Advanced transcriptomic technology has identified a great number of non-coding RNAs (ncRNAs) that are pervasively transcribed in the yeast genome. ncRNAs can be classified into short ncRNAs (<200 nt) and long ncRNAs (lncRNAs; >200 nt). Those transcripts are strictly regulated through transcription and degradation mechanisms to maintain proper cellular homeostasis and prevent aberrant expression. It has been revealed that ncRNAs can play roles in various regulatory processes, particularly in transcriptional regulation. While short ncRNAs are well characterised, the function of lncRNAs remains poorly understood. Both functional and transcriptional profiling have been applied to fill the gap in the lncRNA functions landscape. It has been proven by functional profiling that these long transcripts can serve important cellular roles in gene regulation, RNA metabolism, sexual differentiation and telomeric overhang homeostasis. In addition, transcriptional profiling allowed the characterisation of ncRNAs involved in the cell cycle, colony subpopulation dynamics, virulence and regulatory networks. In this review, we introduce the classification, the cellular fate, the evolution and conservation, the mechanisms of action, and the profiling of yeast ncRNAs.
{"title":"Functional analysis and transcriptional profiling of non-coding RNAs in yeast.","authors":"Tanda Qi,Daniela Delneri,Soukaina Timouma","doi":"10.1042/bcj20253069","DOIUrl":"https://doi.org/10.1042/bcj20253069","url":null,"abstract":"Advanced transcriptomic technology has identified a great number of non-coding RNAs (ncRNAs) that are pervasively transcribed in the yeast genome. ncRNAs can be classified into short ncRNAs (<200 nt) and long ncRNAs (lncRNAs; >200 nt). Those transcripts are strictly regulated through transcription and degradation mechanisms to maintain proper cellular homeostasis and prevent aberrant expression. It has been revealed that ncRNAs can play roles in various regulatory processes, particularly in transcriptional regulation. While short ncRNAs are well characterised, the function of lncRNAs remains poorly understood. Both functional and transcriptional profiling have been applied to fill the gap in the lncRNA functions landscape. It has been proven by functional profiling that these long transcripts can serve important cellular roles in gene regulation, RNA metabolism, sexual differentiation and telomeric overhang homeostasis. In addition, transcriptional profiling allowed the characterisation of ncRNAs involved in the cell cycle, colony subpopulation dynamics, virulence and regulatory networks. In this review, we introduce the classification, the cellular fate, the evolution and conservation, the mechanisms of action, and the profiling of yeast ncRNAs.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"1 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145194920","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}
Histones are critical for eukaryotic cell survival, supporting and packaging DNA into chromatin domains that define gene expression and cellular identity. Fundamental to the establishment of these domains is the adequate histone supply that is tightly regulated from the moment histones are transcribed, synthesized, and recycled, to when they are degraded. In this review, we describe and emphasize each step of the histone supply chain and its impact on chromatin structure and cellular identity. Given the robust studies on histones H3 and H4 supply, we primarily discuss these nucleosome components and their variants while briefly touching on H2A and H2B dynamics. We also highlight central proteins that supervise these processes and relay key studies that explore the consequences and clinical impact of limiting or altering the histone supply chain. Together, these insights underscore the importance of histone homeostasis as a critical determinant of genome stability and cell fate.
{"title":"Histone supply: a precious commodity for cell identity.","authors":"Sara Gonske,Thelma M Escobar,Alejandra Loyola","doi":"10.1042/bcj20253163","DOIUrl":"https://doi.org/10.1042/bcj20253163","url":null,"abstract":"Histones are critical for eukaryotic cell survival, supporting and packaging DNA into chromatin domains that define gene expression and cellular identity. Fundamental to the establishment of these domains is the adequate histone supply that is tightly regulated from the moment histones are transcribed, synthesized, and recycled, to when they are degraded. In this review, we describe and emphasize each step of the histone supply chain and its impact on chromatin structure and cellular identity. Given the robust studies on histones H3 and H4 supply, we primarily discuss these nucleosome components and their variants while briefly touching on H2A and H2B dynamics. We also highlight central proteins that supervise these processes and relay key studies that explore the consequences and clinical impact of limiting or altering the histone supply chain. Together, these insights underscore the importance of histone homeostasis as a critical determinant of genome stability and cell fate.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"17 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145134075","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}
G protein-coupled receptors (GPCRs) are key signal transducers and the target of about one-third of all FDA-approved drugs. Many structural and pharmacological studies rely on disrupted membrane conditions, such as purified receptors in artificial systems or radioligand binding assays using membrane fragments, even though it had not been systematically studied whether membrane integrity affects GPCR function. To address this, we developed Förster resonance energy transfer (FRET)-based GPCR conformation sensors to directly measure receptor activation in both intact and disrupted membranes. Our results show that while some GPCRs remain unaffected, prostanoid receptor conformation sensors exhibit a strong dependence on membrane integrity: their agonist and antagonist potencies decrease up to 30-fold upon membrane disruption, revealing a crucial role of the membrane integrity in ligand-receptor affinity. Validation with wild-type receptors in functional signaling assays confirmed that these effects reflect genuine receptor characteristics rather than unspecific signals from the sensor design. We ruled out several factors that could explain the loss of affinity, but were unable to fully elucidate the mechanism behind this phenomenon. Nevertheless, this effect may introduce bias into structural and pharmacological studies. It is therefore essential to account for membrane integrity and to employ optimized experimental strategies to ensure robust and reliable data interpretation.
{"title":"Membrane disruption attenuates agonist potency in prostanoid receptors.","authors":"Uurtuya Hochban,Imke Wallenstein,Michaela Ulrich,Alwina Bittner,Lisa Spänig,Katharina Klingelhöfer,Sebastian Neumann,Torsten Steinmetzer,Moritz Bünemann,Michael Kurz","doi":"10.1042/bcj20253332","DOIUrl":"https://doi.org/10.1042/bcj20253332","url":null,"abstract":"G protein-coupled receptors (GPCRs) are key signal transducers and the target of about one-third of all FDA-approved drugs. Many structural and pharmacological studies rely on disrupted membrane conditions, such as purified receptors in artificial systems or radioligand binding assays using membrane fragments, even though it had not been systematically studied whether membrane integrity affects GPCR function. To address this, we developed Förster resonance energy transfer (FRET)-based GPCR conformation sensors to directly measure receptor activation in both intact and disrupted membranes. Our results show that while some GPCRs remain unaffected, prostanoid receptor conformation sensors exhibit a strong dependence on membrane integrity: their agonist and antagonist potencies decrease up to 30-fold upon membrane disruption, revealing a crucial role of the membrane integrity in ligand-receptor affinity. Validation with wild-type receptors in functional signaling assays confirmed that these effects reflect genuine receptor characteristics rather than unspecific signals from the sensor design. We ruled out several factors that could explain the loss of affinity, but were unable to fully elucidate the mechanism behind this phenomenon. Nevertheless, this effect may introduce bias into structural and pharmacological studies. It is therefore essential to account for membrane integrity and to employ optimized experimental strategies to ensure robust and reliable data interpretation.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"29 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145182665","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}
Controlling the conformation of dynamic protein, RNA and DNA molecules underpins many biological processes, from the activation of enzymes and induction of signalling cascades to cellular replication. Clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) effectors are enzymes tightly controlled by conformational steps that gate activation of nuclease domains core to their function in bacterial adaptive immunity. These precise conformational checkpoints combined with programmable activation specified by RNA guides have driven the success of CRISPR-Cas tools in biotechnology, medicine and beyond. To illustrate the importance of conformation in controlling CRISPR-Cas activity, we review the discrete conformational checkpoints at play in class 2 CRISPR-Cas systems. Using Cas9, Cas12a and Cas13a as examples, we describe how protein and nucleic acid conformations precisely control the loading of guide RNA, the selection of target nucleic acids and the activation of nuclease domains. Much like a director controls the timing of transitions between scenes in a movie, CRISPR effectors use conformational checkpoints to precisely direct their enzymatic activity.
{"title":"And… cut! - how conformational regulation of CRISPR-Cas effectors directs nuclease activity.","authors":"Roland W Calvert,Gavin J Knott","doi":"10.1042/bcj20240481","DOIUrl":"https://doi.org/10.1042/bcj20240481","url":null,"abstract":"Controlling the conformation of dynamic protein, RNA and DNA molecules underpins many biological processes, from the activation of enzymes and induction of signalling cascades to cellular replication. Clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) effectors are enzymes tightly controlled by conformational steps that gate activation of nuclease domains core to their function in bacterial adaptive immunity. These precise conformational checkpoints combined with programmable activation specified by RNA guides have driven the success of CRISPR-Cas tools in biotechnology, medicine and beyond. To illustrate the importance of conformation in controlling CRISPR-Cas activity, we review the discrete conformational checkpoints at play in class 2 CRISPR-Cas systems. Using Cas9, Cas12a and Cas13a as examples, we describe how protein and nucleic acid conformations precisely control the loading of guide RNA, the selection of target nucleic acids and the activation of nuclease domains. Much like a director controls the timing of transitions between scenes in a movie, CRISPR effectors use conformational checkpoints to precisely direct their enzymatic activity.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"94 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145134092","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}
Tom D Bunney,Hunter G Nyvall,Calum Macrae,Damjan Lalović,Ashley Gregory,Kyle I P Le Huray,Nikita Harvey,Nikos Pinotsis,Antreas C Kalli,Christopher Waudby,John E Burke,Matilda Katan
PLCγ enzymes are key components of intracellular signal transduction processes and are involved in disease development, including immune dysregulation, specific cancer types, and neurodegeneration. Although recognised as important targets for intervention, validated pharmacological tools are lacking. Here, we demonstrate that inhibitory nucleotides bind directly to an allosteric site at the interface between the PLC-core and regulatory-array unique for PLCγ, underlying their specificity for the PLCγ family. This binding site overlaps with the PLCγ autoinhibitory interface, suggesting that the inhibitory impact of nucleotides involves stabilization of autoinhibition. We have also analysed disease-linked variants of PLCγ1 and PLCγ2 to show that multiple mechanisms could underpin their gain-of-function phenotype. While sensitivity of these variants to physiological nucleotide inhibition is reduced, we identified artificial nucleotide compounds that can inhibit such variants not only in vitro but also in cell-based assays. Therefore, our findings suggest a route for development of isozyme specific PLCγ inhibitors allowing further studies of their roles in health and disease.
{"title":"Characterisation of an allosteric site in PLCγ enzymes and implications for development of their specific inhibitors.","authors":"Tom D Bunney,Hunter G Nyvall,Calum Macrae,Damjan Lalović,Ashley Gregory,Kyle I P Le Huray,Nikita Harvey,Nikos Pinotsis,Antreas C Kalli,Christopher Waudby,John E Burke,Matilda Katan","doi":"10.1042/bcj20253358","DOIUrl":"https://doi.org/10.1042/bcj20253358","url":null,"abstract":"PLCγ enzymes are key components of intracellular signal transduction processes and are involved in disease development, including immune dysregulation, specific cancer types, and neurodegeneration. Although recognised as important targets for intervention, validated pharmacological tools are lacking. Here, we demonstrate that inhibitory nucleotides bind directly to an allosteric site at the interface between the PLC-core and regulatory-array unique for PLCγ, underlying their specificity for the PLCγ family. This binding site overlaps with the PLCγ autoinhibitory interface, suggesting that the inhibitory impact of nucleotides involves stabilization of autoinhibition. We have also analysed disease-linked variants of PLCγ1 and PLCγ2 to show that multiple mechanisms could underpin their gain-of-function phenotype. While sensitivity of these variants to physiological nucleotide inhibition is reduced, we identified artificial nucleotide compounds that can inhibit such variants not only in vitro but also in cell-based assays. Therefore, our findings suggest a route for development of isozyme specific PLCγ inhibitors allowing further studies of their roles in health and disease.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"41 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145140137","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}
Inward-rectifier potassium (Kir) channels are essential for regulating various physiological processes and are implicated in several life-threatening diseases, making them key drug targets. KirBac1.1, a well-characterized prokaryotic homolog of Kir channels, is known to undergo anionic lipid-dependent gating. Although the slide helix is an important structural component in the gating mechanism of KirBac1.1, its structural dynamics associated with the anionic lipid-driven activation is not well-understood. Here, we have reconstituted KirBac1.1 in zwitterionic POPC and anionic POPC/POPG membranes to stabilize the inactive and active conformations of the channel, respectively. Our liposome K+ flux assay results show that all the slide helix single-cysteine mutants display PG-driven gating, and increasing the PG from 25 to 40 mol% does not have any linear dependency on both the activation and K+ flux rates. Site-directed NBD fluorescence results suggest that the structural dynamics of the slide helix is significantly altered upon PG-induced activation. For instance, we observe significant changes in hydration dynamics and rotational mobility of slide helix residues between functional states. MEM-based lifetime distribution analysis suggests that the conformational heterogeneity of the slide helix is functional-state dependent. Importantly, membrane penetration depth measurements reveal that the slide helix in the active KirBac1.1 is located ~3 Å deeper within the membrane interface, well supported by increased fluorescence lifetimes. Notably, the non-linear relationship between structural dynamics and PG content highlights the critical role of lipid-protein interactions and membrane surface charge in PG-mediated KirBac1.1 activation. These findings provide valuable insights into Kir channel gating mechanisms, and lipid-dependent gating of other channels.
{"title":"Anionic lipids modulate the membrane localization and conformational dynamics of KirBac1.1 slide helix during lipid-dependent activation.","authors":"Arpan Bysack,Chandrima Jash,H Raghuraman","doi":"10.1042/bcj20253215","DOIUrl":"https://doi.org/10.1042/bcj20253215","url":null,"abstract":"Inward-rectifier potassium (Kir) channels are essential for regulating various physiological processes and are implicated in several life-threatening diseases, making them key drug targets. KirBac1.1, a well-characterized prokaryotic homolog of Kir channels, is known to undergo anionic lipid-dependent gating. Although the slide helix is an important structural component in the gating mechanism of KirBac1.1, its structural dynamics associated with the anionic lipid-driven activation is not well-understood. Here, we have reconstituted KirBac1.1 in zwitterionic POPC and anionic POPC/POPG membranes to stabilize the inactive and active conformations of the channel, respectively. Our liposome K+ flux assay results show that all the slide helix single-cysteine mutants display PG-driven gating, and increasing the PG from 25 to 40 mol% does not have any linear dependency on both the activation and K+ flux rates. Site-directed NBD fluorescence results suggest that the structural dynamics of the slide helix is significantly altered upon PG-induced activation. For instance, we observe significant changes in hydration dynamics and rotational mobility of slide helix residues between functional states. MEM-based lifetime distribution analysis suggests that the conformational heterogeneity of the slide helix is functional-state dependent. Importantly, membrane penetration depth measurements reveal that the slide helix in the active KirBac1.1 is located ~3 Å deeper within the membrane interface, well supported by increased fluorescence lifetimes. Notably, the non-linear relationship between structural dynamics and PG content highlights the critical role of lipid-protein interactions and membrane surface charge in PG-mediated KirBac1.1 activation. These findings provide valuable insights into Kir channel gating mechanisms, and lipid-dependent gating of other channels.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"16 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145083617","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}
Muktesh Athale,Neil Ball,Latifeh Azizi,Irene Valenzuela,Marta Codina,Andrea Martin-Nalda,Vasyl V Mykuliak,Rolle Rahikainen,Benjamin T Goult,Paula Turkki,Vesa P Hytönen
Talin-1 is a central integrin adapter protein connecting cytoplasmic domains of integrins to the cytoskeleton. These talin-1-mediated mechanical linkages are crucial for cellular functions such as cell movement and connections with other cells. Here, we report a patient carrying a missense variant, L353F, in the talin-1 head which is associated with a complex set of symptoms, including skin lesions, blood cell abnormalities, and congenital cataracts. We conducted structural and cellular characterization of this variant. Recombinant talin-1 F2F3 fragment with the corresponding mutation showed a decrease in thermal stability and decreased solubility. Reconstitution of talin-deficient cells with L353F talin-1 revealed decreased cell migration velocity, defects in wound healing capacity, and changes in recruitment of the focal adhesion complex protein paxillin. We also observed decreased levels of activated integrin in cells expressing the talin-1 variant, while integrin-binding affinity was preserved as determined biochemically. These observations suggest that changes in integrin adhesion complex dynamics reflect cellular processes and the multifaceted patient phenotype.
{"title":"De novo talin-1 variant L353F connects multifaceted clinical symptoms to alterations in talin-1 function.","authors":"Muktesh Athale,Neil Ball,Latifeh Azizi,Irene Valenzuela,Marta Codina,Andrea Martin-Nalda,Vasyl V Mykuliak,Rolle Rahikainen,Benjamin T Goult,Paula Turkki,Vesa P Hytönen","doi":"10.1042/bcj20253128","DOIUrl":"https://doi.org/10.1042/bcj20253128","url":null,"abstract":"Talin-1 is a central integrin adapter protein connecting cytoplasmic domains of integrins to the cytoskeleton. These talin-1-mediated mechanical linkages are crucial for cellular functions such as cell movement and connections with other cells. Here, we report a patient carrying a missense variant, L353F, in the talin-1 head which is associated with a complex set of symptoms, including skin lesions, blood cell abnormalities, and congenital cataracts. We conducted structural and cellular characterization of this variant. Recombinant talin-1 F2F3 fragment with the corresponding mutation showed a decrease in thermal stability and decreased solubility. Reconstitution of talin-deficient cells with L353F talin-1 revealed decreased cell migration velocity, defects in wound healing capacity, and changes in recruitment of the focal adhesion complex protein paxillin. We also observed decreased levels of activated integrin in cells expressing the talin-1 variant, while integrin-binding affinity was preserved as determined biochemically. These observations suggest that changes in integrin adhesion complex dynamics reflect cellular processes and the multifaceted patient phenotype.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"37 1","pages":"1337-1352"},"PeriodicalIF":4.1,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145071744","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}
Lydia M Bernabéu-Roda,Geovanny Rivera-Hernández,Virginia Cuéllar,Rafael Núñez,Ángeles Moreno-Ocampo,Christian Sohlenkamp,Otto Geiger,María J Soto,Isabel M López-Lara
Sinorhizobium meliloti is a soil bacterium that can establish beneficial symbiosis with legume plants. The fadD gene encodes a long-chain fatty acyl-coenzyme A (CoA) synthetase. Inactivation of FadD in S. meliloti leads to a pleiotropic phenotype, including the overproduction of several volatile methylketones (MKs). One of them, 2-tridecanone (2-TDC), was found to act as an infochemical that affects important bacterial traits and hampers plant-bacteria interactions. Knowledge about bacterial genes involved in MK production is limited. In wild tomato species, MK synthesis requires intermediates of fatty acid biosynthesis and the activity of the methylketone synthase 2 (MKS2), a thioesterase belonging to the hot dog-fold family. In this study, we have identified SMc03960, a conserved hypothetical protein with homology to bacterial YbgC-like thioesterases, as an ortholog of MKS2 in S. meliloti. Heterologous expression of smc03960 in Escherichia coli results in the formation of several MKs, including 2-TDC, and causes the accumulation of free fatty acids. Purified His-SMc03960 showed thioesterase activity for different acyl groups linked either to acyl carrier protein (ACP) or to CoA with preference for C14-long substrates. Moreover, formation of 2-TDC in vitro was achieved by using His-SMc03960 and 3-oxo-myristoyl-ACP. Although deletion of smc03960 in the wild type or in the fadD mutant does not significantly alter the amount of MKs released by S. meliloti, overexpression of the gene results in increased production of 2-TDC in these two strains. Overall, our data demonstrate that SMc03960 is an acyl-ACP/acyl-CoA thioesterase with broad substrate specificity that contributes to 2-TDC formation.
{"title":"Identification of aSinorhizobium meliloti YbgC-like thioesterase that contributes to the production of the infochemical 2-tridecanone.","authors":"Lydia M Bernabéu-Roda,Geovanny Rivera-Hernández,Virginia Cuéllar,Rafael Núñez,Ángeles Moreno-Ocampo,Christian Sohlenkamp,Otto Geiger,María J Soto,Isabel M López-Lara","doi":"10.1042/bcj20253120","DOIUrl":"https://doi.org/10.1042/bcj20253120","url":null,"abstract":"Sinorhizobium meliloti is a soil bacterium that can establish beneficial symbiosis with legume plants. The fadD gene encodes a long-chain fatty acyl-coenzyme A (CoA) synthetase. Inactivation of FadD in S. meliloti leads to a pleiotropic phenotype, including the overproduction of several volatile methylketones (MKs). One of them, 2-tridecanone (2-TDC), was found to act as an infochemical that affects important bacterial traits and hampers plant-bacteria interactions. Knowledge about bacterial genes involved in MK production is limited. In wild tomato species, MK synthesis requires intermediates of fatty acid biosynthesis and the activity of the methylketone synthase 2 (MKS2), a thioesterase belonging to the hot dog-fold family. In this study, we have identified SMc03960, a conserved hypothetical protein with homology to bacterial YbgC-like thioesterases, as an ortholog of MKS2 in S. meliloti. Heterologous expression of smc03960 in Escherichia coli results in the formation of several MKs, including 2-TDC, and causes the accumulation of free fatty acids. Purified His-SMc03960 showed thioesterase activity for different acyl groups linked either to acyl carrier protein (ACP) or to CoA with preference for C14-long substrates. Moreover, formation of 2-TDC in vitro was achieved by using His-SMc03960 and 3-oxo-myristoyl-ACP. Although deletion of smc03960 in the wild type or in the fadD mutant does not significantly alter the amount of MKs released by S. meliloti, overexpression of the gene results in increased production of 2-TDC in these two strains. Overall, our data demonstrate that SMc03960 is an acyl-ACP/acyl-CoA thioesterase with broad substrate specificity that contributes to 2-TDC formation.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"33 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145036037","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}
Jacquie G Mills,Lydia A Hepburn,Victoria H Cowling
RNA cap formation on RNA polymerase II transcripts is regulated by cellular signalling pathways during development and differentiation, adaptive and innate immune responses, during the cell cycle and in response to oncogene deregulation. Here, we discuss how the RNA cap methyltransferase, RNA guanine-7 methyltransferase (RNMT), functions to complete the 7-methyl-guanosine or m7G cap. The mechanisms by which RNMT is regulated by signalling pathways, co-factors and other enzymes are explored. The m7G cap protects RNA pol II-transcribed RNA from the initiation of transcription and recruits proteins that mediate RNA processing including splicing, 3' cleavage and polyadenylation, nuclear export and translation initiation. Regulation of RNMT has gene-specific impacts with implications for cell function, cell physiology and cell fate decisions.
RNA聚合酶II转录本上的RNA帽形成在发育和分化、适应性和先天免疫反应、细胞周期和癌基因解除调控过程中受到细胞信号通路的调节。在这里，我们讨论了RNA帽甲基转移酶，RNA鸟嘌呤-7甲基转移酶（RNA guanine-7 methyltransferase， RNMT）如何完成7-甲基鸟苷或m7G帽的功能。RNMT通过信号通路，辅助因子和其他酶来调节的机制进行了探索。m7G帽保护RNA pol ii转录的RNA免受转录起始，并招募介导RNA加工的蛋白质，包括剪接、3'切割和聚腺苷化、核输出和翻译起始。RNMT的调控具有基因特异性影响，对细胞功能、细胞生理和细胞命运决定具有影响。
{"title":"RNMT-dependent RNA cap methylation in health and disease.","authors":"Jacquie G Mills,Lydia A Hepburn,Victoria H Cowling","doi":"10.1042/bcj20253170","DOIUrl":"https://doi.org/10.1042/bcj20253170","url":null,"abstract":"RNA cap formation on RNA polymerase II transcripts is regulated by cellular signalling pathways during development and differentiation, adaptive and innate immune responses, during the cell cycle and in response to oncogene deregulation. Here, we discuss how the RNA cap methyltransferase, RNA guanine-7 methyltransferase (RNMT), functions to complete the 7-methyl-guanosine or m7G cap. The mechanisms by which RNMT is regulated by signalling pathways, co-factors and other enzymes are explored. The m7G cap protects RNA pol II-transcribed RNA from the initiation of transcription and recruits proteins that mediate RNA processing including splicing, 3' cleavage and polyadenylation, nuclear export and translation initiation. Regulation of RNMT has gene-specific impacts with implications for cell function, cell physiology and cell fate decisions.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"5 5 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145026048","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}
Firdos Ahmad, Hezlin Marzook, Musa Idris, Omama I Dawuod, Megna Srinivas, Asima Karim, Mohamed A Saleh, Rizwan Qaisar
Glycogen synthase kinase-3α (GSK-3α) is a multifunctional kinase that plays roles in the pathogenesis of various cardiac diseases, including ischemia and pressure overload and ischemia-reperfusion-induced injury. It regulates key cellular processes such as cardiac cell proliferation, apoptosis, metabolism, and inflammation. However, its role in regulating cardiac microRNAs (miRNAs) remains unknown. To explore the role of GSK-3α in regulating miRNAs, we conducted an unbiased miRNA sequencing analysis in human GSK-3α-overexpressing AC16 cardiomyocytes (GOCs) under hypoxic conditions. Transcriptomic analysis demonstrated numerous differentially expressed miRNAs (DEMs) crucial for transcriptional, inflammatory, and various metabolic processes in the cell. Among 184 DEMs, hsa-miR-3934-5p, hsa-miR-139-5p, and hsa-miR-185-5p were the most up-regulated, while hsa-miR-193b-3p, hsa-miR-181a-2-3p, and hsa-miR-369-3p were the most down-regulated in GOC vs. control cells subjected to hypoxia. Gene ontology (GO) term analysis demonstrated a significant set of genes associated with the terms regulation of transcription, cellular protein modification process, cellular aromatic compound metabolic process, and nucleotide binding in GOC. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis further revealed enrichment of key pathways including metabolic, cytokine-cytokine receptor interaction, cyclic adenosine monophosphate (cAMP), and mitogen-activated protein kinase (MAPK) signaling pathways in GOC challenged with hypoxia. Collectively, these findings reveal a novel mechanism by which GSK-3α regulates a network of miRNAs in human cardiomyocytes required for critical transcriptional, metabolic, and signaling responses including the MAPK and inflammatory pathways under hypoxic stress. GSK-3α-mediated miRNA dysregulation may contribute to the pathophysiological changes observed in ischemia-induced cardiac injury.
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