FEBS Open Bio最新文献

{"title":"Sudden anaerobization in Amphibacillus xylanus increases intracellular labile ferrous iron and inhibits cell growth","authors":"Shinya Kimata,&nbsp;Yoichi Sakai,&nbsp;Keisuke Tanaka,&nbsp;Etsuro Yoshimura,&nbsp;Ken Kitano,&nbsp;Morio Ishikawa,&nbsp;Tadahiro Nakamoto,&nbsp;Tsutomu Takayama,&nbsp;Hirofumi Inoue,&nbsp;Kaho Nomura,&nbsp;Tomonori Suzuki,&nbsp;Masataka Uchino,&nbsp;Akira Abe,&nbsp;Youichi Niimura","doi":"10.1002/2211-5463.70255","DOIUrl":"10.1002/2211-5463.70255","url":null,"abstract":"<p><i>Amphibacillus xylanus</i> is an aerotolerant anaerobe that consumes large amounts of oxygen and requires iron as an essential micronutrient during its aerobic growth. However, this bacterium lacks a typical respiratory chain; therefore, intracellular free flavins and their reductases are thought to participate in the reduction of molecular oxygen and ferric iron (Fe³⁺). This system can potentially generate hydroxyl radicals through the Fenton reaction, highlighting the importance of regulating the production of redox-active ferrous iron (Fe²⁺). In this study, we employed a strategy of abruptly switching the cell culture system from aerobic to anaerobic conditions to examine Fe²⁺ production via free flavins. Sudden anaerobization induced growth inhibition and a significant increase in intracellular labile Fe²⁺. Whole-cell ⁵⁷Fe Mössbauer spectroscopy revealed that in aerobic cells, high-spin Fe³⁺ is the major chemical species, whereas in anaerobic conditions, the intracellular iron pool is completely converted into Fe²⁺ and consists of low- and high-spin Fe²⁺ species. Increased Fe²⁺ production was mimicked using cell-free extracts and the reductase activity promoted electron transfer from NADH to Fe³⁺ via physiological concentrations of free flavin adenine dinucleotide under anaerobic conditions. RNA sequencing showed that the electrons of NADH generated through glycolysis and the pyruvate metabolic pathway can flow into a flavoprotein with flavin reductase activity. These findings suggest that the production of labile Fe²⁺ via free flavin is regulated by molecular oxygen, allowing safe iron utilization during the aerobic growth of <i>A. xylanus</i>.</p>","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"16 10","pages":"1911-1924"},"PeriodicalIF":2.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13398963/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147766828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamic photobiology: A collection of experimental protocols for time-resolved structural studies on light-activated proteins","authors":"Sofia M Kapetanaki,&nbsp;Antoine Royant,&nbsp;Briony A Yorke","doi":"10.1002/2211-5463.70303","DOIUrl":"https://doi.org/10.1002/2211-5463.70303","url":null,"abstract":"<p>The study of proteins that sense and respond to light reveals how nature has harnessed light for function while also mitigating its damaging effects through finely tuned molecular mechanisms. Time-resolved optical spectroscopy and time-resolved X-ray solution scattering and diffraction techniques are well-positioned to probe functional transitions triggered by light in photoactive proteins. However, integrating both fields presents technical and conceptual difficulties for many researchers. This <i>FEBS Open Bio</i> ‘In the Limelight’ special issue, Dynamic Photobiology, showcases five research protocols that provide comprehensive and practical guidance for designing and analyzing time-resolved experiments on proteins. The protocols cover studies performed in both solution and crystalline environments using time-resolved femtosecond Vis/IR spectroscopy, time-resolved X-ray solution scattering, and time-resolved serial crystallography at synchrotron and XFEL facilities. These detailed research protocols aim to ease collaboration across fields, acquaint early-career researchers with essential concepts, and offer a comprehensive overview for established researchers.</p>","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"16 10","pages":"1844-1846"},"PeriodicalIF":2.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/2211-5463.70303","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149099394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cyclic azapeptide CD36 ligand attenuates cardiac injury and reduces long-chain fatty acid accumulation after myocardial ischemia–reperfusion in mice","authors":"Jade Gauvin,&nbsp;Naghme Radmannia,&nbsp;David N. Huynh,&nbsp;Liliane Ménard,&nbsp;Caroline Daneault,&nbsp;Maïté Veilleux,&nbsp;Ahsanullah Ahsanullah,&nbsp;André C. Carpentier,&nbsp;William D. Lubell,&nbsp;Matthieu Ruiz,&nbsp;Huy Ong,&nbsp;Sylvie Marleau,&nbsp;Simon-Pierre Gravel","doi":"10.1002/2211-5463.70265","DOIUrl":"10.1002/2211-5463.70265","url":null,"abstract":"<p>Ischemic heart disease remains a leading global cause of death. We investigated the cardioprotective effects of the selective cluster of differentiation-36 receptor (CD36) modulator azapeptide MPE-298 in a mouse model of myocardial ischemia–reperfusion. Given before reperfusion, a single intravenous dose of azapeptide MPE-298 reduced infarct size by 44% of the area-at-risk and transiently decreased left ventricular long-chain fatty acids (LCFA) accumulation, independently of saturation status. Metabolomic profiling identified changes in amino acids that may fuel the tricarboxylic acid cycle and provide substrates for glutathione-dependent antioxidant defense. Gene expression analysis showed transient modulation of oxidative stress and inflammation-associated genes in both heart and adipose tissue. Thus, we conclude that modulation of CD36 by azapeptide MPE-298 exhibits therapeutic potential for treating acute myocardial ischemia and reperfusion by supporting metabolic recovery and limiting excess LCFA uptake.</p>","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"16 10","pages":"1958-1973"},"PeriodicalIF":2.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13399224/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147835732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Polarization-resolved femtosecond Vis/IR spectroscopy tailored for resolving weak signals in biological samples using minimal sample volume","authors":"Clark Zahn,&nbsp;Karsten Heyne","doi":"10.1002/2211-5463.70180","DOIUrl":"10.1002/2211-5463.70180","url":null,"abstract":"<p>Photoreceptor proteins have a variety of functions and properties that are utilized in cells. The starting point is the absorption of light by a chromophore, triggering a cascade of specific reactions in the protein lasting from femtoseconds to seconds. To understand the individual early reaction steps, we need to trace the ultrafast structural dynamics. In this report, we present our approach towards improving the signal-to-noise ratio in polarization-resolved transient infrared (IR) spectroscopy, enabling such measurements. We outline our polarization-resolved ultrafast visible (Vis)-pump/IR-probe spectroscopy setup using IR referencing. The setup is tailored towards tracing small signals of photo-degrading biological samples (e.g. site-specific mutant proteins, that are available only in limited quantities). We provide a comprehensive overview on characterizing the excitation conditions for polarization resolved measurements. The obtained spectra allow for direct tracing of reaction dynamics and conformational changes of molecular groups within the chromophore, protein side chains and hydrogen-bond network.</p>","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"16 10","pages":"1847-1856"},"PeriodicalIF":2.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13398637/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145809972","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"One size does not fit all: An in vitro evaluation of the effects of bezafibrate and medroxyprogesterone acetate on human SH-SY5Y and U-87 MG cancer cells","authors":"Abhishek Kharawatkar,&nbsp;Francesco Michelangeli,&nbsp;Farhat Latif Khanim,&nbsp;Christopher Martin Bunce,&nbsp;William Eustace Basil Johnson","doi":"10.1002/2211-5463.70259","DOIUrl":"10.1002/2211-5463.70259","url":null,"abstract":"<p>Here, we have examined the effects of the repurposed drugs bezafibrate (BEZ) and medroxyprogesterone acetate (MPA) singly and in combination (BaP) on a neuroblastoma (SH-SY5Y) and a glioblastoma (U-87 MG) cell line. BaP was previously shown to inhibit the growth of blood and bone cancers through the generation of reactive oxygen species (ROS) and by targeting lipogenesis. Similarly, in our study, BaP inhibited cell proliferation and induced cell death in both neuroblastoma and glioblastoma cells more effectively than single BEZ or MPA drug treatments, albeit less effectively than in blood cancers. Furthermore, we observed significant increases in ROS levels in both cancer cell lines and reductions in the levels of the lipogenic enzyme, stearoyl-CoA-desaturase 1 (SCD1). Supplementation with the SCD1 product, oleic acid (OA), moderately abrogated the inhibitory effects of BaP on neuroblastoma proliferation. However, this effect was not seen in glioblastoma cultures, where OA supplementation of BaP-treated cells was associated with further decreases in cell proliferation. Lastly, we show that a clinically achievable BaP concentration enhanced the antiproliferative effects of temozolomide on glioblastoma cells. These findings show that drugs that have been successfully repurposed to potentially treat some types of cancers may have use in other cancers, but that their efficacy and mechanisms of action do not necessarily translate from one cancer type to another. Thus, successful drug repurposing requires investigation and optimisation on a case-by-case basis.</p>","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"16 10","pages":"1982-1991"},"PeriodicalIF":2.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13398465/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147766812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hydrostatic pressure activates HIF-1α via β-catenin to promote stemness in breast cancer cells","authors":"Da Zhai,&nbsp;Yong Xu,&nbsp;Jingjing Ma,&nbsp;Ratchanee Duangrat,&nbsp;Chen Yan,&nbsp;Jingyan Liang,&nbsp;Hua Wei,&nbsp;Bin Jiang,&nbsp;Tao-Sheng Li","doi":"10.1002/2211-5463.70267","DOIUrl":"10.1002/2211-5463.70267","url":null,"abstract":"<p>Tumor microenvironment plays a pivotal role in regulating the biological properties of cancer cells. Interstitial fluid hydrostatic pressure (HP) generally increases in malignant solid tumors. While our recent work has demonstrated that elevated HP stabilizes HIF-1α expression in cancer cells, here we further investigate whether elevated HP promotes cancer cells to acquire stemness features. Our results showed that exposure to 50 mmHg HP for 48 h did not significantly change the survival or morphology of human breast cancer cells. However, 50 mmHg HP stimulation significantly increased aldehyde dehydrogenase (ALDH) activity and upregulated HIF-1α and stemness markers (CD44 and SSEA-1) in MCF-7 and BT-474 but not in MDA-MB-453 breast cancer cell lines. Correspondingly, β-catenin was significantly enhanced in MCF-7 and BT-474 breast cancer cell lines under 50 mmHg HP stimulation and was negatively expressed in MDA-MB-453 breast cancer cells. Hypoxia (1% O₂) exposure for 48 h also significantly enhanced the expression of β-catenin only in MCF-7 cells and BT-474 breast cancer cell lines, but increased HIF-1α expression and ALDH activity in all breast cancer cell lines tested, including the β-catenin-deficient MDA-MB-453 cells. Therefore, we conclude that elevated HP in malignant tumors may facilitate the acquisition of ‘stemness’ characteristics of cancer cells by enhancing HIF-1α expression via β-catenin.</p>","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"16 10","pages":"1992-2002"},"PeriodicalIF":2.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13399563/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148143302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A light-triggered Time-Resolved X-ray Solution Scattering (TR-XSS) workflow with application to protein conformational dynamics","authors":"Fatemeh Sabzian-Molaei,&nbsp;Fredrik Orädd,&nbsp;Konstantinos Magkakis,&nbsp;Magnus Andersson","doi":"10.1002/2211-5463.70200","DOIUrl":"10.1002/2211-5463.70200","url":null,"abstract":"<p>Time-resolved X-ray solution scattering (TR-XSS) is a synchrotron-based methodology that enables real-time structural characterization under near-native conditions to provide insight into dynamic and transient structural changes inaccessible to static high-resolution methods such as cryo-electron microscopy (cryo-EM) or X-ray crystallography. Here, we present a workflow for light-triggered TR-XSS experiments that spans data collection, data processing, kinetic analysis, and structural refinement, with accompanying Python scripts. A calcium-transporting P-type ATPase membrane protein (LMCA1) is used as an illustrative example, but the protocol is broadly applicable to diverse protein systems. This workflow offers a practical framework for collecting TR-XSS synchrotron data and subsequent data analysis and interpretation.</p>","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"16 10","pages":"1870-1883"},"PeriodicalIF":2.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13399131/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146156490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Time-restricted feeding prior to Mycobacterium tuberculosis infection reduces tissue CD4+ T cells with limited impact on bacterial clearance","authors":"Ashish Gupta,&nbsp;Nidhi Yadav,&nbsp;Subhasmita Das,&nbsp;R. Rajendra Kumar Reddy,&nbsp;Nupur Sharma,&nbsp;Amol Ratnakar Suryawanshi,&nbsp;Jaswinder Singh Maras,&nbsp;Ranjan Kumar Nanda","doi":"10.1002/2211-5463.70263","DOIUrl":"10.1002/2211-5463.70263","url":null,"abstract":"<p>The effects of time-restricted feeding (TRF) on immune responses during bacterial infection are not well-studied. Here, we subjected mice (6–8 weeks, male) to 8 h of TRF for 30 days and then infected them with a low dose of <i>Mycobacterium tuberculosis</i> (Mtb) H37Rv. During the first 15 days, TRF improved glucose tolerance with marginal weight loss. However, global serum and liver metabolomics alongside liver proteomics indicated that TRF perturbed fatty acid biosynthesis and degradation, steroid hormone biosynthesis, and tyrosine metabolism. Together, these results indicate that TRF potentially affected the distribution and functionality of host immune cells. TRF mice had similar mycobacterial burdens in lungs and spleen at 21 days postinfection but had significantly lower CD3⁺ T cells in bone marrow and CD4⁺ T cells in both bone marrow and lungs. Ultimately, we show that TRF induced changes in amino acid and lipid metabolism persist during Mtb infection.</p>","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"16 10","pages":"1944-1957"},"PeriodicalIF":2.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13398685/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148155921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The crystal structure of the Borrelia burgdorferi nicotinamidase BBE22 resolves a long-standing annotation error","authors":"Kalvis Brangulis","doi":"10.1002/2211-5463.70268","DOIUrl":"10.1002/2211-5463.70268","url":null,"abstract":"<p>Nicotinamidases (PncA) catalyze the hydrolysis of nicotinamide to nicotinic acid, a key step in NAD⁺ salvage pathways. In the Lyme disease spirochete <i>Borrelia burgdorferi</i>, the plasmid-encoded gene <i>bbe22</i> encodes a PncA enzyme that is essential for survival in both mammalian and tick hosts. Previous genetic and biochemical studies demonstrated that translation of <i>B. burgdorferi</i> PncA initiates from a rare non-canonical AUU start codon, resulting in a protein that is 24 residues longer than the sequence currently annotated in major databases. Despite these findings, public resources such as UniProt and KEGG still list a truncated protein beginning at residue 36, which lacks part of the N-terminal region required for enzymatic activity. Here we report the crystal structure of full-length <i>B. burgdorferi</i> PncA determined at 3.2 Å resolution. The structure reveals the canonical fold of bacterial nicotinamidases and clear electron density for a ligand in the active site consistent with nicotinic acid, the product of the enzymatic reaction. Structural comparison with homologous PncA enzymes demonstrates conservation of the catalytic architecture, including residues involved in substrate binding and catalysis. Importantly, the experimentally determined structure confirms that the longer N-terminal sequence described previously is required for formation of the correct fold and active-site geometry, whereas the truncated annotation is structurally inconsistent with the observed fold and with AlphaFold predictions. Our results provide the first structural characterization of <i>B. burgdorferi</i> PncA and resolve the long-standing annotation discrepancy for <i>bbe22</i>, validating the correct protein sequence and providing the structural basis for nicotinamidase activity in this essential metabolic enzyme.</p>","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"16 10","pages":"1974-1981"},"PeriodicalIF":2.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13398362/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147873973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimizing photoexcitation conditions for time-resolved X-ray solution scattering experiments","authors":"Matteo Levantino","doi":"10.1002/2211-5463.70304","DOIUrl":"10.1002/2211-5463.70304","url":null,"abstract":"<p>Investigating the dynamics of biological molecules in real time is crucial to understand their biological function. Time-resolved X-ray solution scattering (TR-XSS) is an experimental technique that allows one to follow large-scale conformational changes of biological molecules in solution induced by a triggering event. In many cases, the triggering event is the absorption of a laser pulse, either by the biological molecule of interest or by photocaged compounds present in solution. Selecting the optimal photoexcitation conditions is a critical step in a TR-XSS experiment and it requires taking into account the laser beam properties, the sample characteristics, and the photoexcitation geometry. This protocol describes how to select the accessible experimental parameters in order to maximize the TR-XSS signal while avoiding nonlinear effects induced by an excessive laser peak power density. The provided set of guidelines will aid the experimentalists in the preparation and realization of their TR-XSS experiments.</p>","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"16 10","pages":"1857-1869"},"PeriodicalIF":2.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13399038/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148445256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}