The Forkhead box O (FOXO) class of transcription factors is evolutionary conserved both structurally and at least in part also functionally. FOXO activation results in transcriptional programs that provide cellular resilience toward exogenous and endogenous challenges, especially challenges that provoke cellular oxidative stress. This FOXO-dependent mechanism of resilience explains by and large the observed longevity phenotype in model organisms where increased FOXO activity extends lifespan. This may even hold for human lifespan as genome-wide association studies show a strong linkage between FOXO3 and human lifespan. Despite decades of studies on FOXOs, there are still many unresolved questions. Here, we discuss some of these knowledge gaps, related to our general understanding of transcriptional control by FOXOs, the role of the intrinsically disordered regions that constitute over 50% of FOXOs sequence, the role of cellular context in determining isoform specificity, and finally, the importance of resilience in understanding FOXO function. The latter, we think, provides context to the evolutionary role of FOXOs. So, rather than providing an exhaustive summary of literature findings, we focus on some of the omissions in our knowledge of FOXO function. Resolving these outstanding questions, we think, will help to provide the necessary insight to know how and when to manipulate FOXO function in a manner that will contribute to healthy aging.
{"title":"The future of Forkhead box O transcription factors.","authors":"Huanjie Huang, Tianshu Gui, Boudewijn Mt Burgering","doi":"10.1042/BCJ20253428","DOIUrl":"https://doi.org/10.1042/BCJ20253428","url":null,"abstract":"<p><p>The Forkhead box O (FOXO) class of transcription factors is evolutionary conserved both structurally and at least in part also functionally. FOXO activation results in transcriptional programs that provide cellular resilience toward exogenous and endogenous challenges, especially challenges that provoke cellular oxidative stress. This FOXO-dependent mechanism of resilience explains by and large the observed longevity phenotype in model organisms where increased FOXO activity extends lifespan. This may even hold for human lifespan as genome-wide association studies show a strong linkage between FOXO3 and human lifespan. Despite decades of studies on FOXOs, there are still many unresolved questions. Here, we discuss some of these knowledge gaps, related to our general understanding of transcriptional control by FOXOs, the role of the intrinsically disordered regions that constitute over 50% of FOXOs sequence, the role of cellular context in determining isoform specificity, and finally, the importance of resilience in understanding FOXO function. The latter, we think, provides context to the evolutionary role of FOXOs. So, rather than providing an exhaustive summary of literature findings, we focus on some of the omissions in our knowledge of FOXO function. Resolving these outstanding questions, we think, will help to provide the necessary insight to know how and when to manipulate FOXO function in a manner that will contribute to healthy aging.</p>","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"483 2","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146112001","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}
Thomas F Grimes, Jacob Pope, Jack Stenning, Taylor E Smith, David G Kent, Simon Baker, William J Brackenbury, Lianne I Willems, Andrew N Holding
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.
{"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":"https://doi.org/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":4.3,"publicationDate":"2026-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yoalli Martínez-Pérez, Ignacio De la Mora-De la Mora, Gloria Hernández-Alcántara, Gabriela López-Herrera, Itzhel García-Torres, Saúl Gómez-Manzo, Alberto Olaya-Vargas, Gloria León-Avila, José Manuel Hernández-Hernandez, Fernando González-Rubio, C Yusiel Flores-Braulio, Luis A Flores-López, Sergio Enríquez-Flores
Acute lymphoblastic leukemia, particularly the T-cell subtype, remains associated with poor outcomes in relapsed and adult patients, highlighting the need for novel therapeutic strategies. Metabolic reprogramming, especially glycolytic dependence, represents a promising target. Triosephosphate isomerase (TPI), a key glycolytic enzyme, undergoes cancer-associated post-translational modifications, including deamidation and phosphorylation. Here, we evaluated the potential of proton pump inhibitors, particularly rabeprazole, to selectively target post-translational modifications-bearing TPI isoforms in Jurkat cell model. Recombinant TPI variants engineered to mimic post-translational modifications exhibited increased reactivity toward thiol-modifying agents and higher predicted binding affinities for proton pump inhibitors compared with wild-type TPI. Consistent with these properties, biochemical assays demonstrated preferential inhibition of the deamidation- and phosphorylation-mimicking proteins, with rabeprazole significantly reducing their enzymatic activity. Native gel electrophoresis of Jurkat cells protein extracts revealed drug-induced accumulation of acidic TPI isoforms, whereas normal T lymphocytes predominantly retained unmodified TPI. Rabeprazole selectively impaired intracellular TPI activity and viability in Jurkat cells, effects enhanced by dichloroacetate co-treatment. This inhibition correlated with marked accumulation of methylglyoxal and advanced glycation end products. Finally, combined dichloroacetate-rabeprazole treatment induced extensive apoptotic death in Jurkat cells while sparing normal lymphocytes. These findings identify post-translational modifications-bearing TPI isoforms as selective metabolic vulnerabilities in Jurkat cells and support the potential repurposing of thiol-modifying agents, particularly, rabeprazole, as targeted antileukemic strategies.
{"title":"Post-translational modifications of triosephosphate isomerase reveal metabolic vulnerabilities in T-ALL. Effect of combining dichloroacetic acid and the PPI rabeprazole.","authors":"Yoalli Martínez-Pérez, Ignacio De la Mora-De la Mora, Gloria Hernández-Alcántara, Gabriela López-Herrera, Itzhel García-Torres, Saúl Gómez-Manzo, Alberto Olaya-Vargas, Gloria León-Avila, José Manuel Hernández-Hernandez, Fernando González-Rubio, C Yusiel Flores-Braulio, Luis A Flores-López, Sergio Enríquez-Flores","doi":"10.1042/BCJ20253451","DOIUrl":"https://doi.org/10.1042/BCJ20253451","url":null,"abstract":"<p><p>Acute lymphoblastic leukemia, particularly the T-cell subtype, remains associated with poor outcomes in relapsed and adult patients, highlighting the need for novel therapeutic strategies. Metabolic reprogramming, especially glycolytic dependence, represents a promising target. Triosephosphate isomerase (TPI), a key glycolytic enzyme, undergoes cancer-associated post-translational modifications, including deamidation and phosphorylation. Here, we evaluated the potential of proton pump inhibitors, particularly rabeprazole, to selectively target post-translational modifications-bearing TPI isoforms in Jurkat cell model. Recombinant TPI variants engineered to mimic post-translational modifications exhibited increased reactivity toward thiol-modifying agents and higher predicted binding affinities for proton pump inhibitors compared with wild-type TPI. Consistent with these properties, biochemical assays demonstrated preferential inhibition of the deamidation- and phosphorylation-mimicking proteins, with rabeprazole significantly reducing their enzymatic activity. Native gel electrophoresis of Jurkat cells protein extracts revealed drug-induced accumulation of acidic TPI isoforms, whereas normal T lymphocytes predominantly retained unmodified TPI. Rabeprazole selectively impaired intracellular TPI activity and viability in Jurkat cells, effects enhanced by dichloroacetate co-treatment. This inhibition correlated with marked accumulation of methylglyoxal and advanced glycation end products. Finally, combined dichloroacetate-rabeprazole treatment induced extensive apoptotic death in Jurkat cells while sparing normal lymphocytes. These findings identify post-translational modifications-bearing TPI isoforms as selective metabolic vulnerabilities in Jurkat cells and support the potential repurposing of thiol-modifying agents, particularly, rabeprazole, as targeted antileukemic strategies.</p>","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146103675","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}
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.
{"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}
Kun Niu,Yi-Fan Zhao,Zi-Xuan Zhang,Yao-Yao Wang,Kai-Di Xiang,Sen Cui,Zhi-Qiang Liu,Yu-Guo Zheng
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.
{"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}
Kaylen R Meeks,Caitlin J Mattingly,Jay C Nix,Oleksii Chuk,Mykola V Protopopov,Olga O Tarkhanova,John J Tanner
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.
{"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}
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.
{"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}
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.
{"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}
Adeya Wyatt,Kevin Hoffer-Hawlik,Ross M Giglio,Elham Azizi,José L McFaline-Figueroa
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.
{"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}
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.
{"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}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号