Biochemical Journal最新文献

Structural Insights and Biophysical Characterization of p90RSK2:ERK2 complex. p90RSK2:ERK2复合物的结构见解和生物物理特性。

IF 4.1 3区生物学

Biochemical Journal Pub Date : 2025-07-25 DOI: 10.1042/bcj20253110

Evan Kobori,Hoang Nguyen,Jian Wu,Katherine Chen,Rodeon Malinovski,Susan Taylor

{"title":"Structural Insights and Biophysical Characterization of p90RSK2:ERK2 complex.","authors":"Evan Kobori,Hoang Nguyen,Jian Wu,Katherine Chen,Rodeon Malinovski,Susan Taylor","doi":"10.1042/bcj20253110","DOIUrl":"https://doi.org/10.1042/bcj20253110","url":null,"abstract":"Kinase domains are often flanked by flexible tails and intrinsically disordered regions (IDRs) that contain conserved motifs. The coordinated action and interplay of IDRs and folded kinase domains is necessary for the proper function of kinases and kinase complexes. Characterization of full length kinases and complexes is often challenging due to the flexible nature of flanking IDRs, yet necessary to fully understand their function and regulation. The p90 ribosomal S6 kinase (RSK) family is an unique kinase family with two distinct, functional kinase domains (NTK and CTK) flanked by flexible tails and a linker. RSK2 forms a stable complex with its activating kinase, ERK2, and here, we use multiple complementary techniques, HDXMS, cryoEM, and Alphafold modeling to study the full length RSK2:ERK2 complex. We find that broadly, ERK2 is more solvent protected than the NTK/CTK. The NTK N-lobe has quite high deuterium uptake, and analysis of published NTK crystal structures suggests that the NTK N-lobe is dynamic and can adopt a wide range of conformations. CryoEM reveals that the RSK2:ERK2 complex adopts a compact shape, and this is consistent with AlphaFold model of the complex hints at a possible additional interface between the NTK and ERK2. Collectively, our approach demonstrates that employing multiple complementary techniques can provide insight into the structure and biophysical characteristics of this challenging to study kinase complex.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"11 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144747817","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}

引用次数: 0

Nitration-driven structural changes in Hsp90 linked to gain of pathological functions. 硝酸驱动的Hsp90结构变化与病理功能的获得有关。

IF 4.1 3区生物学

Biochemical Journal Pub Date : 2025-07-25 DOI: 10.1042/bcj20253230

Tilottama Chatterjee,Alfonso Taboada,Isabelle E Logan,Patience N Paul,Miranda Huerta,Patrick Reardon,Rafael Radi,Ari Zeida,Maria Clara Franco

{"title":"Nitration-driven structural changes in Hsp90 linked to gain of pathological functions.","authors":"Tilottama Chatterjee,Alfonso Taboada,Isabelle E Logan,Patience N Paul,Miranda Huerta,Patrick Reardon,Rafael Radi,Ari Zeida,Maria Clara Franco","doi":"10.1042/bcj20253230","DOIUrl":"https://doi.org/10.1042/bcj20253230","url":null,"abstract":"Protein tyrosine (Y) nitration is an oxidative modification that occurs in pathological conditions such as neurodegenerative diseases and solid tumors. Depending on the location of the tyrosine residue, nitration can modify protein structure and function and affect cellular processes. We previously showed that site-specific nitration of the molecular chaperone Heat shock protein 90 (Hsp90) leads to distinct pathological gain-of-function that cannot be compensated or overcome by native Hsp90. While Hsp90 nitrated on Y33 localizes in mitochondria and decreases mitochondrial metabolism, Hsp90 nitrated on Y56 activates the purinergic receptor and calcium channel P2X7, triggering downstream signaling pathways that can lead to either cell proliferation or apoptosis, depending on the cell type. Herein, using complementary biophysical, biochemical, and in silico methods, we show that nitration on Y33 and Y56 triggers significant site-dependent local and global structural changes, linked to changes in Hsp90 activity. Nitration of these critical residues led to destabilization of Hsp90 dimer and formation of stable oligomeric species, with differential effects on Hsp90 ATPase and chaperone holdase activities depending on the nitrated residue. Molecular dynamics simulations further support the impact of nitration on Y33 and Y56 on the ATP-lid dynamics and the interaction of ATP with R392, critical to Hsp90 ATPase activity. Establishing the molecular basis of nitration-induced structural changes in Hsp90 leading to disease-driving functions is the first step towards the development of therapeutic approaches selectively targeting these pathological variants of Hsp90.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"1 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144737420","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}

引用次数: 0

The peculiar properties of mitochondrial carriers of the SLC25 family. SLC25家族线粒体载体的特殊性质。

IF 4.1 3区生物学

Biochemical Journal Pub Date : 2025-07-23 DOI: 10.1042/bcj20253171

Edmund R S Kunji,Vasiliki Mavridou,Martin S King,Camila Cimadamore-Werthein,Stephany Jaiquel Baron,Scott A Jones,Alannah C King,Roger Springett,Deepak Chand,Shane M Palmer,Denis Lacabanne,Sotiria Tavoulari,Jonathan J Ruprecht

{"title":"The peculiar properties of mitochondrial carriers of the SLC25 family.","authors":"Edmund R S Kunji,Vasiliki Mavridou,Martin S King,Camila Cimadamore-Werthein,Stephany Jaiquel Baron,Scott A Jones,Alannah C King,Roger Springett,Deepak Chand,Shane M Palmer,Denis Lacabanne,Sotiria Tavoulari,Jonathan J Ruprecht","doi":"10.1042/bcj20253171","DOIUrl":"https://doi.org/10.1042/bcj20253171","url":null,"abstract":"With 53 members, the SLC25 mitochondrial carriers form the largest solute carrier family in humans. They transport a wide variety of substrates across the mitochondrial inner membrane to generate chemical energy and to supply molecules and ions for growth and maintenance of cells. They are among the smallest transporters in nature, yet they translocate some of the largest molecules without proton leak. With one exception, they are monomeric and have an unusual three-fold pseudo-symmetric structure. These carriers also have a unique transport mechanism, which is facilitated by six structural elements, meaning that all transmembrane helices move separately, but in a co-ordinated way. In addition, there are three functional elements that are an integral part of the alternating access mechanism, which opens and closes the carrier to the mitochondrial matrix or the intermembrane space. The first is a matrix gate, comprising the matrix salt bridge network and glutamine braces on transmembrane helices H1, H3 and H5. The second is a cytoplasmic gate, containing the cytoplasmic salt bridge network and tyrosine braces on transmembrane helices H2, H4 and H6. The third functional element is a single central substrate-binding site, the access to which is controlled by the opening and closing of the two gates in an alternating way. The electrostatic properties of the binding site facilitate the exchange of charged substrates across the inner membrane in the presence of a high membrane potential. Here, we discuss the extraordinary features of mitochondrial carriers, providing new insights into one of the most complex and dynamic transport mechanisms in nature.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"55 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144701182","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}

引用次数: 0

Evolution of the conformational ensemble and allosteric networks of apoptotic caspases in chordates. 脊索动物凋亡半胱天冬酶的构象集合和变构网络的演化。

IF 4.4 3区生物学

Biochemical Journal Pub Date : 2025-07-22 DOI: 10.1042/BCJ20250001

Isha Joglekar, Mithun Nag Karadi Giridhar, David A Diaz, Ankit Deo, A Clay Clark

{"title":"Evolution of the conformational ensemble and allosteric networks of apoptotic caspases in chordates.","authors":"Isha Joglekar, Mithun Nag Karadi Giridhar, David A Diaz, Ankit Deo, A Clay Clark","doi":"10.1042/BCJ20250001","DOIUrl":"https://doi.org/10.1042/BCJ20250001","url":null,"abstract":"Apoptotic caspases exist not as static structures but as dynamic ensembles in solution, finely tuned by post translational modifications and oligomerization. The fine tuning of this ensemble by cellular cues allows caspases to influence not only apoptotic pathways but also the non-apoptotic pathways in which they are involved. These ensembles span a complex conformational landscape, from well characterized low energy states captured in structural databases to transient high energy intermediates that remain elusive and poorly understood. This limited structural view poses a major barrier to fully understanding how caspase activity is regulated and diversified across cellular contexts. To address this, we integrate evolutionary, folding, and mutational data with molecular dynamics simulations and network analysis to uncover a highly conserved residue network in structural space that has been faithfully passed on in sequence space over 500 million years of vertebrate evolution. This network encodes a high energy intermediate consistently present in the ensemble of all present day vertebrate apoptotic caspases. It not only guides folding but also scaffolds dynamic motions, functioning like a structural backbone that supports the ensemble. Building on this foundation, we identify differentially evolving networks surrounding the conserved core in initiator and effector caspase subfamilies. These variations provide thermodynamic insight into how initiators stabilize monomeric conformations while effectors favor dimeric states, revealing how evolution shapes ensembles to diversify function in protein families. Additionally, we discover conserved hub residues near an allosteric hotspot, distinct from the core network, that regulate the dynamics of surrounding evolving networks and act as control centers that modulate the conformational equilibrium within the apoptotic caspase ensemble.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144697467","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}

引用次数: 0

Comparison of Classical P81 and SVI-P Cation-Exchange Papers in Radiometric Protein Kinase Assays. 经典P81和SVI-P阳离子交换论文在放射蛋白激酶测定中的比较。

IF 4.1 3区生物学

Biochemical Journal Pub Date : 2025-07-22 DOI: 10.1042/bcj20240731

Muhammad Khabib,Lifang Zhang,Ashley Ovens,Abdulhameed Al-Ghabkari,John Scott,Lindsay Sparrow,Martha Blank,Lisa Murray-Segal,Sandra Galic,Morag Park,Christopher Langendorf,Naomi Ling,Ashfaqul Hoque

{"title":"Comparison of Classical P81 and SVI-P Cation-Exchange Papers in Radiometric Protein Kinase Assays.","authors":"Muhammad Khabib,Lifang Zhang,Ashley Ovens,Abdulhameed Al-Ghabkari,John Scott,Lindsay Sparrow,Martha Blank,Lisa Murray-Segal,Sandra Galic,Morag Park,Christopher Langendorf,Naomi Ling,Ashfaqul Hoque","doi":"10.1042/bcj20240731","DOIUrl":"https://doi.org/10.1042/bcj20240731","url":null,"abstract":"Radiometric kinase assays have been widely used due to their high sensitivity and dynamic range. The assay measures the transfer of 32Pi from [γ-32P]-ATP to specific substrates, typically synthetic peptides. The 32P-phosphorylated peptide product is captured by binding it to phosphocellulose paper, specifically P81. Unfortunately, GE Healthcare, the sole supplier of P81, has discontinued its manufacture. Recently, a replacement for P81, SVI-P cation-exchange filter paper, has become available. We have tested SVI-P in various kinase assays, including those for AMPK, Abl, CDK2, and ERK, and found that it performs comparably to P81 in capturing substrates. Additionally, a commercial kinase profiling assay using SVI-P successfully captured a range of peptide and protein substrates from 48 different protein kinases. One minor limitation of SVI-P was the higher background radioactivity; however, this can be addressed through optimisation and extended wash steps. Overall, SVI-P represents a viable alternative for radiometric kinase assays, ensuring continued reliability in both academic and industrial research settings.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"27 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144693474","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}

引用次数: 0

Pharmaco-nutraceutical improvement of the response to obeticholic acid with omega-3 polyunsaturated fatty acids. omega-3多不饱和脂肪酸对欧比胆酸反应的药物营养改善。

IF 4.1 3区生物学

Biochemical Journal Pub Date : 2025-07-22 DOI: 10.1042/bcj20253113

Audrey-Anne Lavoie,Ariane Thérien,Anisia Silva,Emanuel Paré,Anna Ciešlak,William Gagnon,Clémence Desjardins,Mélanie Verreault,Jocelyn Trottier,Marie-Claude Vohl,Jean-Philippe Drouin-Chartier,Jacques Corbeil,Alexandre Caron,Olivier Barbier

{"title":"Pharmaco-nutraceutical improvement of the response to obeticholic acid with omega-3 polyunsaturated fatty acids.","authors":"Audrey-Anne Lavoie,Ariane Thérien,Anisia Silva,Emanuel Paré,Anna Ciešlak,William Gagnon,Clémence Desjardins,Mélanie Verreault,Jocelyn Trottier,Marie-Claude Vohl,Jean-Philippe Drouin-Chartier,Jacques Corbeil,Alexandre Caron,Olivier Barbier","doi":"10.1042/bcj20253113","DOIUrl":"https://doi.org/10.1042/bcj20253113","url":null,"abstract":"Obeticholic acid (OCA) is the second line therapy for primary biliary cholangitis. While efficient in promoting BA detoxification and limiting liver fibrosis, its clinical use is restricted by severe dose-dependent side effects. We tested the hypothesis that adding n-3 polyunsaturated fatty acids, eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids to OCA may improve the therapeutic effect of the low drug dosage. Several liver cell lines were exposed to vehicle, low or high OCA dose (1-20μM) in the presence or absence of EPA/DHA for 24H. To induce ER stress, apoptosis, and fibrosis, HepG2 cells were exposed to a 400μM BA mixture or to 2ng/mL TGF-β. For inflammation analyses, THP-1 cells were activated with 100ng/mL LPS. The impact OCA+EPA/DHA was assessed using transcriptomic (qRT-PCR), proteomic (ELISA, caspase-3), and metabolomic (LC-MS/MS) approaches. The addition of EPA/DHA reinforced the ability of low OCA dose to down-regulate the expression of genes involved in BA synthesis (CYP7A1, CYP8B1) and uptake (NTCP) and to up-regulate MRP2 & 3 genes expression. EPA/DHA also enhanced the anti-inflammatory response of the drug by reducing the expression of the LPS-induced cytokines: TNFα, IL-6, IL-1β and MCP-1 in THP-1 macrophages. OCA+EPA/DHA decreased the expression of BIP, CHOP and COL1A1 genes and the caspase-3 activity. EPA+DHA potentiate the response to low OCA doses on BA toxicity, and provide additional benefits on ER stress, apoptosis, inflammation and fibrosis. These observations support the idea that adding n-3 polyunsaturated fatty acids to the drug may reduce the risk of dose-related side effects in patients treated with OCA.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"17 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144693475","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}

引用次数: 0

Proteomic analysis reveals inhibition of mevalonate and Glycolysis pathways in hepatocytes by 27-hydroxycholesterol. 蛋白质组学分析显示27-羟基胆固醇抑制肝细胞的甲羟戊酸和糖酵解途径。

IF 4.1 3区生物学

Biochemical Journal Pub Date : 2025-07-22 DOI: 10.1042/bcj20253035

Wan-Seog Shim,Seulah Lee,Bakhovuddin Azamov,Chanhee Lee,Yeowon Kang,Kwang Min Lee,Changwan Hong,Sang-Mo Kwon,Koanhoi Kim,Dongjun Lee,Jong Hyuk Yoon,Parkyong Song

{"title":"Proteomic analysis reveals inhibition of mevalonate and Glycolysis pathways in hepatocytes by 27-hydroxycholesterol.","authors":"Wan-Seog Shim,Seulah Lee,Bakhovuddin Azamov,Chanhee Lee,Yeowon Kang,Kwang Min Lee,Changwan Hong,Sang-Mo Kwon,Koanhoi Kim,Dongjun Lee,Jong Hyuk Yoon,Parkyong Song","doi":"10.1042/bcj20253035","DOIUrl":"https://doi.org/10.1042/bcj20253035","url":null,"abstract":"27-Hydroxycholesterol (27OHC), an endogenous oxysterol, has been implicated in various physiological processes, including regulation of estrogen receptor activity and lipid metabolism. However, studies on how 27OHC affects the metabolic changes associated with lipogenesis inhibition in the liver remain limited. This study aimed to investigate the systemic effects of 27OHC on hepatocytes through a comparative proteomic analysis of the proteomes in the 27OHC-treated AML12 cells. Ingenuity Pathway Analysis revealed significant downregulation of certain metabolic pathways, such as cholesterol biosynthesis and glycolysis, which are highly associated with lipid metabolism, following 27OHC treatment. Furthermore, in vitro biochemical analysis revealed significant inhibition of the expression of genes associated with the mevalonate pathway and a decrease in the total cellular cholesterol levels in AML12 cells and primary hepatocytes following 27OHC treatment. In addition, it was observed that 27OHC significantly reduced the transcripts levels of critical glycolytic enzymes such as aldolase, phosphofructokinase, and pyruvate kinase. This inhibition resulted in decreased lactate production and extracellular acidification (ECAR), indicating suppression of glycolytic flux. Concurrently, we proved that downregulation of reactive oxygen species generation and HIF-1α expression following 27OHC treatment partially contributed to glycolysis inhibition. Overall, we demonstrated the inhibitory effects of 27OHC on the hepatic mevalonate pathway and glycolysis, revealing a novel mechanism by which 27OHC regulates lipid metabolism. As the accumulation of cholesterol and lipids promotes hepatic fatty liver disease and increased glycolysis contributes to triacylglycerol maturation, the suppressive effects of 27OHC on hepatic lipid and glucose metabolism may contribute to protect against fatty liver development.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"707 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144693476","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}

引用次数: 0

Structure and activity of the essential UCH family deubiquitinase DUB16 from Leishmania donovani. 多诺瓦利什曼原虫UCH家族去泛素酶DUB16的结构和活性。

IF 4.4 3区生物学

Biochemical Journal Pub Date : 2025-07-09 DOI: 10.1042/BCJ20253107

James A Brannigan, Mohd Kamran, Nathaniel G Jones, Elisa M Nightingale, Eleanor J Dodson, Sarfaraz A Ejazi, Jeremy C Mottram, Nahid Ali, Anthony J Wilkinson

{"title":"Structure and activity of the essential UCH family deubiquitinase DUB16 from Leishmania donovani.","authors":"James A Brannigan, Mohd Kamran, Nathaniel G Jones, Elisa M Nightingale, Eleanor J Dodson, Sarfaraz A Ejazi, Jeremy C Mottram, Nahid Ali, Anthony J Wilkinson","doi":"10.1042/BCJ20253107","DOIUrl":"10.1042/BCJ20253107","url":null,"abstract":"In Leishmania parasites, as for their hosts, the ubiquitin (Ub) proteasome system is important for cell viability. As part of a systematic gene deletion study, it was discovered that four cysteine protease-type deubiquitinases (DUBs) are essential for parasite survival in the promastigote stage, including DUB16. Here, we have purified and characterised recombinant DUB16 from Leishmania donovani, which belongs to the Ub C-terminal hydrolase (UCH) family. DUB16 efficiently hydrolyses C-terminal aminocoumarin and rhodamine conjugates of Ub consistent with proposed cellular roles of UCH-type DUBs in regenerating free monomeric Ub from small molecule Ub adducts arising from adventitious metabolic processes. The crystal structure of DUB16 reveals a typical UCH-type DUB fold, and a relatively short and disordered cross-over loop that appears to restrict access to the catalytic cysteine. At close to stoichiometric enzyme to substrate ratios, DUB16 exhibits DUB activity towards diubiquitins linked through isopeptide bonds between Lys11, Lys48 or Lys63 residues of the proximal Ub and the C-terminus of the distal Ub. With 100-1000-fold higher turnover rates, DUB16 cleaves the ubiquitin-ribosomal L40 fusion protein to give the mature products. A DUB-targeting cysteine-reactive cyanopyrrolidine compound, IMP-1710, inhibits DUB16 activity. IMP-1710 was shown in promastigote cell viability assays to have parasite killing activity with EC50 values of 1-2 μM, comparable with the anti-leishmanial drug, miltefosine. L. mexicana parasites engineered to overproduce DUB16 showed a modest increase in resistance to IMP-1710, providing evidence that IMP-1710 inhibits DUB16 in vivo. While it is highly likely that IMP-1710 has additional targets, these results suggest that DUB16 is a potential target for the development of new anti-leishmanial compounds.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504721","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}

引用次数: 0

The Pseudomonas aeruginosa Type VI secretion system toxin Tse8 evolved from a novel N-carbamoylputrescine amidohydrolase. 铜绿假单胞菌VI型分泌系统毒素Tse8是由一种新型n -氨甲酰腐胺水解酶进化而来的。

IF 4.1 3区生物学

Biochemical Journal Pub Date : 2025-07-09 DOI: 10.1042/bcj20253210

Bin Li,Hamid R Baniasadi,Margaret A Phillips,Anthony J Michael

{"title":"The Pseudomonas aeruginosa Type VI secretion system toxin Tse8 evolved from a novel N-carbamoylputrescine amidohydrolase.","authors":"Bin Li,Hamid R Baniasadi,Margaret A Phillips,Anthony J Michael","doi":"10.1042/bcj20253210","DOIUrl":"https://doi.org/10.1042/bcj20253210","url":null,"abstract":"The polyamine putrescine is synthesized primarily from L-arginine via agmatine in bacteria. There are currently three known routes from agmatine to putrescine, including direct conversion by agmatinase. The other two routes use agmatine deiminase to produce N-carbamoylputrescine from agmatine, then one of two nonhomologous enzymes, putrescine transcarbamylase or N-carbamoylputrescine amidohydrolase (NCPAH) convert N-carbamoylputrescine to putrescine. Here, we functionally identify enzymes from phylogenetically distant bacteria, the gamma-proteobacterium Shewanella oneidensis, and the actinomycetota species Microterricola gilva, that are novel alternative, nonhomologous, noncanonical NCPAHs that we term AguY, which have emerged by convergent evolution. Kinetic analysis indicates that the AguY enzymes are as efficient as the canonical NCPAH from Pseudomonas aeruginosa, in converting N-carbamoylputrescine to putrescine. Genomic evidence suggests that the AguY enzymes may participate in putrescine biosynthetic or agmatine catabolic pathways, and are occasionally encoded in genomes that also encode agmatinase. We show that the Type VI secretion system toxin Tse8 from Pseudomonas aeruginosa has evolved from AguY. It is formally possible that AguY evolved directly or indirectly from the ancient glutamine amidohydrolase GatA, a component of the transamidosome, an RNA/protein complex required for production of glutamine-charged tRNA. Our study provides a further example of the prevalence of convergent evolution and horizontal gene transfer in polyamine biosynthesis, suggesting pervasive selective pressure to evolve polyamine metabolism in bacteria.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"37 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144645895","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}

引用次数: 0

Cyanobacterial redox carriers support photosynthesis in a purple phototrophic bacterium. 蓝藻氧化还原载体支持紫色光养细菌的光合作用。

IF 4.1 3区生物学

Biochemical Journal Pub Date : 2025-07-08 DOI: 10.1042/bcj20253114

Adam Bowie,Andrew Hitchcock,Matthew Proctor,Elizabeth Martin,David Swainsbury,C Hunter

{"title":"Cyanobacterial redox carriers support photosynthesis in a purple phototrophic bacterium.","authors":"Adam Bowie,Andrew Hitchcock,Matthew Proctor,Elizabeth Martin,David Swainsbury,C Hunter","doi":"10.1042/bcj20253114","DOIUrl":"https://doi.org/10.1042/bcj20253114","url":null,"abstract":"In oxygenic and anoxygenic photosynthesis, excitation energy migrates from a surrounding antenna to specialised chlorophyll (Chl) or bacteriochlorophyll (BChl) pigments housed within a reaction centre (RC) complex. Here, a charge-separated state is formed within a few picoseconds, and an electron moves along a series of cofactors until it arrives at a quinone or iron-sulfur centre acceptor. Further photochemical cycles rely on rapid re-reduction of the photo-oxidised RC, usually by small, soluble metalloproteins which vary considerably between different phototrophic clades. In the purple phototrophic bacterium Rhodobacter (Rba.) sphaeroides, the electron carrier cytochrome c2 (cyt c2) shuttles between the periplasmic faces of the cytochrome bc1 complex and the reaction centre-light harvesting 1 (RC-LH1) core complex, the location of the BChl special pair (P865865). By contrast, in the model cyanobacterium Synechocystis sp. PCC 6803, electrons are transferred from cytochrome b6f to photosystem I (PSI) via two isofunctional redox carrier proteins, cytochrome c6 (cyt c6) and plastocyanin (Pc). In this paper, we demonstrate that both cyt c6 and Pc can substitute for cyt c2 in silico, in vitro and in vivo, even though their electrostatic properties may be counter-productive for binding the RC-LH1 complex. Interestingly, whilst P865865++ reduction was highest with cyt c2 and the full physiological RC-LH1 complex, both Synechocystis proteins were more compatible with the RC-only complex lacking the surrounding LH1 antenna. Taken together, this suggests the subunits that constitute the LH1 ring improve both the donor side activity and selectivity of the Rba. sphaeroides RC complex.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"74 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144640239","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}

引用次数: 0