Understanding metal transport in plants has always been critical. Several gene families have been identified in the last two decades that have aided in the understanding of channelized metal transport, including their uptake, distribution, and storage in plants. Identifying Yellow Stripe-like (YSL) genes has contributed to an improved understanding of metal homeostasis in plants, especially monocots. Several studies have demonstrated that these genes play a role in transporting metals complexed with phytosiderophores (PS) and/or nicotianamine (NA). In the current review, we have discussed and opinionated the signalling role of YSL protein in maintaining inter and intracellular metal homeostasis in plants. Although the genes are known to have a broader range of metal substrate specificity, these are primary iron (Fe) transporters, and a detailed Fe transport in plants is discussed. Furthermore, based on recent findings, alternative functions of these genes are also discussed. Overall, we provide a broader overview of YSL protein in modulating the Fe mobilization and provides evidence of the expanding functions in plants.
{"title":"The multifaceted role of YSL proteins: Iron transport and emerging functions in plant metal homeostasis","authors":"Anil Kumar , Riya Joon , Gourav Singh , Jagtar Singh , Ajay Kumar Pandey","doi":"10.1016/j.bbagen.2025.130792","DOIUrl":"10.1016/j.bbagen.2025.130792","url":null,"abstract":"<div><div>Understanding metal transport in plants has always been critical. Several gene families have been identified in the last two decades that have aided in the understanding of channelized metal transport, including their uptake, distribution, and storage in plants. Identifying Yellow Stripe-like (YSL) genes has contributed to an improved understanding of metal homeostasis in plants, especially monocots. Several studies have demonstrated that these genes play a role in transporting metals complexed with phytosiderophores (PS) and/or nicotianamine (NA). In the current review, we have discussed and opinionated the signalling role of YSL protein in maintaining inter and intracellular metal homeostasis in plants. Although the genes are known to have a broader range of metal substrate specificity, these are primary iron (Fe) transporters, and a detailed Fe transport in plants is discussed. Furthermore, based on recent findings, alternative functions of these genes are also discussed. Overall, we provide a broader overview of YSL protein in modulating the Fe mobilization and provides evidence of the expanding functions in plants.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 6","pages":"Article 130792"},"PeriodicalIF":2.8,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143620150","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 : 2025-03-12DOI: 10.1016/j.bbagen.2025.130793
Christopher C Perry, Reinhard W Schulte, Ryan N Fuller, Nathan R Wall, Kevin E Nick, Magdalena Wegrzyn, Jamie R Milligan
X-irradiation has extensive applications in therapy and considerable attention has been devoted to the radiosensitizing properties of nanoparticles composed of high atomic number elements, particularly gold. Low energy electrons and/or heterogenous catalysis are widely suspected to be involved in radiosensitization, but there is uncertainty about their contributions. Because of their greater surface area to volume ratio relative to spherical particles per unit mass of gold, nanostars permit more low energy electrons to escape and posses an increased catalytic activity. Condensed DNA represents a highly useful model for mammalian chromatin, particularly with respect to the types and yields of DNA damage produced by ionizing radiation. Here we describe the incorporation of spherical gold nanoparticles and of gold nanostars into a condensed DNA model system. The resulting self-assembled micron-sized co-aggregates involve an intimate association between gold and DNA, maximizing the opportunity for the production of DNA damage. After increasing the ionic strength, the co-condensate becomes disaggregated and the DNA is available for subsequent assays. This model system provides a previously unavailable tool for examining the mechanisms of radiosensitization of DNA damage by gold nanoparticles with implications for possible applications in radiotherapy.
X 射线在治疗中有着广泛的应用，人们对由高原子序数元素（尤其是金）组成的纳米粒子的辐射敏感特性给予了极大的关注。人们普遍怀疑低能电子和/或异质催化作用参与了放射增敏作用，但对它们的贡献还不确定。与单位质量的球形金粒子相比，纳米金星的表面积与体积比更大，因此可允许更多的低能电子逸出，并具有更强的催化活性。凝结 DNA 是哺乳动物染色质的一个非常有用的模型，特别是在电离辐射产生的 DNA 损伤类型和损伤率方面。在这里，我们描述了将球形金纳米粒子和金纳米星融入凝聚 DNA 模型系统的过程。由此产生的自组装微米级共聚物涉及金与 DNA 之间的紧密结合，最大限度地增加了产生 DNA 损伤的机会。增加离子强度后，共聚物会分解，DNA 可用于后续检测。该模型系统为研究金纳米粒子对 DNA 损伤的放射增敏机制提供了一种前所未有的工具，对放射治疗的可能应用具有重要意义。
{"title":"Integrating gold nanostars into condensed DNA.","authors":"Christopher C Perry, Reinhard W Schulte, Ryan N Fuller, Nathan R Wall, Kevin E Nick, Magdalena Wegrzyn, Jamie R Milligan","doi":"10.1016/j.bbagen.2025.130793","DOIUrl":"https://doi.org/10.1016/j.bbagen.2025.130793","url":null,"abstract":"<p><p>X-irradiation has extensive applications in therapy and considerable attention has been devoted to the radiosensitizing properties of nanoparticles composed of high atomic number elements, particularly gold. Low energy electrons and/or heterogenous catalysis are widely suspected to be involved in radiosensitization, but there is uncertainty about their contributions. Because of their greater surface area to volume ratio relative to spherical particles per unit mass of gold, nanostars permit more low energy electrons to escape and posses an increased catalytic activity. Condensed DNA represents a highly useful model for mammalian chromatin, particularly with respect to the types and yields of DNA damage produced by ionizing radiation. Here we describe the incorporation of spherical gold nanoparticles and of gold nanostars into a condensed DNA model system. The resulting self-assembled micron-sized co-aggregates involve an intimate association between gold and DNA, maximizing the opportunity for the production of DNA damage. After increasing the ionic strength, the co-condensate becomes disaggregated and the DNA is available for subsequent assays. This model system provides a previously unavailable tool for examining the mechanisms of radiosensitization of DNA damage by gold nanoparticles with implications for possible applications in radiotherapy.</p>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":" ","pages":"130793"},"PeriodicalIF":2.8,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143630138","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}
Operons, clusters of genes under a single promoter, often exhibit a specific gene order influencing their physiological function. While functional relatedness is a known factor for clustering, the underlying drivers of gene ordering remain unclear. To investigate this, we analyzed the pdu operon, encoding proteins for 1,2 Pdu bacterial microcompartment. Our bioinformatics revealed no link between the sequence similarity and proximity of the genes in the operon. However quantitative mapping of protein-protein interactions within the operon using a barrage of spectroscopic tools showed a strong correlation between interaction strength and gene proximity. Our data thus indicates that protein-protein interactions play a significant role in determining gene order within the pdu operon, potentially contributing to the efficient assembly and function of these microcompartments.
{"title":"Protein-protein interactions as determinants of operon architecture","authors":"Silky Bedi, S.M. Rose, Simerpreet Kaur , Preeti Negi , Sharmistha Sinha","doi":"10.1016/j.bbagen.2025.130794","DOIUrl":"10.1016/j.bbagen.2025.130794","url":null,"abstract":"<div><div>Operons, clusters of genes under a single promoter, often exhibit a specific gene order influencing their physiological function. While functional relatedness is a known factor for clustering, the underlying drivers of gene ordering remain unclear. To investigate this, we analyzed the <em>pdu</em> operon, encoding proteins for 1,2 Pdu bacterial microcompartment. Our bioinformatics revealed no link between the sequence similarity and proximity of the genes in the operon. However quantitative mapping of protein-protein interactions within the operon using a barrage of spectroscopic tools showed a strong correlation between interaction strength and gene proximity. Our data thus indicates that protein-protein interactions play a significant role in determining gene order within the <em>pdu</em> operon, potentially contributing to the efficient assembly and function of these microcompartments.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 6","pages":"Article 130794"},"PeriodicalIF":2.8,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143629471","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 : 2025-03-09DOI: 10.1016/j.bbagen.2025.130791
Shilian Pang , Yurao Chen , Zemao Zheng , Luoshai Wang , Ronghuai Chen , Ming He , Xiang Zhao , Juan Yao , Liyan Jin
Background
The progression of Esophageal Squamous Cell Carcinoma (ESCC) can be dissected with greater precision using multi-omics and single-cell RNA sequencing (scRNA-seq) compared to traditional methodologies. These advanced approaches enable a comprehensive understanding of cellular heterogeneity and molecular dynamics, offering higher resolution insights into cancer development. Moreover, analyzing transcription factor regulatory networks provides innovative avenues for identifying cancer biomarkers and therapeutic targets, driving new perspectives in cancer research.
Objective
To explore the molecular mechanisms and cellular dynamics of ESCC.
Methods
Utilizing bulk-RNA-seq and single-cell transcriptomics, our study identify major cell types, transcriptomic gene and function changes during ESCC progression. Validation experiments in clinical sample tissues and ESCC cell lines to confirm core regulation factor in ESCC.
Results
We identified six major cell types in the ESCC scRNA-seq dataset and revealed profound shifts in cellular composition and transcriptional profiles. Notably, STAT3 was found to be a core regulator in ESCC and negatively regulated LHPP expression at promoter sites. Elevated STAT3 and reduced LHPP expression were consistently observed in patient samples, highlighting their inverse relationship in ESCC pathogenesis.
Conclusion
This study integrates bulk-seq and scRNA-seq data to reveal the pivotal role of STAT3 in ESCC. STAT3 negatively regulates LHPP expression, driving tumor progression. These findings underscore the therapeutic potential of targeting STAT3 in ESCC. Key words: ESCC, single-cell transcriptomics, ESCC microenvironment, STAT3.
{"title":"STAT3-orchestrated gene expression signatures and tumor microenvironment in esophageal squamous cell carcinoma uncovered by single-cell sequencing","authors":"Shilian Pang , Yurao Chen , Zemao Zheng , Luoshai Wang , Ronghuai Chen , Ming He , Xiang Zhao , Juan Yao , Liyan Jin","doi":"10.1016/j.bbagen.2025.130791","DOIUrl":"10.1016/j.bbagen.2025.130791","url":null,"abstract":"<div><h3>Background</h3><div>The progression of Esophageal Squamous Cell Carcinoma (ESCC) can be dissected with greater precision using multi-omics and single-cell RNA sequencing (scRNA-seq) compared to traditional methodologies. These advanced approaches enable a comprehensive understanding of cellular heterogeneity and molecular dynamics, offering higher resolution insights into cancer development. Moreover, analyzing transcription factor regulatory networks provides innovative avenues for identifying cancer biomarkers and therapeutic targets, driving new perspectives in cancer research.</div></div><div><h3>Objective</h3><div>To explore the molecular mechanisms and cellular dynamics of ESCC.</div></div><div><h3>Methods</h3><div>Utilizing bulk-RNA-seq and single-cell transcriptomics, our study identify major cell types, transcriptomic gene and function changes during ESCC progression. Validation experiments in clinical sample tissues and ESCC cell lines to confirm core regulation factor in ESCC.</div></div><div><h3>Results</h3><div>We identified six major cell types in the ESCC scRNA-seq dataset and revealed profound shifts in cellular composition and transcriptional profiles. Notably, STAT3 was found to be a core regulator in ESCC and negatively regulated LHPP expression at promoter sites. Elevated STAT3 and reduced LHPP expression were consistently observed in patient samples, highlighting their inverse relationship in ESCC pathogenesis.</div></div><div><h3>Conclusion</h3><div>This study integrates bulk-seq and scRNA-seq data to reveal the pivotal role of STAT3 in ESCC. STAT3 negatively regulates LHPP expression, driving tumor progression. These findings underscore the therapeutic potential of targeting STAT3 in ESCC. <strong>Key words:</strong> ESCC, single-cell transcriptomics, ESCC microenvironment, STAT3.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 6","pages":"Article 130791"},"PeriodicalIF":2.8,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603879","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 : 2025-03-07DOI: 10.1016/j.bbagen.2025.130787
Sayoko Ito-Harashima, Natsuko Miura
Compartmentalization of multiple enzymes in cellulo and in vitro is a means of controlling the cascade reaction of metabolic enzymes. The compartmentation of enzymes through liquid–liquid phase separation may facilitate the reversible control of biocatalytic cascade reactions, thereby reducing the transcriptional and translational burden. This has attracted attention as a potential application in bioproduction. Recent research has demonstrated the existence and regulatory mechanisms of various enzyme compartments within cells. Mounting evidence suggests that enzyme compartmentation allows in vitro and in vivo regulation of cellular metabolism. However, the comprehensive regulatory mechanisms of enzyme condensates in cells and ideal organization of cellular systems remain unknown. This review provides an overview of the recent progress in multiple enzyme compartmentation in cells and summarizes strategies to reconstruct multiple enzyme assemblies in vitro and in cellulo. By examining parallel examples, we have evaluated the consensus and future perspectives of enzyme condensation.
{"title":"Compartmentation of multiple metabolic enzymes and their preparation in vitro and in cellulo","authors":"Sayoko Ito-Harashima, Natsuko Miura","doi":"10.1016/j.bbagen.2025.130787","DOIUrl":"10.1016/j.bbagen.2025.130787","url":null,"abstract":"<div><div>Compartmentalization of multiple enzymes <em>in cellulo</em> and <em>in vitro</em> is a means of controlling the cascade reaction of metabolic enzymes. The compartmentation of enzymes through liquid–liquid phase separation may facilitate the reversible control of biocatalytic cascade reactions, thereby reducing the transcriptional and translational burden. This has attracted attention as a potential application in bioproduction. Recent research has demonstrated the existence and regulatory mechanisms of various enzyme compartments within cells. Mounting evidence suggests that enzyme compartmentation allows <em>in vitro</em> and <em>in vivo</em> regulation of cellular metabolism. However, the comprehensive regulatory mechanisms of enzyme condensates in cells and ideal organization of cellular systems remain unknown. This review provides an overview of the recent progress in multiple enzyme compartmentation in cells and summarizes strategies to reconstruct multiple enzyme assemblies <em>in vitro</em> and <em>in cellulo</em>. By examining parallel examples, we have evaluated the consensus and future perspectives of enzyme condensation.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 6","pages":"Article 130787"},"PeriodicalIF":2.8,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584449","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 : 2025-03-07DOI: 10.1016/j.bbagen.2025.130789
Miao Zhu, Xuying Wang, Xinran Li
Glutamate receptor-like (GLRs) genes play essential roles in plant growth and development, and in coping with environmental stresses; however, information on GLR genes in Dendrobium species is lacking. We identified 25 GLR genes in three Dendrobium species, which were classified into three subfamilies based on their phylogenetic relationships. These genes have been relatively conserved during evolution. Analysis of cis-acting elements and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes annotations revealed the complexity and diversity of GLR gene regulation and functions. Further, gene expression analysis showed that different GLR members exhibited different expression patterns during Dendrobium growth and development, and some were involved in pathogen infection and in response to hormones. These results provide important information on the GLR gene family of Dendrobium, and a foundation for further functional, and trait regulation and improvement studies.
{"title":"Genome-wide identification and expression analysis of glutamate receptor-like genes in three Dendrobium species","authors":"Miao Zhu, Xuying Wang, Xinran Li","doi":"10.1016/j.bbagen.2025.130789","DOIUrl":"10.1016/j.bbagen.2025.130789","url":null,"abstract":"<div><div>Glutamate receptor-like (<em>GLRs</em>) genes play essential roles in plant growth and development, and in coping with environmental stresses; however, information on <em>GLR</em> genes in <em>Dendrobium</em> species is lacking. We identified 25 <em>GLR</em> genes in three <em>Dendrobium</em> species, which were classified into three subfamilies based on their phylogenetic relationships. These genes have been relatively conserved during evolution. Analysis of cis-acting elements and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes annotations revealed the complexity and diversity of <em>GLR</em> gene regulation and functions. Further, gene expression analysis showed that different <em>GLR</em> members exhibited different expression patterns during <em>Dendrobium</em> growth and development, and some were involved in pathogen infection and in response to hormones. These results provide important information on the <em>GLR</em> gene family of <em>Dendrobium,</em> and a foundation for further functional, and trait regulation and improvement studies.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 6","pages":"Article 130789"},"PeriodicalIF":2.8,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584451","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 : 2025-03-06DOI: 10.1016/j.bbagen.2025.130790
Chikashi Obuse , Jun-ichi Nakayama
Heterochromatin is a highly condensed chromatin structure observed in the nuclei of eukaryotic cells. It plays a pivotal role in repressing undesired gene expression and establishing functional chromosomal domains, including centromeres and telomeres. Heterochromatin is characterized by specific histone modifications and the formation of higher-order chromatin structures mediated by proteins, such as HP1 and Polycomb repressive complexes (PRCs), which recognize the specific histone modifications. Recent studies have identified the involvement of non-coding RNAs (ncRNAs) and intrinsically disordered proteins (IDPs) in heterochromatin, leading to the proposal of a new model in which liquid-liquid phase separation (LLPS) contributes to heterochromatin formation and function. This emerging model not only broadens our understanding of heterochromatin's molecular mechanisms but also provides insights into its dynamic regulation depending on cellular context. Such advancements pave the way for exploring heterochromatin's role in genome organization and stability, as well as its implications in development and disease.
{"title":"Functional involvement of RNAs and intrinsically disordered proteins in the assembly of heterochromatin","authors":"Chikashi Obuse , Jun-ichi Nakayama","doi":"10.1016/j.bbagen.2025.130790","DOIUrl":"10.1016/j.bbagen.2025.130790","url":null,"abstract":"<div><div>Heterochromatin is a highly condensed chromatin structure observed in the nuclei of eukaryotic cells. It plays a pivotal role in repressing undesired gene expression and establishing functional chromosomal domains, including centromeres and telomeres. Heterochromatin is characterized by specific histone modifications and the formation of higher-order chromatin structures mediated by proteins, such as HP1 and Polycomb repressive complexes (PRCs), which recognize the specific histone modifications. Recent studies have identified the involvement of non-coding RNAs (ncRNAs) and intrinsically disordered proteins (IDPs) in heterochromatin, leading to the proposal of a new model in which liquid-liquid phase separation (LLPS) contributes to heterochromatin formation and function. This emerging model not only broadens our understanding of heterochromatin's molecular mechanisms but also provides insights into its dynamic regulation depending on cellular context. Such advancements pave the way for exploring heterochromatin's role in genome organization and stability, as well as its implications in development and disease.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 6","pages":"Article 130790"},"PeriodicalIF":2.8,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143578456","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 : 2025-03-05DOI: 10.1016/j.bbagen.2025.130788
Shubham Joshi , Rohit Joshi
Understanding the responses of Himalayan medicinal plants to multifactorial stresses is crucial in the face of increasing environmental challenges, primarily characterised by frequent temperature and water availability fluctuations. The present study investigates the physiological, biochemical, and transcript variations in the critically endangered Himalayan medicinal plant Nardostachys jatamansi subjected to cold (15 °C and 10 °C for 30 days), drought (6 % PEG for 30 days), and heat stress (30 °C for 24 h). The primary impact of stress was observed through reduced plant biomass and chlorophyll fluorescence. The effects of abiotic stresses were also evident in the modulation of electrolyte leakage, MDA content and H2O2 accumulation. Accumulation of reactive oxygen species was confirmed through DAB and NBT staining, alongside increased DPPH and ABTS radical scavenging activity. Differential expression profiling of the RBOH family transcripts further substantiated the production of ROS. Enhanced enzymatic and non-enzymatic activities were observed under each abiotic stress condition. Additionally, genes specific to the regulatory mevalonate (MVA) pathway (TPS9; HMGR) and the methylerythritol phosphate (MEP) pathway (DXS1; DXR) were found to be differentially regulated. Moreover, differential expression profiling of abiotic stress signalling regulatory transcripts CRLK1, CRLK2, CaM6 and ICE1 was also discovered. These findings provide valuable insights into the physiological and biochemical profiling of N. jatamansi in response to extreme environmental conditions, significantly aiding our understanding of the adaptation strategies of alpine vegetation for their conservation.
{"title":"Quantifying redox signalling regulatory transcriptional dynamics in Nardostachys jatamansi under abiotic stress response","authors":"Shubham Joshi , Rohit Joshi","doi":"10.1016/j.bbagen.2025.130788","DOIUrl":"10.1016/j.bbagen.2025.130788","url":null,"abstract":"<div><div>Understanding the responses of Himalayan medicinal plants to multifactorial stresses is crucial in the face of increasing environmental challenges, primarily characterised by frequent temperature and water availability fluctuations. The present study investigates the physiological, biochemical, and transcript variations in the critically endangered Himalayan medicinal plant <em>Nardostachys jatamansi</em> subjected to cold (15 °C and 10 °C for 30 days), drought (6 % PEG for 30 days), and heat stress (30 °C for 24 h). The primary impact of stress was observed through reduced plant biomass and chlorophyll fluorescence. The effects of abiotic stresses were also evident in the modulation of electrolyte leakage, MDA content and H<sub>2</sub>O<sub>2</sub> accumulation. Accumulation of reactive oxygen species was confirmed through DAB and NBT staining, alongside increased DPPH and ABTS radical scavenging activity. Differential expression profiling of the RBOH family transcripts further substantiated the production of ROS. Enhanced enzymatic and non-enzymatic activities were observed under each abiotic stress condition. Additionally, genes specific to the regulatory mevalonate (MVA) pathway (<em>TPS9</em>; <em>HMGR</em>) and the methylerythritol phosphate (MEP) pathway (<em>DXS1</em>; <em>DXR</em>) were found to be differentially regulated. Moreover, differential expression profiling of abiotic stress signalling regulatory transcripts <em>CRLK1</em>, <em>CRLK2</em>, <em>CaM6</em> and <em>ICE1</em> was also discovered. These findings provide valuable insights into the physiological and biochemical profiling of <em>N. jatamansi</em> in response to extreme environmental conditions, significantly aiding our understanding of the adaptation strategies of alpine vegetation for their conservation.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 6","pages":"Article 130788"},"PeriodicalIF":2.8,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143578455","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 : 2025-03-02DOI: 10.1016/j.bbagen.2025.130786
Andy Y.W. Lam , Yukihide Tomari , Kotaro Tsuboyama
In order for a protein to function, it must fold into its proper three-dimensional structure. Otherwise, improperly folded proteins are typically prone to aggregate through a process that is detrimental to cellular health. It is widely known that a diverse group of proteins, called molecular chaperones, function to promote proper folding of other proteins and prevent aggregation. In contrast, intrinsically disordered proteins (IDPs) lack substantial tertiary structures, but nonetheless serve important functional roles. In some cases, IDPs have been observed to display remarkably chaperone-like activities, where they stabilize the activities of client proteins and prevent their aggregation. While it was previously thought that chaperone-like IDPs were mainly utilized by extremophilic organisms in their survival of extreme stress, we recently showed that a group of chaperone-like IDPs, we named heat-resistant obscure (Hero) proteins, are also widespread in non-extremophile animals, including humans and flies. Thus, we should consider the possibility that IDPs serve significant chaperone-like functions in protein stabilization relevant to physiological conditions. However, as most of our understanding of how chaperones function is based on insights from their structured domains, it is unclear how chaperone-like IDPs elicit chaperone-like effects without these structures. Here we summarize our understanding of Hero proteins to date and, based on experimental evidence, outline the features that are likely important for their protein stabilizing activities. We draw on concepts from the studies of chaperones and chaperone-like IDPs, in order to draft potential models of how chaperone-like IDPs achieve chaperone-like effects in the absence of well-defined structures.
{"title":"No structure, no problem: Protein stabilization by Hero proteins and other chaperone-like IDPs","authors":"Andy Y.W. Lam , Yukihide Tomari , Kotaro Tsuboyama","doi":"10.1016/j.bbagen.2025.130786","DOIUrl":"10.1016/j.bbagen.2025.130786","url":null,"abstract":"<div><div>In order for a protein to function, it must fold into its proper three-dimensional structure. Otherwise, improperly folded proteins are typically prone to aggregate through a process that is detrimental to cellular health. It is widely known that a diverse group of proteins, called molecular chaperones, function to promote proper folding of other proteins and prevent aggregation. In contrast, intrinsically disordered proteins (IDPs) lack substantial tertiary structures, but nonetheless serve important functional roles. In some cases, IDPs have been observed to display remarkably chaperone-like activities, where they stabilize the activities of client proteins and prevent their aggregation. While it was previously thought that chaperone-like IDPs were mainly utilized by extremophilic organisms in their survival of extreme stress, we recently showed that a group of chaperone-like IDPs, we named heat-resistant obscure (Hero) proteins, are also widespread in non-extremophile animals, including humans and flies. Thus, we should consider the possibility that IDPs serve significant chaperone-like functions in protein stabilization relevant to physiological conditions. However, as most of our understanding of how chaperones function is based on insights from their structured domains, it is unclear how chaperone-like IDPs elicit chaperone-like effects without these structures. Here we summarize our understanding of Hero proteins to date and, based on experimental evidence, outline the features that are likely important for their protein stabilizing activities. We draw on concepts from the studies of chaperones and chaperone-like IDPs, in order to draft potential models of how chaperone-like IDPs achieve chaperone-like effects in the absence of well-defined structures.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 6","pages":"Article 130786"},"PeriodicalIF":2.8,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143555735","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 : 2025-02-21DOI: 10.1016/j.bbagen.2025.130779
Pedro Almeida , Inês Alves , Ângela Fernandes , Cláudia Lima , Rui Freitas , Isaac Braga , Jorge Correia , Carmen Jerónimo , Salomé S. Pinho
Cell wall glycans isolated from microorganisms are long known to provoke strong immune responses piloted by innate immune cell populations, including monocytes, in the context of Trained Immunity (TI). However, the contribution of yeast-derived mannan in the reprogramming of monocytes remains ill-defined. Here, we demonstrated that TI is often accompanied by an altered gene expression profile of selected glycan-binding proteins expressed by monocytes, including DC-SIGN and Dectin-2. Additionally, we showed that mannan, a mannose rich glycan, can trigger an enhanced immune phenotype compatible with TI in healthy monocytes, with glycan-primed cells exhibiting enhanced pro-inflammatory cytokine secretion (TNFα and IL-6) and higher activation (CD86) levels. Furthermore, the glycan-mediated priming of monocytes also imposed alterations to the expression of certain Glycan-Binding Proteins, such as DC-SIGN. Importantly, we established that these mannan-trained immune cells displayed an improved capacity to kill tumor cells in vitro. Lastly, we confirmed that monocytes from non-muscle invasive bladder cancer patients treated with BCG instillations presented a TI phenotype, as was revealed by the higher cytokine production and activation. Altogether, this study lays the foundations for exploiting the immunological potential of glycan-derived pathogens in reprogramming innate immune cells towards an effective anti-tumor immune response.
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