Biochemical Journal最新文献

{"title":"ChIP happens: from biochemical origins to the modern omics toolbox for understanding steroid hormone receptors.","authors":"Thomas F Grimes, Jacob Pope, Jack Stenning, Taylor E Smith, David G Kent, Simon Baker, William J Brackenbury, Lianne I Willems, Andrew N Holding","doi":"10.1042/BCJ20253216","DOIUrl":"10.1042/BCJ20253216","url":null,"abstract":"<p><p>Nuclear steroid hormone receptors (SHRs) are ligand-activated transcription factors that mediate cellular responses to steroid hormones (SHs) through regulating gene expression. Understanding the SHR function is crucial for elucidating SH-driven physiology and pathology, including their roles in normal development, metabolism and reproduction, alongside their aberrant function in cancer, endocrine disorders and inflammatory diseases. Investigating the mechanisms that underscore SHR signalling and regulation is therefore essential for advancing our knowledge of both normal physiology and disease and is vital to the development of novel therapeutic strategies. In this review, we examine a range of methods for studying SHR interactions with chromatin and coregulator proteins, from classical biochemical assays to more advanced approaches such as PL-MS, RIME and ChIP. We also highlight potential future innovations in the field, including in situ Calling Cards and UV-induced photocross-linking RIME (UVXL-RIME), that may overcome current methodological limitations, in turn enabling the study of SHRs in increasingly physiologically relevant contexts.</p>","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"483 2","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12905503/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146103723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rules of the road: how to turn off kinesin motors.","authors":"Zhenyu Tan,Alex Missman,Michael A Cianfrocco","doi":"10.1042/bcj20253135","DOIUrl":"https://doi.org/10.1042/bcj20253135","url":null,"abstract":"Intracellular organization is crucial for supporting cell function in an ever-changing environment. The eukaryotic microtubule cytoskeleton and its associated motor proteins are the vast molecular highways and motor vehicles that connect, position, and transport cellular cargoes, ranging from the cell nucleus to vesicles to mitotic spindles. The kinesin superfamily of motor proteins carries out a diverse array of functions and is thus a key player in these processes. While the mechanochemical cycle of kinesins has been extensively studied, mechanisms of kinesin activation and inhibition are not well understood. Over the past five years, several publications have significantly advanced our understanding of kinesin regulation, showing how inesin motors are turned off via autoinhibition and kinesin-binding protein. In this review, we will delve into these recent findings to introduce some 'rules of the road' in a model that captures the complexities of kinesin regulation.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"140 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146069814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Construction and regulation of microbial cell factories for enhancing the biosynthesis of O-acetyl-L-homoserine in Escherichia coli W3110 Biosynthesis of O-acetyl-L-homoserine in E. coli.","authors":"Kun Niu,Yi-Fan Zhao,Zi-Xuan Zhang,Yao-Yao Wang,Kai-Di Xiang,Sen Cui,Zhi-Qiang Liu,Yu-Guo Zheng","doi":"10.1042/bcj20243022","DOIUrl":"https://doi.org/10.1042/bcj20243022","url":null,"abstract":"O-Acetyl-L-homoserine (OAH) is a versatile platform compound with extensive potential applications. It is a key precursor for the synthesis of L-methionine and adenosylmethionine. Currently, the microbial fermentation process for the production of OAH still face challenges, such as low fermentation yield and long fermentation period. In this study, the supply of key precursors, including L-aspartic acid, L-homoserine and acetyl-CoA, were firstly enhanced, which increased the OAH production from 7.25 g/L to 12.95 g/L in shaking flask fermentation. Subsequently, the non-oxidative glycolysis pathway (NOG pathway) was constructed and optimized to minimize the carbon loss and improve the carbon sources utilization, resulting in an increase in OAH production to 15.59 g/L. Finally, by accelerating cell division and enhancing the glucose transport system, OAH production was further improved to 17.23 g/L. The OAH production of the engineered strain OAH23 achieved a production level of 66.25 g/L in a 5-L bioreactor for 68 h, with the yield of 0.41 g/g glucose. The metabolic regulation strategy outlined in this study offers valuable insights for the efficient biosynthesis of OAH and other acetylated amino acids in E. coli.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"50 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146044553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Serendipitous Discovery of an Allosteric Inhibitor Binding Groove in the Proline Biosynthetic Enzyme Pyrroline-5-Carboxylate Reductase 1 (PYCR1).","authors":"Kaylen R Meeks,Caitlin J Mattingly,Jay C Nix,Oleksii Chuk,Mykola V Protopopov,Olga O Tarkhanova,John J Tanner","doi":"10.1042/bcj20250278","DOIUrl":"https://doi.org/10.1042/bcj20250278","url":null,"abstract":"Δ1-pyrroline-5-carboxylate (P5C) reductase 1 (PYCR1) catalyzes the NAD(P)H-dependent conversion of L-P5C to L-proline and is one of the most consistently upregulated metabolic enzymes in cancer cells. High PYCR1 expression is associated with adverse clinical outcomes, and its knockdown inhibits tumor proliferation and metastasis, motivating inhibitor discovery. All structurally validated PYCR1 inhibitors to date bind in the active site and are anchored in the L-P5C binding pocket by an anionic functional group, typically carboxylate. Seeking inhibitors with alternative anchors, we used X-ray crystallography to screen 22 fragment-like compounds (MW = 189-343 Da) from docking that represent six different carboxylic acid isosteres. Surprisingly, only one compound bound in the active site. Four other compounds were found in three adjacent remote sites located in oligomer interfaces. The compounds bind 7 Å from NADH and 10-14 Å from L-P5C, and the intervening space is blocked by protein for inhibitors in Sites 1A/1B and open for inhibitors in Site 2. Together, the three binding sites define a ligand binding hot spot groove that spans 33 Å. The remote binders inhibit PYCR1 activity with K values from the mixed model of inhibition of 32 μM to 2 mM. Co-crystal structures of PYCR1 with combinations of allosteric inhibitors, NADH, and L-P5C/proline analogs suggest the inhibitors can bind to the ternary PYCR1-L-P5C-NAD(P)H complex in addition to the free enzyme, consistent with a mixed mechanism of inhibition. The discovery of an allosteric inhibitor binding groove that accommodates multiple fragments heralds a new era of PYCR1 inhibitor design.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"37 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146015170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clostridium beijerinckii displays a soluble [FeFe]-hydrogenase/formate dehydrogenase enzyme complex that links H2 and CO2 metabolism.","authors":"Sabrina Dezzani,Abdulrahman Alogaidi,Anca Pordea,Simone Morra","doi":"10.1042/bcj20253323","DOIUrl":"https://doi.org/10.1042/bcj20253323","url":null,"abstract":"The production of biofuels by bacterial fermentation receives sustained attention due to the need to develop novel circular and sustainable technologies. Clostridium beijerinckii produces both hydrogen (H2) and carbon-based biofuels acetone, butanol, and ethanol (ABE solvents). H2 metabolism in C. beijerinckii is complex and mostly unexplored. Seven hydrogenase genes are contained in the genome, but their exact physiological role is unknown. Here, we report on the characterisation of a novel heterotetrameric soluble enzyme complex composed of an [FeFe]-hydrogenase component stably bound to a formate dehydrogenase subunit, which we name CbFdh/Hyd. We show that the four subunits form a stable complex that can be conveniently overexpressed and purified recombinantly. CbFdh/Hyd is highly sensitive to atmospheric oxygen and displays reversible catalytic features, including H2 evolution, H2 uptake, formate oxidation, and the ability to split formate into H2 and CO2 (formate hydrogen lyase activity, FHL) as well as the opposite reaction, H2-driven CO2 reduction (HDCR). CbFdh/Hyd displays functional and spectroscopic features very similar to Fdh/Hyd complexes previously described in acetogens, suggesting that this enzyme is at the basis of the previously reported unconventional ability of C. beijerinckii to fix CO2 into acetate and butyrate. CbFdh/Hyd could also represent a key player in H2 production metabolism by degrading formate produced from the decarboxylation of pyruvate.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"64 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146021698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural basis for sequence-specific DNA recognition by a group IId WRKY transcription factor GhWRKY17 in cotton.","authors":"Qin Xiao,Yu Wang,Xinci Shang,Yichang Chen,Ming Zhang,Yinhao Zhou,Xiaolei Huang,Su Qin,Jinrong Min,Guoqiang Xu,Yanli Liu","doi":"10.1042/bcj20250191","DOIUrl":"https://doi.org/10.1042/bcj20250191","url":null,"abstract":"WRKY transcription factors, a plant-specific family of transcriptional regulators, are classified into four groups (I-IV) and play pivotal roles in plant defense, development, and stress responses. These proteins are characterized by conserved WRKY domains that preferentially bind to the W-box cis-element C/TTGACC/T in target gene promoters. In Gossypium hirsutum (Gh; upland cotton), the group IId member GhWRKY17 regulates cotton fiber development by activating downstream target genes such as GhHOX3 through promoter W-box binding. However, the structural basis for its DNA recognition specificity remains elusive. Here, we present the 1.8 Å resolution crystal structure of the GhWRKY17 WRKY domain in complex with the GhHOX3 promoter DNA-the first structural characterization of a group IId WRKY protein. Structural analysis reveals that it consists of four antiparallel β-strands, with the β2-strand (harboring the conserved 249WRKYGQK255 motif) and β3-strand co-operatively engaging the DNA major groove. Key residues (R250, K251, Y252, Q254, K255, R264, Y266, Y267) form an intricate hydrogen-bonding network essential for recognizing the extended G/TTTGACC motif. Comparative structural analyses with group I/IIa/III WRKY-DNA complexes reveal that GhWRKY17's dual-strand engagement and extensively hydrogen bond-mediated specific interaction represent novel mechanistic features distinguishing group IId members from other WRKY subgroups, emphasizing the necessity for subgroup-specific investigations. These findings not only establish a structural paradigm for group IId WRKY function but also provide molecular insights for engineering cotton fiber traits through transcriptional regulation.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"8 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146021699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An expanded role for single-cell chemical genomics profiling in drug discovery.","authors":"Adeya Wyatt,Kevin Hoffer-Hawlik,Ross M Giglio,Elham Azizi,José L McFaline-Figueroa","doi":"10.1042/bcj20253273","DOIUrl":"https://doi.org/10.1042/bcj20253273","url":null,"abstract":"The integration of single-cell genomics into the chemical genetics paradigm is reshaping how researchers profile drug activity, prioritize lead candidates, and uncover new therapeutic opportunities. Traditional chemical genetic approaches, though instrumental in linking compounds to cellular phenotypes, often rely on bulk measurements that obscure important cellular heterogeneity and limit insight into mechanisms of action. By contrast, single-cell technologies offer a transformative view of how compounds influence diverse cell types and states, capturing nuanced molecular responses that further our understanding of efficacy, resistance, and polypharmacology. From cancer to neurodegenerative disorders and other disease contexts, single-cell chemical profiling enables a more precise annotation of drug-induced effects, revealing differential responses across cellular subpopulations. These methods help identify both beneficial and adverse outcomes that may not be readily predicted by a compound's structure or known targets, enhancing preclinical prioritization and supporting rational drug repurposing strategies. As these technologies mature, advances in multiplexing, multimodal profiling, and computational analysis are expanding their scalability and applicability to increasingly complex models. The resulting data-rich assays are poised to bridge critical gaps between compound screening and clinical relevance. This review highlights the evolution of chemical genomics toward single-cell resolution and outlines emerging opportunities to leverage these methods throughout the drug discovery pipeline, from early preclinical prioritization to late-stage repurposing, ultimately accelerating the development of safer, more effective therapies.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"99 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146005036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Macrophage-specific N-terminal Truncation of Plin2 Limits the Size of Lipid Droplets.","authors":"Yaru Tian,Xiaolong Huang,Yuanyuan Wei","doi":"10.1042/bcj20253345","DOIUrl":"https://doi.org/10.1042/bcj20253345","url":null,"abstract":"Lipid droplets (LDs) are dynamic organelles that exhibit cell-type-specific heterogeneity in size, composition, and abundance to support diverse cellular functions. However, the molecular mechanisms regulating this functional diversity remain poorly understood. Here, we identified a cell-type-specific truncated isoform of Plin2, which was present in macrophages but absent in adipocytes. Using N-terminal HA- and C-terminal FLAG-tagged Plin2 constructs combined with immunoprecipitation-mass spectrometry analysis in HEK293T cells or macrophages, we confirmed the N-terminal truncation and mapped the deletion site to residues 40-44. Ectopic expression of this truncated variant significantly reduced LD size in both macrophages and HEK293T cells. These findings reveal that macrophages modulate lipid storage by expressing distinct Plin2 protein variants, suggesting new therapeutic targets for lipid metabolism disorders.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"7 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145956039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and functional characterization of two CXCL17 paralogs from zebrafish.","authors":"Jie Yu,Wen-Feng Hu,Juan-Juan Wang,Ya-Li Liu,Zeng-Guang Xu,Zhan-Yun Guo","doi":"10.1042/bcj20253418","DOIUrl":"https://doi.org/10.1042/bcj20253418","url":null,"abstract":"C-X-C motif chemokine ligand 17 (CXCL17) and its receptor G protein-coupled receptor 25 (GPR25) have been identified as a significant pair in regulating immunity, but CXCL17 orthologs have not yet been identified from non-mammalian vertebrates. This study aimed to identify and characterize non-mammalian CXCL17 orthologs based on key features of mammalian CXCL17s, such as a C-terminal Xaa-Pro-Yaa motif, a signal peptide, and six cysteine residues. Two possible CXCL17 paralogs were identified from zebrafish (Danio rerio): Dr-CXCL17 (encoded by zgc:158701) and Dr-CXCL17-like (encoded by si:dkey-112a7.5). Both are previously uncharacterized proteins with unknown functions because they lack overall sequence similarity to known mammalian CXCL17s. For functional characterization, recombinant Dr-CXCL17 and Dr-CXCL17-like were prepared via overexpression in Escherichia coli and subsequent in vitro refolding and their activity was tested using NanoLuc Binary Technology (NanoBiT)-based β-arrestin recruitment assays, NanoBiT-based ligand‒receptor binding assays, and chemotaxis assays. The results showed that both Dr-CXCL17 and Dr-CXCL17-like tightly bound to and efficiently activated zebrafish GPR25 (Dr-GPR25) and induced chemotactic movement in transfected human embryonic kidney (HEK) 293T cells expressing the receptor. Deletion of three C-terminal residues in both paralogs almost eliminated their binding, activation, and chemotactic effects, which suggests that this fragment is crucial for their function. Homologs of Dr-CXCL17 or Dr-CXCL17-like were retrieved from several other ray-finned fish species, indicating that two CXCL17 paralogs are present in certain fish species and function as endogenous agonists for the fish GPR25 receptor. The identification of fish CXCL17 orthologs suggests that the CXCL17‒GPR25 pair likely originated in ancient fishes and was conserved across vertebrate lineages. This work represents the first identification of CXCL17 orthologs in non-mammalian vertebrates, paving the way for future functional studies of this ligand‒receptor pair.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"3 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145949596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular foundations of collagen triple helical assembly: the central role of prolyl-4-hydroxylation.","authors":"Ashutosh Joshi, Bhaskar Mondal, Trayambak Basak","doi":"10.1042/BCJ20253467","DOIUrl":"10.1042/BCJ20253467","url":null,"abstract":"<p><p>Collagen, the principal structural protein of the extracellular matrix, has been pivotal in the evolution of multicellular life. Among its posttranslational modifications (PTMs), prolyl-4-hydroxylation stands out as the most conserved and functionally critical. This hydroxylation not only facilitates polyproline II-like helicity in single collagen strands but also underpins the stability and integrity of the triple helix. In this review, we summarize the molecular foundations of collagen assembly, emphasizing both thermodynamic and stereo-electronic contributions of 4-hydroxyproline (4-Hyp). Insights from collagen-mimetic peptides are highlighted to elucidate main-chain torsional preferences, the positional dependence of proline ring puckering, and the correlation between 4-Hyp and enhanced thermal stability. Parallel discussions explore stereo-electronic effects revealed through quantum chemical studies, particularly charge-transfer interactions that modulate pyrrolidine ring conformation and peptide bond geometry. Finally, we summarize advances from periodic quantum mechanical calculations that quantify interstrand binding energies across different tripeptide motifs. Together, these findings provide a molecular-level perspective on how prolyl-4-hydroxylation has shaped the unique stability and evolution of collagenous helicity.</p>","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"483 2","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12862961/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145931473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}