Pub Date : 2025-11-15DOI: 10.1016/j.biochi.2025.11.006
Karolina Zygmunt , Kacper Żukowski , Katarzyna Piórkowska , Grzegorz Smołucha , Alicja Wierzbicka , Wojciech Witarski
The co-culture of fibroblasts and muscle cells is essential for obtaining cultured meat using in vitro techniques. While fibroblasts are known to promote myogenesis through cell-cell interactions, their paracrine effects and associated transcriptomic changes remain unknown. This study aimed to investigate the paracrine effect of fibroblasts on myogenesis, focusing on transcriptome profiling. Muscle satellite cells (isolated enzymatically) and fibroblasts (isolated through the explant culture) were co-cultured in 0.4 μm transwell plates for 5 days of proliferation and 24 and 72 h of differentiation. RNA-Seq and protein analysis (Western Blot, ELISA, immunofluorescence) were used to assess changes in myogenic marker expression. RNA-Seq revealed changes in many genes involved in myogenesis, such as upregulation of EGR1, IL6, and SOCS3 and downregulation of ITGA7. ELISA showed significantly higher MyHC levels at the proliferation stage in the co-culture group (p = 0.0183), with no significant differences at differentiation stages. To summarize, fibroblasts promote early myogenic differentiation and could modulate the extent of myogenic differentiation.
{"title":"Paracrine effect of fibroblasts on the proliferation and differentiation of bovine satellite cells in vitro","authors":"Karolina Zygmunt , Kacper Żukowski , Katarzyna Piórkowska , Grzegorz Smołucha , Alicja Wierzbicka , Wojciech Witarski","doi":"10.1016/j.biochi.2025.11.006","DOIUrl":"10.1016/j.biochi.2025.11.006","url":null,"abstract":"<div><div>The co-culture of fibroblasts and muscle cells is essential for obtaining cultured meat using <em>in vitro</em> techniques. While fibroblasts are known to promote myogenesis through cell-cell interactions, their paracrine effects and associated transcriptomic changes remain unknown. This study aimed to investigate the paracrine effect of fibroblasts on myogenesis, focusing on transcriptome profiling. Muscle satellite cells (isolated enzymatically) and fibroblasts (isolated through the explant culture) were co-cultured in 0.4 μm transwell plates for 5 days of proliferation and 24 and 72 h of differentiation. RNA-Seq and protein analysis (Western Blot, ELISA, immunofluorescence) were used to assess changes in myogenic marker expression. RNA-Seq revealed changes in many genes involved in myogenesis, such as upregulation of EGR1, IL6, and SOCS3 and downregulation of ITGA7. ELISA showed significantly higher MyHC levels at the proliferation stage in the co-culture group (p = 0.0183), with no significant differences at differentiation stages. To summarize, fibroblasts promote early myogenic differentiation and could modulate the extent of myogenic differentiation.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"241 ","pages":"Pages 26-43"},"PeriodicalIF":3.0,"publicationDate":"2025-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145543953","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}
Pub Date : 2025-11-11DOI: 10.1016/j.biochi.2025.11.003
Surajit Gandhi , Dileep Vasudevan
Anti-silencing function 1 (ASF1) is a highly conserved histone chaperone essential for the dynamics of nucleosome structure, facilitating assembly and histone exchange during important cellular processes such as replication, repair, and transcription. Although ASF1 has been well characterised in model organisms, its properties in protozoan parasites remain poorly explored. This study investigates the structural and functional adaptation of ASF1 from the early-diverging eukaryotic pathogen Entamoeba histolytica that causes amoebiasis in humans. Phylogenetic and sequence analyses place EhASF1 in a distinct clade and indicate that it contains a remarkably acidic C-terminal extension, like yeast ASF1, but different in length and composition compared to metazoan homologs. Recombinant EhASF1 was expressed successfully and purified, and a predominant β-sheet secondary structural composition was confirmed by circular dichroism spectroscopy. A variety of biophysical approaches, such as size-exclusion chromatography, sedimentation velocity analytical centrifugation (SV-AUC), and small-angle X-ray scattering, revealed EhASF1 to be a monomer in solution with an elongated, flexible structure. Interaction studies indicated that EhASF1 has selective binding specificity to histone H3/H4 dimer, wherein isothermal titration calorimetry established a 1:1 stoichiometric interaction with a micromolar binding affinity. Further, an in vitro nucleosome assembly assay established that EhASF1 can promote the deposition of histones onto DNA and thereby confirming its function as a histone chaperone. This study establishes EhASF1 as the first characterised histone chaperone from E. histolytica, reporting conserved chromatin assembly mechanisms and illuminating the evolution of histone chaperones from ancient eukaryotic pathogens.
抗沉默功能1 （Anti-silencing function 1, ASF1）是一种高度保守的组蛋白伴侣蛋白，对核小体结构的动力学至关重要，在复制、修复和转录等重要细胞过程中促进组蛋白的组装和交换。虽然ASF1已经在模式生物中得到了很好的表征，但它在原生动物寄生虫中的特性仍然很少被探索。本研究研究了引起人类阿米巴病的早期分化真核病原体溶组织内阿米巴的ASF1的结构和功能适应性。系统发育和序列分析将EhASF1置于一个独特的进化支中，并表明它含有一个明显的酸性c端延伸，就像酵母ASF1一样，但与后生动物同源物相比，其长度和组成不同。成功表达并纯化了重组EhASF1，通过圆二色光谱分析证实了其主要的β-sheet二级结构组成。各种生物物理方法，如粒径排除色谱、沉降速度分析离心（SV-AUC）和小角度x射线散射，显示EhASF1在溶液中是一个具有细长柔性结构的单体。相互作用研究表明EhASF1对组蛋白H3/H4二聚体具有选择性结合特异性，其中等温滴定量热法建立了具有微摩尔结合亲和力的1:1化学计量相互作用。此外，体外核小体组装试验证实EhASF1可以促进组蛋白沉积到DNA上，从而确认其作为组蛋白伴侣的功能。本研究确定了EhASF1是首个来自溶组织杆菌的组蛋白伴侣蛋白，报告了保守的染色质组装机制，并阐明了来自古代真核病原体的组蛋白伴侣蛋白的进化。
{"title":"Characterisation of Entamoeba histolytica anti-silencing function 1 as a histone chaperone","authors":"Surajit Gandhi , Dileep Vasudevan","doi":"10.1016/j.biochi.2025.11.003","DOIUrl":"10.1016/j.biochi.2025.11.003","url":null,"abstract":"<div><div>Anti-silencing function 1 (ASF1) is a highly conserved histone chaperone essential for the dynamics of nucleosome structure, facilitating assembly and histone exchange during important cellular processes such as replication, repair, and transcription. Although ASF1 has been well characterised in model organisms, its properties in protozoan parasites remain poorly explored. This study investigates the structural and functional adaptation of ASF1 from the early-diverging eukaryotic pathogen <em>Entamoeba histolytica</em> that causes amoebiasis in humans. Phylogenetic and sequence analyses place EhASF1 in a distinct clade and indicate that it contains a remarkably acidic C-terminal extension, like yeast ASF1, but different in length and composition compared to metazoan homologs. Recombinant EhASF1 was expressed successfully and purified, and a predominant β-sheet secondary structural composition was confirmed by circular dichroism spectroscopy. A variety of biophysical approaches, such as size-exclusion chromatography, sedimentation velocity analytical centrifugation (SV-AUC), and small-angle X-ray scattering, revealed EhASF1 to be a monomer in solution with an elongated, flexible structure. Interaction studies indicated that EhASF1 has selective binding specificity to histone H3/H4 dimer, wherein isothermal titration calorimetry established a 1:1 stoichiometric interaction with a micromolar binding affinity. Further, an in vitro nucleosome assembly assay established that EhASF1 can promote the deposition of histones onto DNA and thereby confirming its function as a histone chaperone. This study establishes EhASF1 as the first characterised histone chaperone from <em>E. histolytica,</em> reporting conserved chromatin assembly mechanisms and illuminating the evolution of histone chaperones from ancient eukaryotic pathogens.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"241 ","pages":"Pages 72-85"},"PeriodicalIF":3.0,"publicationDate":"2025-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145515290","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}
Pub Date : 2025-11-07DOI: 10.1016/j.biochi.2025.11.002
Muhammad Mubashshir , Mohd Ovais
Chemical pollutants bioaccumulate in aquatic animals and can reach humans, causing adverse health effects. Pollution of aquatic ecosystems from industrialization and anthropogenic xenobiotics is a global issue. Poikilothermic animals possess pigment cells called integumentary melanophores, derived from neural crest cells, which contain melanin and can detect environmental pollution. These melanophores serve as effective bioassay tools for pharmacological drugs and chemical contaminants. Studies show pollutants like Aroclor 1242 and naphthalene influence crustacean color changes, indicating pollutant impact on chromatophores. Fish melanophores are sensitive to various pollutants and function as sensors of ecological stress, while both melanophores and erythrophores act as bioindicators of water contamination. Exposure to contaminants can cause morphological damage to fish scales, including chromatophore scattering and lepidont disruption. In amphibians, insecticides such as dimethoate lead to melanophore degeneration and bleaching. Melanophore-based toxicity sensors have potential for detecting hazardous substances in drinking water and can also identify bacterial toxins and pathogenic bacteria through cell-based biosensing. Acute pigment dispersion occurs rapidly within minutes to hours, whereas morphological changes appear over days to months. This review explores acute physiological and long-term morphological responses of melanophores in fish, amphibians, and even crustaceans exposed to aquatic pollutants. It distinguishes between short-term pigment translocation as a marker of acute toxicity and longer-term structural changes indicating chronic environmental stress. The review critically evaluates the advantages and limitations of melanophore-based biomonitoring and underscores their potential for in vitro sensing of diverse aquatic contaminants, including bacterial toxins.
{"title":"Melanophore: A biosensor for water pollution analysis","authors":"Muhammad Mubashshir , Mohd Ovais","doi":"10.1016/j.biochi.2025.11.002","DOIUrl":"10.1016/j.biochi.2025.11.002","url":null,"abstract":"<div><div>Chemical pollutants bioaccumulate in aquatic animals and can reach humans, causing adverse health effects. Pollution of aquatic ecosystems from industrialization and anthropogenic xenobiotics is a global issue. Poikilothermic animals possess pigment cells called integumentary melanophores, derived from neural crest cells, which contain melanin and can detect environmental pollution. These melanophores serve as effective bioassay tools for pharmacological drugs and chemical contaminants. Studies show pollutants like Aroclor 1242 and naphthalene influence crustacean color changes, indicating pollutant impact on chromatophores. Fish melanophores are sensitive to various pollutants and function as sensors of ecological stress, while both melanophores and erythrophores act as bioindicators of water contamination. Exposure to contaminants can cause morphological damage to fish scales, including chromatophore scattering and lepidont disruption. In amphibians, insecticides such as dimethoate lead to melanophore degeneration and bleaching. Melanophore-based toxicity sensors have potential for detecting hazardous substances in drinking water and can also identify bacterial toxins and pathogenic bacteria through cell-based biosensing. Acute pigment dispersion occurs rapidly within minutes to hours, whereas morphological changes appear over days to months. This review explores acute physiological and long-term morphological responses of melanophores in fish, amphibians, and even crustaceans exposed to aquatic pollutants. It distinguishes between short-term pigment translocation as a marker of acute toxicity and longer-term structural changes indicating chronic environmental stress. The review critically evaluates the advantages and limitations of melanophore-based biomonitoring and underscores their potential for in vitro sensing of diverse aquatic contaminants, including bacterial toxins.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"241 ","pages":"Pages 16-25"},"PeriodicalIF":3.0,"publicationDate":"2025-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145484092","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}
Pub Date : 2025-11-05DOI: 10.1016/j.biochi.2025.11.001
Hubert Schaller, Philippe Soudant
{"title":"Lipids: from sea to fork","authors":"Hubert Schaller, Philippe Soudant","doi":"10.1016/j.biochi.2025.11.001","DOIUrl":"10.1016/j.biochi.2025.11.001","url":null,"abstract":"","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"239 ","pages":"Pages 1-3"},"PeriodicalIF":3.0,"publicationDate":"2025-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145472545","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}
Pub Date : 2025-11-01DOI: 10.1016/j.biochi.2025.05.003
Oriana Puidebat, Sylvain Egloff
Cyclin-Dependent Kinase 9 (CDK9) is a critical regulator of transcriptional elongation, functioning within the Positive Transcription Elongation Factor b (P-TEFb) complex alongside Cyclin T1. P-TEFb facilitates the release of RNA polymerase II (RNAPII) from promoter-proximal pausing, thereby enabling productive transcriptional elongation. CDK9 activity is tightly controlled by the 7SK small nuclear ribonucleoprotein (7SK snRNP) complex, comprising 7SK snRNA, LARP7, MEPCE, and HEXIM1/2. Under homeostatic conditions, the 7SK snRNP sequesters and inactivates a fraction of P-TEFb, maintaining it in a repressed state. However, in response to cellular stress or increased transcriptional demand, P-TEFb is released from 7SK snRNP, activating CDK9 to ensure precise, context-dependent transcriptional control. This regulatory switch allows dynamic adaptation to environmental and intracellular cues. Emerging evidence implicates 7SK snRNP deregulation in cancer progression. This review explores the intricate interplay between 7SK snRNP and CDK9, highlighting how disruptions in individual 7SK snRNP components drive transcriptional imbalances, amplify oncogenic programs, and promote a tumorigenic environment.
{"title":"The 7SK snRNP complex: a critical regulator in carcinogenesis","authors":"Oriana Puidebat, Sylvain Egloff","doi":"10.1016/j.biochi.2025.05.003","DOIUrl":"10.1016/j.biochi.2025.05.003","url":null,"abstract":"<div><div>Cyclin-Dependent Kinase 9 (CDK9) is a critical regulator of transcriptional elongation, functioning within the Positive Transcription Elongation Factor b (P-TEFb) complex alongside Cyclin T1. P-TEFb facilitates the release of RNA polymerase II (RNAPII) from promoter-proximal pausing, thereby enabling productive transcriptional elongation. CDK9 activity is tightly controlled by the 7SK small nuclear ribonucleoprotein (7SK snRNP) complex, comprising 7SK snRNA, LARP7, MEPCE, and HEXIM1/2. Under homeostatic conditions, the 7SK snRNP sequesters and inactivates a fraction of P-TEFb, maintaining it in a repressed state. However, in response to cellular stress or increased transcriptional demand, P-TEFb is released from 7SK snRNP, activating CDK9 to ensure precise, context-dependent transcriptional control. This regulatory switch allows dynamic adaptation to environmental and intracellular cues. Emerging evidence implicates 7SK snRNP deregulation in cancer progression. This review explores the intricate interplay between 7SK snRNP and CDK9, highlighting how disruptions in individual 7SK snRNP components drive transcriptional imbalances, amplify oncogenic programs, and promote a tumorigenic environment.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"238 ","pages":"Pages 3-8"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082693","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}
Hybrid internal-terminal exons function as either internal or terminal exons. Their evolutionary origins remain unclear. Here, we investigate the phylogenetic origin and regulation of a hybrid exon, 9A9′, in the TPM1 gene encoding tropomyosin alpha-1. We demonstrate that exon 9A9′ was originally terminal in non-vertebrate deuterostomes and switched to internal in vertebrates through the exonization of a downstream exon, 9B. While the terminal nature of exon 9A9′ was lost in most vertebrates, it was conserved in amphibians and coelacanths where it behaves as a hybrid internal-terminal exon. Using Xenopus laevis as a model, we show that the preservation of terminal exon 9A9′ in the tpm1 gene likely arose from evolutionary pressures to mitigate the developmental toxicity linked to exon 9B inclusion during neurulation. We identify two peculiarities of terminal exon 9A9': it lies downstream of an AG-independent intron, and its definition is supported by an intronic cis-regulatory element, the UTE, which enhances recognition of the weak cleavage-polyadenylation site. Our findings characterize the molecular mechanisms underlying the regulation of hybrid internal-terminal exons and reveal how evolutionary pressures can reactivate vestigial traits to resolve developmental challenges. This work broadens our understanding of alternative splicing evolution and its significance in vertebrate development.
{"title":"Insights into the evolution and regulation of hybrid internal-terminal exons from tropomyosin exon 9A in Xenopus laevis","authors":"Agnès Méreau, Hubert Lerivray, Justine Viet, Serge Hardy, Luc Paillard , Yann Audic","doi":"10.1016/j.biochi.2025.07.009","DOIUrl":"10.1016/j.biochi.2025.07.009","url":null,"abstract":"<div><div>Hybrid internal-terminal exons function as either internal or terminal exons. Their evolutionary origins remain unclear. Here, we investigate the phylogenetic origin and regulation of a hybrid exon, 9A9′, in the <em>TPM1</em> gene encoding tropomyosin alpha-1. We demonstrate that exon 9A9′ was originally terminal in non-vertebrate deuterostomes and switched to internal in vertebrates through the exonization of a downstream exon, 9B. While the terminal nature of exon 9A9′ was lost in most vertebrates, it was conserved in amphibians and coelacanths where it behaves as a hybrid internal-terminal exon. Using <em>Xenopus laevis</em> as a model, we show that the preservation of terminal exon 9A9′ in the <em>tpm1</em> gene likely arose from evolutionary pressures to mitigate the developmental toxicity linked to exon 9B inclusion during neurulation. We identify two peculiarities of terminal exon 9A9': it lies downstream of an AG-independent intron, and its definition is supported by an intronic <em>cis</em>-regulatory element, the UTE, which enhances recognition of the weak cleavage-polyadenylation site. Our findings characterize the molecular mechanisms underlying the regulation of hybrid internal-terminal exons and reveal how evolutionary pressures can reactivate vestigial traits to resolve developmental challenges. This work broadens our understanding of alternative splicing evolution and its significance in vertebrate development.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"238 ","pages":"Pages 29-42"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144621465","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 emergence of antibiotic resistance has rendered the treatment of bacterial infections exceedingly challenging, with diseases caused by resistant strains often resulting in significant morbidity and mortality. Consequently, it is crucial to investigate the mechanisms underlying antibiotic resistance. Outer membrane vesicles (OMVs) are nanoscale spheres characterized by a double membrane structure, released by Gram-negative bacteria (GNB). While the mechanisms governing OMV biogenesis remain under investigation, three models have been proposed. These vesicles have been implicated in enhancing bacterial survival during antibiotic treatment and contributing to the onset and development of drug resistance through various pathways. OMVs function as a secretion system, delivering cargo that mediates intercellular communication to neighboring cells, and their closed structure facilitates this molecular delivery. Vesicles released into the extracellular compartment can protect bacteria from antibiotic treatment by promoting horizontal gene transfer, inactivating or binding antibiotics, influencing biofilm formation, and mediating bacterial gene mutations, among other mechanisms. Many studies have demonstrated that OMVs play a critical role during antibiotic exposure. An in-depth understanding of the mechanisms of OMVs in the development of bacterial drug resistance could help develop more effective therapeutic strategies to prevent persistent bacterial infections. This review focuses on summarising the latest evidence on the involvement of OMVs in the development of drug resistance, to provide ideas for future studies.
{"title":"Mechanisms of outer membrane vesicles in bacterial drug resistance: Insights and implications","authors":"Xianyu Zhang, Wenbo Ding, Jianyu Yang, Linran Gao, Qianying Wang, Jingjing Wang, Yu Luo, Xin Yuan, Baoyu Sun, Jifei Yang, Yujiao Zhou, Liyuan Sun","doi":"10.1016/j.biochi.2025.07.024","DOIUrl":"10.1016/j.biochi.2025.07.024","url":null,"abstract":"<div><div>The emergence of antibiotic resistance has rendered the treatment of bacterial infections exceedingly challenging, with diseases caused by resistant strains often resulting in significant morbidity and mortality. Consequently, it is crucial to investigate the mechanisms underlying antibiotic resistance. Outer membrane vesicles (OMVs) are nanoscale spheres characterized by a double membrane structure, released by Gram-negative bacteria (GNB). While the mechanisms governing OMV biogenesis remain under investigation, three models have been proposed. These vesicles have been implicated in enhancing bacterial survival during antibiotic treatment and contributing to the onset and development of drug resistance through various pathways. OMVs function as a secretion system, delivering cargo that mediates intercellular communication to neighboring cells, and their closed structure facilitates this molecular delivery. Vesicles released into the extracellular compartment can protect bacteria from antibiotic treatment by promoting horizontal gene transfer, inactivating or binding antibiotics, influencing biofilm formation, and mediating bacterial gene mutations, among other mechanisms. Many studies have demonstrated that OMVs play a critical role during antibiotic exposure. An in-depth understanding of the mechanisms of OMVs in the development of bacterial drug resistance could help develop more effective therapeutic strategies to prevent persistent bacterial infections. This review focuses on summarising the latest evidence on the involvement of OMVs in the development of drug resistance, to provide ideas for future studies.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"238 ","pages":"Pages 77-90"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144719206","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}
Pub Date : 2025-11-01DOI: 10.1016/j.biochi.2025.07.025
Cecilia Díaz , Jennifer Rivera , Arturo Chang-Castillo , Fabián Bonilla , Natalia Ortiz , Adriana Alfaro-Chinchilla , Mahmood Sasa
Centruroides limbatus and Centruroides bicolor are phylogenetically related species with different geographical distributions. The scarce envenomation cases in Costa Rica suggest they are probably ‘mammal harmless’, but their venom's effect on other animals has been poorly characterized. We aimed to describe the protein venom composition of C. limbatus and C. bicolor, in the context of their trophic habits and prey specificity.
We applied a proteomics shotgun approach to analyze the composition of venom peptides of C. limbatus and compare them with those expressed by C. bicolor. We also tested the venom's lethal effect on insects and their ability to induce paralysis.
Among the recovered NaTxs, there were C. bicolor Cbi1, C. suffusus CssIX, C. noxius Cn11, C. gracilis Cg2, and C. vittatus β-toxins. Regarding KTxs, we identified ergtoxins, limbatotoxins, and hongotoxins, all peptides commonly found in Centruroides venoms, as well as C. noxius cobatoxin-1 and C. margaritatus Cm39.
Regarding lethality, as demonstrated with other buthid venoms, crickets were very sensitive, whereas mealworms were the most resistant. The current study shows that these scorpion species display similar venom compositions, including previously identified peptides from other Centruroides with and without medical importance, and as expected, they show only minor specificity differences.
缘形蜈蚣和双色蜈蚣是系统亲缘关系密切的物种，但地理分布不同。哥斯达黎加的罕见中毒案例表明，它们可能是“对哺乳动物无害的”，但它们的毒液对其他动物的影响却没有得到很好的描述。我们旨在描述C. limbatus和C. bicolor的蛋白质毒液组成，在他们的营养习惯和猎物特异性的背景下。我们采用蛋白质组学鸟枪法分析了唇形锥虫毒液肽的组成，并与双色锥虫表达的毒液肽进行了比较。我们还测试了毒液对昆虫的致命作用以及它们诱导瘫痪的能力。在回收的natx中，有双色C. Cbi1、suffusus C. cs6、C. noxius C. Cn11、C. gracilis Cg2和C. vittatus β-毒素。对于KTxs，我们鉴定出了ergtoxins， limbatotoxins和honggotoxins，这些肽都是在弓形虫毒液中常见的肽，以及C.毒素cobatoxin-1和C. margaritatus Cm39。在致死率方面，与其他虫毒一样，蟋蟀对虫毒非常敏感，而粉虫对虫毒的抵抗力最强。目前的研究表明，这些蝎子种类显示出相似的毒液成分，包括先前从其他有和没有医学意义的森特罗维德蛛中鉴定出的肽，正如预期的那样，它们只显示出微小的特异性差异。
{"title":"Venomics and insect prey specificity of the Central American scorpion Centruroides limbatus (Pocock, 1898) and its comparison with close species Centruroides bicolor (Pocock, 1898)","authors":"Cecilia Díaz , Jennifer Rivera , Arturo Chang-Castillo , Fabián Bonilla , Natalia Ortiz , Adriana Alfaro-Chinchilla , Mahmood Sasa","doi":"10.1016/j.biochi.2025.07.025","DOIUrl":"10.1016/j.biochi.2025.07.025","url":null,"abstract":"<div><div><em>Centruroides limbatus</em> and <em>Centruroides bicolor</em> are phylogenetically related species with different geographical distributions. The scarce envenomation cases in Costa Rica suggest they are probably ‘mammal harmless’, but their venom's effect on other animals has been poorly characterized. We aimed to describe the protein venom composition of <em>C. limbatus</em> and <em>C. bicolor</em>, in the context of their trophic habits and prey specificity.</div><div>We applied a proteomics shotgun approach to analyze the composition of venom peptides of <em>C. limbatus</em> and compare them with those expressed by <em>C. bicolor</em>. We also tested the venom's lethal effect on insects and their ability to induce paralysis.</div><div>Among the recovered NaTxs, there were <em>C. bicolor</em> Cbi1, <em>C. suffusus</em> CssIX, <em>C. noxi</em><em>us</em> Cn11<em>, C. gracilis</em> Cg2, and <em>C. vittatus</em> β-toxins. Regarding KTxs, we identified ergtoxins, limbatotoxins, and hongotoxins, all peptides commonly found in <em>Centruroides</em> venoms, as well as <em>C. noxi</em><em>us</em> cobatoxin-1 and <em>C. margaritatus</em> Cm39.</div><div>Regarding lethality, as demonstrated with other buthid venoms, crickets were very sensitive, whereas mealworms were the most resistant. The current study shows that these scorpion species display similar venom compositions, including previously identified peptides from other <em>Centruroides</em> with and without medical importance, and as expected, they show only minor specificity differences.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"238 ","pages":"Pages 91-101"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144719217","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}
Ribosomal proteins (RPs), key components of ribosomes, are traditionally associated with protein synthesis. However, emerging evidence suggests their involvement in diverse cellular functions beyond ribosomal biogenesis and translation, including transcriptional regulation. This study aimed at investigating the potential of RPs as transcriptional regulators by analyzing their interacting protein network. A subset of RP interactors exhibiting transcriptional regulatory functions was subjected to Gene Ontology analysis to identify enriched functional pathways. The results indicated that these interactions may play a role in different cellular pathways relevant to a number of biological processes, including cancer. To further explore this hypothesis, a virtual knockdown of RPL5 was performed in ovarian and breast cancer public data. As proof of concept the same experiments were conducted in vitro to validate the computational findings, confirming the potential of RPL5 in transcriptional regulation in cancer. This seminal study provides a foundation for future investigations into the multifaceted roles of RPs in the regulation of gene expression in physiological and pathological contexts.
{"title":"Master of disguise: ribosomal protein L5 beyond translation","authors":"Guglielmo Rambaldelli , Lorenza Bacci , Daniela Pollutri , Kamil Filipek , Marianna Penzo","doi":"10.1016/j.biochi.2025.03.009","DOIUrl":"10.1016/j.biochi.2025.03.009","url":null,"abstract":"<div><div>Ribosomal proteins (RPs), key components of ribosomes, are traditionally associated with protein synthesis. However, emerging evidence suggests their involvement in diverse cellular functions beyond ribosomal biogenesis and translation, including transcriptional regulation. This study aimed at investigating the potential of RPs as transcriptional regulators by analyzing their interacting protein network. A subset of RP interactors exhibiting transcriptional regulatory functions was subjected to Gene Ontology analysis to identify enriched functional pathways. The results indicated that these interactions may play a role in different cellular pathways relevant to a number of biological processes, including cancer. To further explore this hypothesis, a virtual knockdown of RPL5 was performed in ovarian and breast cancer public data. As proof of concept the same experiments were conducted <em>in vitro</em> to validate the computational findings, confirming the potential of RPL5 in transcriptional regulation in cancer. This seminal study provides a foundation for future investigations into the multifaceted roles of RPs in the regulation of gene expression in physiological and pathological contexts.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"238 ","pages":"Pages 65-72"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143789395","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}
Pub Date : 2025-11-01DOI: 10.1016/j.biochi.2025.07.022
Nora Halgasova , Lucia Bocanova , Jacob A. Bauer , Barbora Niku , Kristina Papayova , Gabriela Bukovska
Replication protein gp41 from bacteriophage BFK20 is a 537 residue SF2 family helicase. The N-terminal two-thirds of the gp41 sequence is homologous to XPB/Ssl2-like helicases, but no clear homology to any known and characterized protein could be found for the C-terminal one-third. We prepared and studied the following gp41 mutant recombinant proteins: deletion mutant gp41L481, missing the last 56 C-terminal amino acids (482–537), and five point mutants, each substituting a single amino acid from this region with alanine (K516A, R518A, D520A, D521A and E522A). We tested the ATPase activities, DNA binding abilities, thermal stabilities and protein-ATP interactions of each isolated protein and compared them with wild-type-like protein gp41HN. The ATPase activity and DNA binding ability of gp41L481 were significantly lower than gp41HN. The K516A and R518A mutations resulted in an almost total loss of ATPase activity, while the D521A mutation produced a lesser loss. The K516A mutation also significantly reduced the DNA binding ability of the mutant protein. All point mutants were less stable than the wild-type protein to a greater or lesser extent, and ATP had a significant stabilizing effect on most tested proteins. We conclude that the amino-acids at the extreme C-terminus of gp41 are important for its ATPase activity, DNA binding ability and protein-ATP interactions. BFK20 gp41 is an example of a phage helicase whose accessory domain significantly affects its properties and it provides additional evidence for the importance of accessory domains for helicase function.
{"title":"The extreme C-terminal region of the phage BFK20 gp41 helicase has a role in DNA binding, protein-ATP interactions and ATPase activity","authors":"Nora Halgasova , Lucia Bocanova , Jacob A. Bauer , Barbora Niku , Kristina Papayova , Gabriela Bukovska","doi":"10.1016/j.biochi.2025.07.022","DOIUrl":"10.1016/j.biochi.2025.07.022","url":null,"abstract":"<div><div>Replication protein gp41 from bacteriophage BFK20 is a 537 residue SF2 family helicase. The N-terminal two-thirds of the gp41 sequence is homologous to XPB/Ssl2-like helicases, but no clear homology to any known and characterized protein could be found for the C-terminal one-third. We prepared and studied the following gp41 mutant recombinant proteins: deletion mutant gp41L481, missing the last 56 C-terminal amino acids (482–537), and five point mutants, each substituting a single amino acid from this region with alanine (K516A, R518A, D520A, D521A and E522A). We tested the ATPase activities, DNA binding abilities, thermal stabilities and protein-ATP interactions of each isolated protein and compared them with wild-type-like protein gp41HN. The ATPase activity and DNA binding ability of gp41L481 were significantly lower than gp41HN. The K516A and R518A mutations resulted in an almost total loss of ATPase activity, while the D521A mutation produced a lesser loss. The K516A mutation also significantly reduced the DNA binding ability of the mutant protein. All point mutants were less stable than the wild-type protein to a greater or lesser extent, and ATP had a significant stabilizing effect on most tested proteins. We conclude that the amino-acids at the extreme C-terminus of gp41 are important for its ATPase activity, DNA binding ability and protein-ATP interactions. BFK20 gp41 is an example of a phage helicase whose accessory domain significantly affects its properties and it provides additional evidence for the importance of accessory domains for helicase function.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"238 ","pages":"Pages 43-57"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144710282","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}
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