Journal of Biological Chemistry最新文献_第6页

Abstract 1076 Creation of a new genomically recoded organism with a single non-degenerate stop codon [摘要]1076 .一个具有单一非退化终止密码子的新基因组编码生物的创建

IF 4.8 2区生物学

Journal of Biological Chemistry Pub Date : 2025-06-13 DOI: 10.1016/j.jbc.2025.110145

Jesse Rinehart, Farren Isaacs, Michael Grome

引用次数: 0

Abstract 2355 Production of Preassembled Protein Nanopores and Their Characterization in Unsupported Lipid Bilayers 2355无负载脂质双分子层中预组装蛋白纳米孔的制备及其表征

IF 4.8 2区生物学

Journal of Biological Chemistry Pub Date : 2025-06-13 DOI: 10.1016/j.jbc.2025.110159

Lisa Keranen Burden, Annika Evenson, Sarah Koeneman, Rich Michael, Daniel Burden

引用次数: 0

Abstract 2057 Development of a Quantum Dot-Based Cell-Free Cadmium Biosensor Component with Multiplexing Potential for the Detection of Heavy Metals in Fluids 2057基于量子点的无细胞镉生物传感器组件的研制及其多路复用潜力，用于检测流体中重金属

IF 4.8 2区生物学

Journal of Biological Chemistry Pub Date : 2025-06-13 DOI: 10.1016/j.jbc.2025.110156

Sara Desai, Era Srivastava, Kevin Liu, Meghna Thakur, Gregory Ellis, Igor Medintz, Divita Mathur

引用次数: 0

Cover 封面

IF 4.8 2区生物学

Journal of Biological Chemistry Pub Date : 2025-06-13 DOI: 10.1016/s0021-9258(25)02049-6

引用次数: 0

Abstract 1302 Phylogenetic and structure guided design of metal sensitive transcription factors 1302金属敏感转录因子的系统发育和结构导向设计

IF 4.8 2区生物学

Journal of Biological Chemistry Pub Date : 2025-06-13 DOI: 10.1016/j.jbc.2025.110148

Claire Schleicher, Nathan Novy, Srivatsan Raman

引用次数: 0

Abstract 1141 A blueprint for biomolecular condensation driven by bacterial microcompartment encapsulation peptides 摘要：细菌微室包封肽驱动生物分子缩聚的蓝图

IF 4.8 2区生物学

Journal of Biological Chemistry Pub Date : 2025-06-13 DOI: 10.1016/j.jbc.2025.110147

Daniel Trettel, Cesar López, Eliana Rodrigquez, Babetta Marrone, Raul Gonzalez-Esquer

引用次数: 0

Abstract 2425 Large serine integrases: how do they know which way to go? 大型丝氨酸整合酶：它们如何知道该走哪条路？

IF 4.8 2区生物学

Journal of Biological Chemistry Pub Date : 2025-06-13 DOI: 10.1016/j.jbc.2025.110161

Phoebe Rice, Heewhan Shin, Femi Olorunniji, Phoebe Rice

引用次数: 0

Nanobodies targeting EGFR provide insight into conformations stabilized by glioblastoma mutations. 靶向EGFR的纳米体提供了对胶质母细胞瘤突变稳定构象的见解。

IF 4 2区生物学

Journal of Biological Chemistry Pub Date : 2025-06-12 DOI: 10.1016/j.jbc.2025.110374

Sean M Watson, Edward P Harvey, Novalia Pishesha, Hidde L Ploegh, Timothy A Springer

{"title":"Nanobodies targeting EGFR provide insight into conformations stabilized by glioblastoma mutations.","authors":"Sean M Watson, Edward P Harvey, Novalia Pishesha, Hidde L Ploegh, Timothy A Springer","doi":"10.1016/j.jbc.2025.110374","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.110374","url":null,"abstract":"Oncogenic mutations in the epidermal growth factor receptor (EGFR) promote tumorigenesis by stabilizing active or pre-active receptor conformations. Most EGFR-driven cancers are characterized by kinase domain mutations that directly activate the receptor. However, brain cancers such as glioblastoma multiforme (GBM) uniquely harbor mutations in the EGFR ectodomain that allosterically activate the kinase domain. Despite significant advances in understanding the physiologic and pathogenic roles of EGFR, the conformational characteristics that define ligand-independent EGFR activation in GBM remain poorly understood. In this study, we use naïve and post-immune yeast-displayed nanobody libraries to discover four nanobody groups that with benchmark nanobodies define a total of five groups with unique binding signatures and specificities for GBM mutation-stabilized conformational states. Nanobodies in groups 1 and 2 block ligand, selectively bind the inactive, tethered conformation, and favor wild-type EGFR over GBM-stabilized conformations. In contrast, nanobodies in groups 4 and 5 do not block ligand, target active or pre-active conformations, and selectively bind GBM-stabilized conformations. Additionally, nanobodies in group 3 block ligand and appear to be conformation agnostic. We observed domain-specific bias in the nanobodies' selectivity for GBM mutations, suggesting that mutations across different ectodomain regions stabilize distinct conformations. This work advances our understanding of EGFR conformational equilibria in the context of GBM. The observed cooperativity and mutation-dependent binding of nanobodies emphasize their utility in dissecting EGFR activation mechanisms and in developing targeted therapies for EGFR-driven cancers, including GBM.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":" ","pages":"110374"},"PeriodicalIF":4.0,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Regulation of Steady State Ribosomal Transcription in Mycobacterium tuberculosis: Intersection of Sigma Subunits, Superhelicity, and Transcription Factors. 结核分枝杆菌稳定状态核糖体转录的调控：Sigma亚基、超螺旋和转录因子的交叉。

IF 4 2区生物学

Journal of Biological Chemistry Pub Date : 2025-06-12 DOI: 10.1016/j.jbc.2025.110369

Ana Ruiz Manzano, Drake Jensen, Eric A Galburt

{"title":"Regulation of Steady State Ribosomal Transcription in Mycobacterium tuberculosis: Intersection of Sigma Subunits, Superhelicity, and Transcription Factors.","authors":"Ana Ruiz Manzano, Drake Jensen, Eric A Galburt","doi":"10.1016/j.jbc.2025.110369","DOIUrl":"10.1016/j.jbc.2025.110369","url":null,"abstract":"Ribosomal RNA (rRNA) regulation in Mycobacterium tuberculosis (Mtb) is tightly linked to nutrient availability, growth phase, and global gene expression, influencing Mtb's adaptability and pathogenicity. Unlike most bacteria, Mtb has a single ribosomal operon with two promoters, rrnAP3 and rrnAP1, and a high ratio of sigma (σ) factors to genome size. While σA is the primary driver of ribosomal transcription, σB has been suggested to contribute under various conditions, though its role remains unclear. Here, we quantify steady-state transcription rates in reconstituted reactions and demonstrate that σA-driven transcription from rrnAP3 dominates rRNA production, with minimal contributions from σB or rrnAP1. Kinetic analysis suggests that σB holoenzymes exhibit slower DNA unwinding and holoenzyme recycling. We also show that transcription factors CarD and RbpA reverse and buffer, respectively, the stimulatory effects of negative superhelicity on σA-driven rRNA transcription. Finally, we identify the N-terminal 205 amino acids of σA as a key determinant of its increased activity relative to σB. Our findings reveal the intricate interplay of promoter sequence, σ factor identity, DNA superhelicity, and transcription factors in shaping transcription initiation kinetics to ultimately influence rRNA production in Mtb.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":" ","pages":"110369"},"PeriodicalIF":4.0,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

ATPase-dependent duplex nucleic acid unwinding by SARS-CoV-2 nsP13 relies on facile binding and translocation along single-stranded nucleic acid. SARS-CoV-2 nsP13依赖atp酶的双核酸解绕依赖于单链核酸的易结合和易位。

IF 4 2区生物学

Journal of Biological Chemistry Pub Date : 2025-06-12 DOI: 10.1016/j.jbc.2025.110373

Jinwoo Park, Yong-Joo Jeong, Khushbu Chauhan, Hye Ran Koh, Dong-Eun Kim

{"title":"ATPase-dependent duplex nucleic acid unwinding by SARS-CoV-2 nsP13 relies on facile binding and translocation along single-stranded nucleic acid.","authors":"Jinwoo Park, Yong-Joo Jeong, Khushbu Chauhan, Hye Ran Koh, Dong-Eun Kim","doi":"10.1016/j.jbc.2025.110373","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.110373","url":null,"abstract":"Nonstructural protein 13 (nsP13) of severe acute respiratory syndrome coronary virus (SARS-CoV-2) is a superfamily 1 helicase, which is essential for viral RNA replication. This protein can unwind dsRNA and DNA with a 5' single-stranded tail in the 5'-3' direction. Previous studies have demonstrated that nsP13 efficiently unwinds double-stranded nucleic acids with a single-stranded tail through a cooperative translocation fueled by ATP hydrolysis. However, the mechanism underlying the aforementioned unwinding remains unclear. In this study, we hypothesized that the differences in unwinding efficiency among duplex nucleic acids are driven by the ATP hydrolysis-induced changes in the binding affinity of nsP13 to a single-stranded tail. When nsP13 unwinds dsDNA with a 5' single-stranded tail, a long 5' single-stranded tail enhances ATP hydrolysis and promotes DNA unwinding efficiency. When the slowly hydrolyzable ATP analog adenosine-5'-O-3-thiotriphosphate was used for dsDNA unwinding by nsP13, duplex DNA unwinding was largely diminished, whereas the binding affinity onto the single-stranded DNA was more enhanced compared with ATP. Thus, unhindered ATP hydrolysis may allow nsP13 to bind and translocate along the single-stranded nucleic acid, resulting in the efficient unwinding of duplex nucleic acids.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":" ","pages":"110373"},"PeriodicalIF":4.0,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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