Biochimica et biophysica acta. General subjects最新文献

{"title":"Beyond protein folding: The pleiotropic functions of PPIases in cellular processes and microbial virulence","authors":"Roopshali Rakshit ,&nbsp;Aayush Bahl ,&nbsp;Arunima Arunima ,&nbsp;Saurabh Pandey ,&nbsp;Deeksha Tripathi","doi":"10.1016/j.bbagen.2024.130754","DOIUrl":"10.1016/j.bbagen.2024.130754","url":null,"abstract":"<div><div>Peptidyl prolyl cis/trans isomerases (PPIases), a ubiquitously distributed superfamily of enzymes, associated with signal transduction, trafficking, assembly, biofilm formation, stress tolerance, cell cycle regulation, gene expression and tissue regeneration, is a key regulator of metabolic disorders and microbial virulence. This review assumes an integrative approach, to provide a holistic overview of the structural and functional diversity of PPIases, examining their conformational dynamics, cellular distribution, and physiological significance. We explore their intricate involvement in cellular processes and virulence modulation in both eukaryotic and prokaryotic systems. Additionally, we evaluate the potential of these molecular chaperones as drug targets and vaccine candidates, emphasizing their relevance in therapeutic development. By synthesizing recent findings and providing a broader perspective on these proteins, this review aims to enhance our understanding of their multifaceted roles in biology and their potential applications in medicine.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 2","pages":"Article 130754"},"PeriodicalIF":2.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142891751","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}

{"title":"From non-coding to coding: The importance of long non-coding RNA translation in de novo gene birth","authors":"Taichi Shiraishi,&nbsp;Akinobu Matsumoto","doi":"10.1016/j.bbagen.2024.130747","DOIUrl":"10.1016/j.bbagen.2024.130747","url":null,"abstract":"<div><div>Recent emerging evidence demonstrates that some long non-coding RNAs (lncRNAs) can indeed be translated into functional polypeptides. These discoveries are pivotal for understanding de novo gene birth, the process by which new genes evolve from previously non-genic regions. In this review, we first introduce key methods, such as Ribo-seq and translation initiation site detection by translation complex analysis, for identifying coding sequences within lncRNAs and highlight examples of functional polypeptides derived from lncRNAs across species. These polypeptides play essential roles in maintaining cellular homeostasis and contribute to pathological processes, including cancer. However, because not all lncRNA-derived polypeptides appear to be functional, these lncRNAs may act as gene reservoirs. We also discuss how lncRNAs change their intracellular localization, how lncRNA-derived polypeptides evade immune surveillance, and how they gradually evolve into typical coding RNAs, providing evidence for the evolutionary model of de novo gene birth.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 2","pages":"Article 130747"},"PeriodicalIF":2.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142871064","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}

{"title":"Structural investigation of erdafitinib, an anticancer drug, with ctDNA: A spectroscopic and computational study","authors":"Mohd Amir ,&nbsp;Mohd Aamir Qureshi ,&nbsp;Javed Musarrat ,&nbsp;Saleem Javed","doi":"10.1016/j.bbagen.2024.130751","DOIUrl":"10.1016/j.bbagen.2024.130751","url":null,"abstract":"<div><div>The interaction of drugs with DNA is crucial for understanding their mechanism of action, particularly in the context of gene expression regulation. Erdafitinib (EDB), a pan-FGFR (fibroblast growth factor receptor) inhibitor approved by the FDA, is a potent anticancer agent used primarily in the treatment of urothelial carcinoma. In this study, the binding interaction between EDB and calf thymus DNA (ctDNA) was assessed using molecular docking, UV-absorption spectroscopy, fluorescence spectroscopy, and circular dichroism (CD) spectroscopy. The absorption spectra indicated a hypochromic effect when EDB was combined with ctDNA. The binding constant (K_a) of EDB-ctDNA complex was calculated as 7.84 × 10³ M⁻¹, corresponds to a free energy change (ΔG) value of approximately −5.06 kcal/mol, indicating a moderate binding affinity. Fluorometric analysis revealed a static binding mechanism in the ground state, with a bimolecular enhancement constant (K_B) of 7.56 × 10¹¹ M⁻¹. Displacement experiments demonstrated that EDB preferentially binds to the minor groove of ctDNA, with a Ksv value of 5.14 × 10⁴ M⁻¹. Further, KI quenching and CD spectroscopy confirmed the minor groove binding mode, which was associated with a decrease in the T_m from 68.28 °C to 65.84 °C, reflecting a destabilizing effect on DNA helix. Molecular docking supported these findings, showing that EDB exhibits a strong affinity for the minor groove of ctDNA and hydrogen bonding and Vander Waal interactions are the major forces involved in the binding. These results suggest that EDB primarily binds to the minor groove of ctDNA, which may play a role in its anticancer activity.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 2","pages":"Article 130751"},"PeriodicalIF":2.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142891771","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}

{"title":"Unraveling the intricate tapestry of bamboo transcription factors in abiotic stress signaling and resilience with special reference to moso bamboo family","authors":"Anita Kumari ,&nbsp;Sudhir K. Sopory ,&nbsp;Rohit Joshi","doi":"10.1016/j.bbagen.2024.130755","DOIUrl":"10.1016/j.bbagen.2024.130755","url":null,"abstract":"<div><div>The abiotic stress tolerance mechanism in plants is regulated by multiple physiological, biochemical, and molecular processes; hence, omics approaches to underpin these mechanisms are essential. It is clear that transcription factors (TFs) are one of the fundamental molecular switches that play a crucial role in modulating, regulating, and orchestrating plants in response to various climatic vagaries. Several reports are available now, focusing on understanding the roles of TFs, including those in Poaceae family in regulating different biological processes and stress responses. However, research on bamboo TFs' regulatory role in providing abiotic stress tolerance is limited. Hence the present review offers innovative insights into unraveling the molecular regulation of known family of TFs in different species of bamboo which have been identified as regulators of transcript abundance in numerous genes responsive to various abiotic stresses. Additionally, this review highlights recent discoveries concerning bamboo TFs, encompassing their classification, promoter analysis and functional dynamics in response to different abiotic stresses. Attempt has also been made to delve into the molecular interplay and cross-talk among these TFs during abiotic stresses, thus proposing potential strategies for enhancing the intricate regulatory networks involved in the adaptive responses of bamboo species.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 2","pages":"Article 130755"},"PeriodicalIF":2.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142908760","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}

{"title":"Computational analysis of the alpha−2 domain of apolipoprotein B − 100, a potential triggering factor in LDL aggregation","authors":"Joanne Jennifer E. Tan ,&nbsp;Marvin M. Bilog ,&nbsp;Adam A. Profit ,&nbsp;Francisco M. Heralde III ,&nbsp;Ruel Z.B. Desamero","doi":"10.1016/j.bbagen.2024.130742","DOIUrl":"10.1016/j.bbagen.2024.130742","url":null,"abstract":"&lt;div&gt;&lt;div&gt;Atherosclerosis, the major underlying cause of cardiovascular disease, is believed to arise from the accumulation of low-density lipoprotein (LDL) in the arterial subendothelial space, ultimately leading to plaque formation. It is proposed that the accumulation of LDL is linked to its intrinsic aggregation propensity. Although the native LDL is not prone to aggregation, LDL(−), an electronegative LDL characterized in the plasma, has been shown to prime LDL aggregation in a domino-like behavior similar to amyloidogenic proteins. LDL(−) has also been observed to have a misfolded apolipoprotein B-100 (apo B-100), a huge protein consisting of 4563 amino acid residues. As misfolding of proteins is commonly associated with amyloid formation, apo B-100 is therefore being considered as the possible triggering factor in LDL aggregation. Previous computational studies have implicated the α2 domain to be the aggregation-prone region of apo B-100. In this study, the amyloidogenic properties of the α2 domain of apo B-100 were interrogated using both &lt;em&gt;in silico&lt;/em&gt; and &lt;em&gt;in vitro&lt;/em&gt; techniques.&lt;/div&gt;&lt;div&gt;Since the crystal structure of the 570-amino acid α2 domain of apo B-100 is yet to be solved, we used several secondary structure prediction tools to model putative helical regions that make up the α2 domain. The stability of each of the 17 helices thus identified was further probed using molecular dynamics (MD), with the least stable of the helices considered as potentially amyloidogenic. In a 100 ns simulation window, helices &lt;strong&gt;&lt;em&gt;k&lt;/em&gt;&lt;/strong&gt; (YFEKLVGFIDDAVK), &lt;strong&gt;&lt;em&gt;m&lt;/em&gt;&lt;/strong&gt; (YHQFVDETNDKIREVTQRLNGEIQA), and &lt;strong&gt;&lt;em&gt;p&lt;/em&gt;&lt;/strong&gt; (QQELQRYLSLVGQVYS) were the least stable and appeared to transition to β-structures, the hallmark of amyloidogenesis. When the simulation was extended to longer times, only helices &lt;strong&gt;&lt;em&gt;k&lt;/em&gt;&lt;/strong&gt; and &lt;strong&gt;&lt;em&gt;p&lt;/em&gt;&lt;/strong&gt; formed stable β-sheets that persisted. Analysis of the data indicates that the final β-sheet conformation was stabilized by the π-π stacking interactions between the aromatic rings of Tyr-1 and Phe-8 for helix &lt;strong&gt;&lt;em&gt;k&lt;/em&gt;&lt;/strong&gt; and likely π-π stacking contacts between Arg-6 guanidino group and Tyr-15 ring for helix &lt;strong&gt;&lt;em&gt;p&lt;/em&gt;&lt;/strong&gt;.&lt;/div&gt;&lt;div&gt;Based on the &lt;em&gt;in silico&lt;/em&gt; work, we proceeded to synthesize and spectroscopically characterize helices &lt;strong&gt;&lt;em&gt;k&lt;/em&gt;&lt;/strong&gt;, &lt;strong&gt;&lt;em&gt;m&lt;/em&gt;&lt;/strong&gt;&lt;sub&gt;&lt;strong&gt;&lt;em&gt;17&lt;/em&gt;&lt;/strong&gt;&lt;/sub&gt;&lt;sub&gt;&lt;strong&gt;&lt;em&gt;–&lt;/em&gt;&lt;/strong&gt;&lt;/sub&gt;&lt;sub&gt;&lt;strong&gt;&lt;em&gt;25&lt;/em&gt;&lt;/strong&gt;&lt;/sub&gt; (QRLNGEIQA), and &lt;strong&gt;&lt;em&gt;p&lt;/em&gt;&lt;/strong&gt;. As expected, &lt;strong&gt;&lt;em&gt;k&lt;/em&gt;&lt;/strong&gt; and &lt;strong&gt;&lt;em&gt;p&lt;/em&gt;&lt;/strong&gt; formed detectable amyloids, with the latter appearing to be substantially more amyloidogenic based on kinetic aggregation assays. Amyloid fibrils formed by &lt;strong&gt;&lt;em&gt;p&lt;/em&gt;&lt;/strong&gt; were confirmed using circular dichroism spectroscopy and transmission electron microscopy. Data obtained could be ex","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 2","pages":"Article 130742"},"PeriodicalIF":2.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833772","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}

{"title":"Synthesis of spherical and rods-like titanium oxide nanoparticles (TiO2 NPs) and evaluation of their cytotoxicity towards colon cells in vitro","authors":"Bartosz Klebowski ,&nbsp;Karolina Kosinska ,&nbsp;Agnieszka Bukowska ,&nbsp;Piotr M. Zieliński ,&nbsp;Magdalena Parlinska-Wojtan ,&nbsp;Joanna Depciuch","doi":"10.1016/j.bbagen.2024.130743","DOIUrl":"10.1016/j.bbagen.2024.130743","url":null,"abstract":"<div><div>Titanium oxide nanoparticles (TiO₂ NPs) are currently used as ingredients in medicines and sunscreens. Unfortunately, recent information about TiO₂ NPs indicates their undesirable biological effect on colon cells. Therefore, the aim of this work was to synthesize and evaluate the physicochemical characterization of spherical (TiO₂ NSs) and rods-like (TiO₂ NRs) NPs, followed by assessment their cytotoxicity. For this purpose, both normal colon epithelial cells (CRL-1790) and cancerous colon cells (SW480) were used. Scanning transmission electron microscopy (STEM) showed that TiO₂ NSs with a diameter of ≈10 nm and TiO₂ NRs with the size of the longer axis ≈25 nm and shorter axis ≈3 nm were obtained. Based on the selected area electron diffraction (SAED) patterns, it was found that crystalline phases were obtained for both TiO₂ NPs. The UV–Vis spectra showed no contamination of TiO₂ NPs. Zeta potential values were 9.7 mV and 3.1 mV for NSs and NRs, respectively. Cytotoxicity of TiO₂ NPs was assessed using the MTS (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxy-methoxy-phenyl)-2-(4-sulfophenyl)-2H-tetrazolium) test for various concentration of NPs. The cytotoxic effect for both TiO₂ NPs was visible for concentration of 75 μg/ml (for CRL-1790) and 50 μg/ml (for SW480) and higher, and it did not depend on the shape. Moreover, both types of TiO₂ NPs (in higher concentration) induce the generation of reactive oxygen species (ROS) in cells cultured with these NPs. Holotomographic microscopy studies showed increased cellular uptake of TiO₂ NPs by SW480. The obtained results for the synthesized TiO₂ NPs are a promising prospect for their use in biomedical application.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 2","pages":"Article 130743"},"PeriodicalIF":2.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833775","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}

{"title":"Reduction in MCP-1 production in preadipocytes is mediated by PPARγ activation and JNK/SIRT1 signaling","authors":"Atsushi Sawamoto,&nbsp;Ibuki Itagaki,&nbsp;Satoshi Okuyama,&nbsp;Mitsunari Nakajima","doi":"10.1016/j.bbagen.2024.130737","DOIUrl":"10.1016/j.bbagen.2024.130737","url":null,"abstract":"<div><div>Obesity-induced monocyte chemoattractant protein 1 (MCP-1) production leads to the infiltration of monocytes/macrophages into white adipose tissue (WAT), which contributes to systemic insulin resistance. Peroxisome proliferator-activated receptor gamma (PPARγ) agonists are known to reduce MCP-1 production in both humans and mice; however, the underlying mechanism in WAT remains unclear. Here, we propose a novel mechanism for the reduction in MCP-1 production in preadipocytes. The PPARγ agonist rosiglitazone (RSG) reduced MCP-1 production and secretion in response to lipopolysaccharide (LPS) in 3T3-L1 preadipocytes and mouse stromal vascular fraction–derived primary preadipocytes. Both RSG and SP600125 (a c-Jun N-terminal kinase (JNK) inhibitor) inhibited LPS-induced degradation of silent information regulator 2 homolog 1 (SIRT1), a negative regulator of MCP-1 production in 3T3-L1 preadipocytes. Furthermore, RSG inhibited LPS-induced activation of nuclear factor-κB. These effects of RSG were abolished in 3T3-L1 preadipocytes transfected with <em>Pparg</em> siRNA. These findings highlight a novel mechanism by which PPARγ activation inhibits JNK/SIRT1 signaling in preadipocytes and contributes to the reduction in MCP-1 production, suggesting that preadipocytes could be a potential therapeutic target for the treatment of insulin resistance.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 2","pages":"Article 130737"},"PeriodicalIF":2.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142821763","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}

{"title":"Dose-responsive effects of endothelial cell-sourced exosomes on vascular cell proliferation and phenotype transition","authors":"Yangyang Xiao ,&nbsp;Dan Zou ,&nbsp;Jianan Liu ,&nbsp;Fanfan Dai ,&nbsp;Ansha Zhao ,&nbsp;Ping Yang","doi":"10.1016/j.bbagen.2024.130745","DOIUrl":"10.1016/j.bbagen.2024.130745","url":null,"abstract":"<div><div>Endothelial cell-sourced exosomes are potential participants in the process of atherosclerosis, and their function is mainly affected by concentration. By studying the effects of exosome concentrations on vascular cells, atherosclerosis can be better intervened. In this study, exosomes with concentrations of 0, 0.07, 0.35, 1.75 and 8.75 μg/mL were set to interact with endothelial cells, macrophages and smooth muscle cells respectively. The results suggested that EC-Exo altered vascular cells' proliferation, migration and nitric oxide release abilities, increasing with EC-Exo concentrate from 0 to 1.75 μg/mL and varing with cell types at 8.75 μg/mL. The effects of exosome on cells is dose-responsive，and endothelial cells-sourced exosome favors vascular repair within the concentration of 0.35–1.75 μg/mL，showing potential for atherosclerosis regulation.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 2","pages":"Article 130745"},"PeriodicalIF":2.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845530","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}

{"title":"Insight into the intercalation of N-substituted acridine-9-amines into DNA based on spectroscopic and calorimetric analysis","authors":"Krzysztof Żamojć ,&nbsp;Dan Milaș ,&nbsp;Ola Grabowska ,&nbsp;Dariusz Wyrzykowski ,&nbsp;Magdalena Mańkowska ,&nbsp;Karol Krzymiński","doi":"10.1016/j.bbagen.2024.130741","DOIUrl":"10.1016/j.bbagen.2024.130741","url":null,"abstract":"<div><div>The study delves into the binding properties of acridine-9-amine and its selected, mainly <em>N</em>-substituted derivatives (A9As), with calf thymus deoxyribonucleic acid (CT-DNA). This investigation, conducted using UV–Vis spectrophotometry, steady-state fluorescence spectroscopy and isothermal titration calorimetry, provides insights into the relationship between their structure and activity. The absorption spectra of the A9As exhibited a slight red shift and significant hypochromic effects, while the fluorescence emission intensities decreased in the presence of CT-DNA. These results suggest that all fluorescent substrates intercalate into the double helix of native DNA to varying degrees. The binding constants for the A9As/CT-DNA complexes (log(<em>K</em>_A) were determined using various techniques in the range from 2.59 to 5.50). The thermodynamic parameters of A9As binding to DNA were obtained from ITC measurements (Δ<em>G</em> from – 7.51 to – 6.75 kcal·mol⁻¹, Δ<em>H</em> from – 11.58 to – 3.83 kcal·mol⁻¹, and <em>T</em>Δ<em>S</em> from – 4.83 to 3.68 kcal·mol⁻¹) and indicated that the formation of all the investigated A9As–DNA complexes is an enthalpy-driven process. The study also discusses the influence of the emitters' structure and electronic properties of substituents on intercalation efficiency. This knowledge serves as a guide for further research and offers directions for functionalising new acridines as potential reagents. It also provides the latest information on the ability of intercalation to DNA, which can be instrumental in studies on the mechanism of binding small aromatic molecules to DNA and can potentially contribute to new anticancer drug designs.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 2","pages":"Article 130741"},"PeriodicalIF":2.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142852299","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}

{"title":"The methylome of clonal seagrass shoots shows age-associated variation and differentiation of roots from other tissues","authors":"Anne M.L. Nilsen ,&nbsp;Galice Hoarau ,&nbsp;Irina Smolina ,&nbsp;James A. Coyer ,&nbsp;Christoffer Boström ,&nbsp;Martina E.L. Kopp ,&nbsp;Alexander Jueterbock","doi":"10.1016/j.bbagen.2024.130748","DOIUrl":"10.1016/j.bbagen.2024.130748","url":null,"abstract":"<div><div>Factors influencing variance of DNA methylation in vegetatively reproducing plants, both terrestrial plants and aquatic seagrasses, is just beginning to be understood. Improving our knowledge of these mechanisms will increase understanding of transgenerational epigenetics in plant clones, of the relationship between DNA methylation and seagrass development, and of the drivers of epigenetic variation, which may underly acclimation in clonally reproducing plants. Here, we sampled leaves, rhizomes and roots of three physically and spatially separated ramet sections from a clonally propagated field of the seagrass <em>Zostera marina</em>. Using reduced methylome sequencing, we studied variations in the methylome of seagrass <em>Zostera marina</em> between the sampled tissue types and across age groups. Our analysis of ramets of different ages showed variations in methylation between older and younger samples in both specific methylation patterns and global methylation levels. Our analysis of tissue types showed a marked differentiation of the roots from the rhizomes and leaves, which showed more similar methylation patterns. These findings are in agreement with the strong connection of DNA methylation and plant development and tissue differentiation. We also suggest an effect of differential environmental exposures on the methylome of the younger versus the older ramets due to the forming of molecular stress memories.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 2","pages":"Article 130748"},"PeriodicalIF":2.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142884785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}