Biochimica et biophysica acta. General subjects最新文献

{"title":"Characterization of the intracellular polyphosphate granules of the phototrophic green sulfur bacterium Chlorobaculum tepidum","authors":"Alexandros Lyratzakis,&nbsp;Michail Kalogerakis,&nbsp;Katerina Polymerou,&nbsp;Apostolos Spyros,&nbsp;Georgios Tsiotis","doi":"10.1016/j.bbagen.2024.130718","DOIUrl":"10.1016/j.bbagen.2024.130718","url":null,"abstract":"<div><div>The ability to generate polyphosphate (polyP) granules is important for survival for bacteria during resistance to diverse environmental stresses, however the genesis of polyP granules is poorly understood. <em>Chlorobaculum tepidum</em> (<em>Cba tepidum</em>) is a thermophilic green sulfur anoxygenic phototrophic bacterium which uses reduced sulfur compounds as electron donors. The presence of electron rich granules inside the <em>Cba tepidum</em> was reported, but no further information was provided. In this work we used cell thin sections at three different time points of cultivation to observe the biogenesis of the inclusions over time, and the in cell total phosphate concentration was monitored over time as well. Furthermore, the elemental analysis (EDS) of the electron rich inclusions showed the presence of phosphorus and oxygen. The existence of polyphosphate was demonstrated by ³¹P NMR spectroscopy of cell lysates. Finally, we show that the biogenesis of the phosphorus granules correlates with an abundance of proteins that are closely related to polyphosphate metabolism.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387595","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":"FCS videos: Fluorescence correlation spectroscopy in space and time","authors":"Thorsten Wohland ,&nbsp;Shao Ren Sim ,&nbsp;Marc Demoustier ,&nbsp;Shambhavi Pandey ,&nbsp;Rutuparna Kulkarni ,&nbsp;Daniel Aik","doi":"10.1016/j.bbagen.2024.130716","DOIUrl":"10.1016/j.bbagen.2024.130716","url":null,"abstract":"<div><div>Fluorescence Correlation Spectroscopy (FCS), invented more than 50 years ago is a widely used tool providing information on molecular processes in a variety of samples from materials to life sciences. In the last two decades FCS was multiplexed and ultimately made into an imaging technique that provided maps of molecular parameters over whole sample cross-section. However, it was still limited by a measurement time on the order of minutes. With the improvement of FCS time resolution to seconds using deep learning, we extend here FCS to so-called FCS videos that can provide information how the molecular parameters determined by Imaging FCS change in space and time. This opens up new possibilities for the investigation of molecular processes. Here, we demonstrate the feasibility of the approach and show FCS video applications to lipid bilayers and cell membranes.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142340408","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":"Establishment of the Meyer-Overton correlation in an artificial membrane without protein","authors":"Atsushi Matsumoto ,&nbsp;Yukifumi Uesono","doi":"10.1016/j.bbagen.2024.130717","DOIUrl":"10.1016/j.bbagen.2024.130717","url":null,"abstract":"<div><h3>Background</h3><div>The potency of anesthetics with various structures increases exponentially with lipophilicity, which is the Meyer-Overton (MO) correlation discovered over 120 years ago. The MO correlation was also observed with various biological effects and chemicals, including alcohols; thus, the correlation represents a fundamental relationship between chemicals and organisms. The MO correlation was explained by the lipid and protein theories, although the principle remains unknown because these are still debating.</div></div><div><h3>Methods</h3><div>The gentle hydration method was used to form giant unilamellar vesicles (GUVs) consisting of high- and low-melting phospholipids and cholesterol in the presence of <em>n</em>-alcohols (C₂-C₁₂). Confocal fluorescence microscopy was used to determine the percentage of GUVs with domains in relation to the <em>n</em>-alcohol concentrations.</div></div><div><h3>Results</h3><div><em>n</em>-Alcohols inhibited the domain formation of GUVs, and the half inhibitory concentration (IC₅₀) in the aqueous phase (<em>C</em>_w) decreased exponentially with increasing chain length (lipophilicity). In contrast, the membrane concentrations (<em>C</em>_m) of alcohols for the inhibition, which is a product of the membrane-water partition coefficient and the IC₅₀ values, remained constant irrespective of the chain length.</div></div><div><h3>Conclusions</h3><div>The MO correlation is established in GUVs, which supports the lipid theory. When alcohols reach the same critical concentration in the membrane, similar biological effects appear irrespective of the chain length, which is the principle underlying the MO correlation.</div></div><div><h3>General significance</h3><div>The protein theory states that a highly lipophilic compound targets minor membrane proteins due to the low <em>C</em>_w. However, our lipid theory states that the compound targets various membrane proteins due to the high <em>C</em>_m.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142340407","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}

{"title":"SecM leader peptide as an allosteric translation inhibitor: a molecular dynamics study","authors":"G.I. Makarov,&nbsp;T.M. Makarova","doi":"10.1016/j.bbagen.2024.130715","DOIUrl":"10.1016/j.bbagen.2024.130715","url":null,"abstract":"<div><div>The SecM leader peptide regulates translation of the SecA protein, being a part of the Sec translocase, that reversibly arrests the ribosome. In the present study the structure of the SecM complex with the <em>E. coli</em> A/A,P/P–ribosome was obtained by means of docking and molecular dynamics simulation methods. It has been established that binding of the SecM leader peptide in the nascent peptide exit tunnel leads to a turn of the aminoacylating proline residue away from the C–terminal SecM glycine residue, which is adverse to the peptidyltransferase reaction. Besides, the SecM binding leads to a disturbance of the A–tRNA contacts with the tip of the H38 helix of the 23S rRNA (the A–site finger, ASF) and ribosomal protein uL16. Allosteric interrelation between these events has been proved by a construction of networks of concerted changes in non–covalent interactions throughout the whole ribosome, whereupon the A1614 and A751 residues of the 23S rRNA in the exit tunnel that formed stacking interactions with the SecM residues during the MD simulations, were found to be the principal triggers, inducing crucial alterations in the A–tRNA binding. The allosteric signal from the SecM peptide to the ASF, according to our model, is transmitted through ribosomal protein uL22, and there is reason to believe that this sensor is used not only by the SecM leader peptide, but also by other peptides that cause translation arrest.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142340409","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":"Multispectral and molecular simulation of the interaction of human α1-acid glycoprotein with palbociclib","authors":"Shao-Liang Jiang ,&nbsp;Yu-Ting Wu ,&nbsp;Wang-Cai Chen ,&nbsp;Jia-Ping Huang ,&nbsp;Dong Chen ,&nbsp;Li Li ,&nbsp;Liang Han ,&nbsp;Jie-Hua Shi","doi":"10.1016/j.bbagen.2024.130712","DOIUrl":"10.1016/j.bbagen.2024.130712","url":null,"abstract":"<div><div>Palbociclib, a selective CDK4/6 inhibitor with potent anti-tumor effects, was investigated for its interaction with human α1-acid glycoprotein (HAG). Spectral analysis revealed that palbociclib forms a ground state complex with HAG, exhibiting binding constant (K_b) of 10⁴ M⁻¹ at the used temperature range. The interaction between the two was determined to be driven mainly by hydrogen bonding and hydrophobic forces. Multispectral studies indicated that the bound palbociclib altered the secondary structure of HAG and reduced polarity around Trp and Tyr amino acids. And, molecular docking and dynamics simulations verified the experimental findings. Finally, most of the metal ions present in plasma, such as K⁺, Cu²⁺, Ca²⁺, Mg²⁺, Ni²⁺, Fe³⁺, and Co²⁺, are detrimental to the binding of palbociclib to HAG, with the exception of Zn²⁺, which is favorable.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142307036","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":"METTL3-driven m6A modification of lncRNA FAM230B suppresses ferroptosis by modulating miR-27a-5p/BTF3 axis in gastric cancer","authors":"Yejia Cui ,&nbsp;Meicen Pu ,&nbsp;Yanting Gong ,&nbsp;Runchao Li ,&nbsp;Xiaokang Wang ,&nbsp;Jinjun Ye ,&nbsp;Haohai Huang ,&nbsp;Dan Liao ,&nbsp;Yufeng Yang ,&nbsp;Aiping Yin ,&nbsp;Jiale Li ,&nbsp;Yuling Deng ,&nbsp;Zhen Tian ,&nbsp;Rong Pu","doi":"10.1016/j.bbagen.2024.130714","DOIUrl":"10.1016/j.bbagen.2024.130714","url":null,"abstract":"<div><div>Our previous research revealed the apoptosis-inhibiting effect of lncRNA FAM230B in gastric cancer (GC). While its role on ferroptosis of GC remain unexplored. In this study, the m6A level and RNA stability regulation of METTL3 on FAM230B was detected by m6A quantification, stability assays, MeRIP, and their interaction was confirmed by RIP, and RNA pull-down assays. The level of ferroptosis was detected by flow cytometry, MDA and GSH level assessments, and electron microscopy. Gene expression was detected by quantitative real-time PCR, western blot, and immunofluorescence. The miR-27a-5p and BTF3 interaction was predicted with TargetScan and confirmed by dual-luciferase assay. Here, elevated levels of METTL3 and FAM230B were observed in GC tissues and cell lines. METTL3 was confirmed to bind with FAM230B RNA. Furthermore, silencing METTL3 reduced FAM230B m6A levels and stability, leading to decreased FAM230B and increased miR-27a-5p expressions. FAM230B knockdown favored ferroptosis and increased BTF3 expression, while its overexpression mitigated erastin-induced ferroptosis in GC cells. Additionally, BTF3 overexpression was found to negate miR-27a-5p's ferroptosis-promoting effects in GC cells. Collectively, our study demonstrates that the m6A modification of FAM230B by METTL3 plays a crucial role in promoting GC progression by reducing ferroptosis, through the modulation of the miR-27a-5p/BTF3 axis.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142279976","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":"Sonodynamic inactivation of gram-negative and gram-positive bacteria in the presence of phenothiazine compounds toluidine blue and azurin A","authors":"Ming-Qin Qian ,&nbsp;Zheng Xiang ,&nbsp;Xin Wang","doi":"10.1016/j.bbagen.2024.130711","DOIUrl":"10.1016/j.bbagen.2024.130711","url":null,"abstract":"<div><h3>Background</h3><p>Sonodynamic antimicrobial chemotherapy (SACT) is an effective antimicrobial treatment that can avoid the production of drug-resistant bacteria. Design and development of new high-efficiency sonosensitizers play a key role in the practical application of SACT.</p></div><div><h3>Methods</h3><p>The bacteriostatic effects of two phenothiazine compounds, toluidine blue (TB) and azure A (AA) combined with ultrasonic (US) on <em>Escherichia coli</em> (<em>E. coli</em>) and <em>Staphylococcus aureus</em> (<em>S. aureus</em>) were studied, and the sonodynamic antibacterial activities of TB and AA were compared. The reactive oxygen species (ROS) and the types of ROS produced in the sonodynamic system were detected and the sonodynamic mechanisms of TB and AA were proposed.</p></div><div><h3>Results</h3><p>The sonodynamic bacteriostasis mediated by TB and AA increased with the increasing concentration of sonosensitizer, the extension of sonication time and the increase of reaction temperature. The production of ROS was the main reason that TB and AA had excellent sonodynamic antibacterial performance. Singlet oxygen (¹O₂) and hydroxyl radical (•OH) were the main ROS types in the sonodynamic antibacterial system. The ROS produced by the combined action of AA and US was higher than that of TB.</p></div><div><h3>Conclusion</h3><p>Both TB and AA displayed excellent sonodynamic antibacterial activities. Moreover, AA had a higher sonodynamic activity than TB. The electron donation effect and steric hindrance effect of the methyl group of phenothiazine parent nucleus of TB might be the cause of the decrease of its sonodynamic activity. These results would provide a valuable reference for the further study of phenothiazines sonosensitizers and their clinical application in SACT.</p></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142240800","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":"Glucose induced regulation of iron transporters implicates kidney iron accumulation","authors":"Rajiv Kumar ,&nbsp;Diksha Kulshreshtha ,&nbsp;Ayushi Aggarwal ,&nbsp;Somya Asthana ,&nbsp;Amit Dinda ,&nbsp;Chinmay K. Mukhopadhyay","doi":"10.1016/j.bbagen.2024.130713","DOIUrl":"10.1016/j.bbagen.2024.130713","url":null,"abstract":"<div><p>Increased iron level is detected in rat kidney and human urine in diabetic condition and implicated in associated nephropathy. However, the biological cue and mechanism of the iron accumulation remain unclear. Here we reveal that glucose increases iron uptake by promoting transferrin receptor 1 (TFRC) in kidney cells by a translational mechanism but does not alter expression of endosomal iron transporter DMT1. Glucose decreases iron exporter ferroportin (FPN) by a protein degradation mechanism. Hepcidin is known to bind at Cys-326 residue in promoting degradation of human ferroportin. When Cys-326 was mutated to Ser in human-FPN-FLAG and expressed in kidney cells, glucose still could degrade FPN-FLAG implicating involvement of hepcidin independent mechanism in glucose induced ferroportin degradation. Chronic hyperglycemia was generated in rats by administering streptozotocin (STZ) with periodic insulin injection to determine the level of iron homeostasis components. Increased TFRC and decreased ferroportin levels were detected in hyperglycemic rat kidney by Western blot and immunohistochemistry analyses. Hepcidin mRNA was not significantly altered in kidney but was marginally decreased in liver. Perls' staining and non-heme iron estimation showed an elevated iron level in hyperglycemic rat kidney. These results suggest that high glucose dysregulates iron transport components resulting iron accumulation in diabetic kidney.</p></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142240801","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":"Resistance-based directed evolution of nanobodies for higher affinity in prokaryotes","authors":"Yue Hu,&nbsp;Li Huo,&nbsp;Weiwei Chen,&nbsp;Jinhua Shen,&nbsp;Wenyi Wang","doi":"10.1016/j.bbagen.2024.130710","DOIUrl":"10.1016/j.bbagen.2024.130710","url":null,"abstract":"<div><p>A prokaryotic resistance-based directed evolution system leveraging protein-fragment complementation assay (PCA) was devised, and its proficiency in detecting protein-protein interactions and discriminating varying degrees of binding affinity was demonstrated by two well-characterized protein pairs. Furthermore, we constructed a random mutant library based on the GBP^R36K/E45K mutant, characterized by almost no affinity towards EGFP. This library was subjected to PCA-based prokaryotic directed evolution, resulting in the isolation of back-mutated variants. In summary, we have established an expedited, cost-effective, and structural information-independent PCA-based prokaryotic directed evolution platform for nanobody affinity maturation, featuring tunable screening stringency via modulation of antibiotic concentrations.</p></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142153084","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":"Structure and function of N-acetylglucosaminyltransferase V (GnT-V)","authors":"Reina F. Osuka ,&nbsp;Takahiro Yamasaki ,&nbsp;Yasuhiko Kizuka","doi":"10.1016/j.bbagen.2024.130709","DOIUrl":"10.1016/j.bbagen.2024.130709","url":null,"abstract":"<div><h3>Background</h3><p>The β1,6-GlcNAc branch in <em>N</em>-glycans, produced by a glycosyltransferase <em>N</em>-acetylglucosaminyltransferase V (GnT-V or MGAT5), is associated with cancer and autoimmune diseases.</p></div><div><h3>Scope</h3><p>Here, we summarize the structure and activity regulation of GnT-V. We also describe the roles of the β1,6-GlcNAc branch on glycoproteins in cells and the phenotypes of <em>Mgat5</em>-deficient mice, focusing on cancer and the immune system.</p></div><div><h3>Major conclusions</h3><p>GnT-V has a unique structure for substrate recognition, and its activity and function are regulated by shedding. The glycans produced by GnT-V play pivotal roles in the differentiation of neural cells, cancer malignancy and immunotherapy, and the development of autoimmune diseases by regulating the functions and cell surface residency of glycoproteins.</p></div><div><h3>General significance</h3><p>Controlling the expression or activity of GnT-V could be a therapeutic option against cancer and autoimmune diseases. Future work should clarify how GnT-V selectively modifies the specific glycoproteins or <em>N</em>-glycosylation sites <em>in vivo</em>.</p></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142131723","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}