth. Mimicking natural selection, scientists have learned to tailor these biocatalysts through recursive cycles of mutation, selection and amplification, often relying on screening large protein libraries to productively modulate the complex interplay between protein structure, dynamics and function. Here we show that by removing destabilizing mutations at the library design stage and taking advantage of recent advances in gene synthesis, we can accelerate the evolution of a computationally designed enzyme. In only five rounds of evolution, we generated a Kemp eliminase—an enzymatic model system for proton transfer from carbon—that accelerates the proton abstraction step >108-fold over the uncatalyzed reaction. Recombining the resulting variant with a previously evolved Kemp eliminase HG3.17, which exhibits similar activity but differs by 29 substitutions, allowed us to chart the topography of the designer enzyme’s fitness landscape, highlighting that a given protein scaffold can accommodate several, equally viable solutions to a specific catalytic problem.<figure></figure>","PeriodicalId":18832,"journal":{"name":"Nature chemical biology","volume":null,"pages":null},"PeriodicalIF":14.8,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142166054","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}

引用次数: 0

Substrate interactions guide cyclase engineering and lasso peptide diversification 底物相互作用引导环化酶工程和套索肽多样化

IF 14.8 1区生物学

Nature chemical biology Pub Date : 2024-09-11 DOI: 10.1038/s41589-024-01727-w

Susanna E. Barrett, Song Yin, Peter Jordan, John K. Brunson, Jessica Gordon-Nunez, Gabriella Costa Machado da Cruz, Christopher Rosario, Bethany K. Okada, Kelsey Anderson, Thomas A. Pires, Ruoyang Wang, Diwakar Shukla, Mark J. Burk, Douglas A. Mitchell

{"title":"Substrate interactions guide cyclase engineering and lasso peptide diversification","authors":"Susanna E. Barrett, Song Yin, Peter Jordan, John K. Brunson, Jessica Gordon-Nunez, Gabriella Costa Machado da Cruz, Christopher Rosario, Bethany K. Okada, Kelsey Anderson, Thomas A. Pires, Ruoyang Wang, Diwakar Shukla, Mark J. Burk, Douglas A. Mitchell","doi":"10.1038/s41589-024-01727-w","DOIUrl":"https://doi.org/10.1038/s41589-024-01727-w","url":null,"abstract":"Lasso peptides are a diverse class of naturally occurring, highly stable molecules kinetically trapped in a distinctive [1]rotaxane conformation. How the ATP-dependent lasso cyclase constrains a relatively unstructured substrate peptide into a low entropy product has remained a mystery owing to poor enzyme stability and activity in vitro. In this study, we combined substrate tolerance data with structural predictions, bioinformatic analysis, molecular dynamics simulations and mutational scanning to construct a model for the three-dimensional orientation of the substrate peptide in the lasso cyclase active site. Predicted peptide cyclase molecular contacts were validated by rationally engineering multiple, phylogenetically diverse lasso cyclases to accept substrates rejected by the wild-type enzymes. Finally, we demonstrate the utility of lasso cyclase engineering by robustly producing previously inaccessible variants that tightly bind to integrin αvβ8, which is a primary activator of transforming growth factor β and, thus, an important anti-cancer target.<figure></figure>","PeriodicalId":18832,"journal":{"name":"Nature chemical biology","volume":null,"pages":null},"PeriodicalIF":14.8,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142166059","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}

引用次数: 0

Complex structure and activation mechanism of arginine kinase McsB by McsA 精氨酸激酶 McsB 的复合结构和 McsA 激活机制

IF 14.8 1区生物学

Nature chemical biology Pub Date : 2024-09-04 DOI: 10.1038/s41589-024-01720-3

Kai Lu, Bingnan Luo, Xuan Tao, Yongbo Luo, Mingjun Ao, Bin Zheng, Xiang Xu, Xiaoyan Ma, Jingling Niu, Huinan Li, Yanxuan Xie, Zhennan Zhao, Peng Zheng, Guanbo Wang, Song Gao, Chao Wang, Wei Xia, Zhaoming Su, Zong-Wan Mao

{"title":"Complex structure and activation mechanism of arginine kinase McsB by McsA","authors":"Kai Lu, Bingnan Luo, Xuan Tao, Yongbo Luo, Mingjun Ao, Bin Zheng, Xiang Xu, Xiaoyan Ma, Jingling Niu, Huinan Li, Yanxuan Xie, Zhennan Zhao, Peng Zheng, Guanbo Wang, Song Gao, Chao Wang, Wei Xia, Zhaoming Su, Zong-Wan Mao","doi":"10.1038/s41589-024-01720-3","DOIUrl":"https://doi.org/10.1038/s41589-024-01720-3","url":null,"abstract":"Protein phosphorylation is a pivotal post-translational modification modulating various cellular processes. In Gram-positive bacteria, the protein arginine kinase McsB, along with its activator McsA, has a key role in labeling misfolded and damaged proteins during stress. However, the activation mechanism of McsB by McsA remains elusive. Here we report the cryo-electron microscopy structure of a tetrameric McsA–McsB complex at 3.41 Å resolution. Biochemical analysis indicates that the homotetrameric assembly is essential for McsB’s kinase activity. The conserved C-terminal zinc finger of McsA interacts with an extended loop in McsB, optimally orienting a critical catalytic cysteine residue. In addition, McsA binding decreases the CtsR’s affinity for McsB, enhancing McsB’s kinase activity and accelerating the turnover rate of CtsR phosphorylation. Furthermore, McsA binding also increases McsB’s thermostability, ensuring its activity under heat stress. These findings elucidate the structural basis and activation mechanism of McsB in stress response.<figure></figure>","PeriodicalId":18832,"journal":{"name":"Nature chemical biology","volume":null,"pages":null},"PeriodicalIF":14.8,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142130900","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}

引用次数: 0

Endogenous cell membrane interactome mapping for the GLP-1 receptor in different cell types 不同细胞类型中 GLP-1 受体的内源性细胞膜相互作用组图谱

IF 14.8 1区生物学

Nature chemical biology Pub Date : 2024-09-03 DOI: 10.1038/s41589-024-01714-1

Ting Dang, Jie Yu, Zhihe Cao, Bingjie Zhang, Shanshan Li, Ye Xin, Lingyun Yang, Ronghui Lou, Min Zhuang, Wenqing Shui

引用次数: 0

Illuminating GPCR trafficking 阐明 GPCR 的贩运

IF 14.8 1区生物学

Nature chemical biology Pub Date : 2024-09-02 DOI: 10.1038/s41589-024-01699-x

Michelle L. Halls

引用次数: 0

An engineered trafficking biosensor reveals a role for DNAJC13 in DOR downregulation 工程化贩运生物传感器揭示了DNAJC13在DOR下调中的作用

IF 14.8 1区生物学

Nature chemical biology Pub Date : 2024-09-02 DOI: 10.1038/s41589-024-01705-2

Brandon Novy, Aleksandra Dagunts, Tatum Weishaar, Emily E. Holland, Hayden Adoff, Emily Hutchinson, Monica De Maria, Martin Kampmann, Nikoleta G. Tsvetanova, Braden T. Lobingier

{"title":"An engineered trafficking biosensor reveals a role for DNAJC13 in DOR downregulation","authors":"Brandon Novy, Aleksandra Dagunts, Tatum Weishaar, Emily E. Holland, Hayden Adoff, Emily Hutchinson, Monica De Maria, Martin Kampmann, Nikoleta G. Tsvetanova, Braden T. Lobingier","doi":"10.1038/s41589-024-01705-2","DOIUrl":"https://doi.org/10.1038/s41589-024-01705-2","url":null,"abstract":"Trafficking of G protein-coupled receptors (GPCRs) through the endosomal–lysosomal pathway is critical to homeostatic regulation of GPCRs following activation with agonist. Identifying the genes involved in GPCR trafficking is challenging due to the complexity of sorting operations and the large number of cellular proteins involved in the process. Here, we developed a high-sensitivity biosensor for GPCR expression and agonist-induced trafficking to the lysosome by leveraging the ability of the engineered peroxidase APEX2 to activate the fluorogenic substrate Amplex UltraRed (AUR). We used the GPCR–APEX2/AUR assay to perform a genome-wide CRISPR interference screen focused on identifying genes regulating expression and trafficking of the δ-opioid receptor (DOR). We identified 492 genes consisting of both known and new regulators of DOR function. We demonstrate that one new regulator, DNAJC13, controls trafficking of multiple GPCRs, including DOR, through the endosomal–lysosomal pathway by regulating the composition of the endosomal proteome and endosomal homeostasis.<figure></figure>","PeriodicalId":18832,"journal":{"name":"Nature chemical biology","volume":null,"pages":null},"PeriodicalIF":14.8,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142118188","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}

引用次数: 0

Engineering artificial non-coding RNAs for targeted protein degradation 工程化人工非编码 RNA，实现有针对性的蛋白质降解

IF 14.8 1区生物学

Nature chemical biology Pub Date : 2024-08-30 DOI: 10.1038/s41589-024-01719-w

Congcong Cao, Aolin Li, Chaojie Xu, Baorui Wu, Lin Yao, Yuchen Liu

引用次数: 0

µMap proximity labeling in living cells reveals stress granule disassembly mechanisms 活细胞中的 µMap 近距离标记揭示了应力颗粒的解体机制

IF 14.8 1区生物学

Nature chemical biology Pub Date : 2024-08-30 DOI: 10.1038/s41589-024-01721-2

Chenmengxiao (Roderick) Pan, Steve D. Knutson, Sean W. Huth, David W. C. MacMillan

{"title":"µMap proximity labeling in living cells reveals stress granule disassembly mechanisms","authors":"Chenmengxiao (Roderick) Pan, Steve D. Knutson, Sean W. Huth, David W. C. MacMillan","doi":"10.1038/s41589-024-01721-2","DOIUrl":"https://doi.org/10.1038/s41589-024-01721-2","url":null,"abstract":"Phase-separated condensates are membrane-less intracellular structures comprising dynamic protein interactions that organize essential biological processes. Understanding the composition and dynamics of these organelles advances our knowledge of cellular behaviors and disease pathologies related to granule dysregulation. In this study, we apply microenvironment mapping with a HaloTag-based platform (HaloMap) to characterize intracellular stress granule dynamics in living cells. After validating the robustness and sensitivity of this approach, we then profile the stress granule proteome throughout the formation and disassembly and under pharmacological perturbation. These experiments reveal several ubiquitin-related modulators, including the HECT (homologous to E6AP C terminus) E3 ligases ITCH and NEDD4L, as well as the ubiquitin receptor toll-interacting protein TOLLIP, as key mediators of granule disassembly. In addition, we identify an autophagy-related pathway that promotes granule clearance. Collectively, this work establishes a general photoproximity labeling approach for unraveling intracellular protein interactomes and uncovers previously unexplored regulatory mechanisms of stress granule dynamics.<figure></figure>","PeriodicalId":18832,"journal":{"name":"Nature chemical biology","volume":null,"pages":null},"PeriodicalIF":14.8,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142101699","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}

引用次数: 0