FEBS LettersPub Date : 2024-12-31DOI: 10.1002/1873-3468.15093
Giulia Zanetti, Jeffrey B. Klarenbeek, Kees Jalink
{"title":"Cytosolic-enhanced dark Epac-based FRET sensors allow for intracellular cAMP detection in live cells via FLIM","authors":"Giulia Zanetti, Jeffrey B. Klarenbeek, Kees Jalink","doi":"10.1002/1873-3468.15093","DOIUrl":"10.1002/1873-3468.15093","url":null,"abstract":"<p>Fluorescence resonance energy transfer (FRET)-based biosensors are powerful tools for studying second messengers with high temporal and spatial resolution. FRET is commonly detected by ratio imaging, but fluorescence lifetime imaging microscopy (FLIM), which measures the donor fluorophore's lifetime, offers a robust and more quantitative alternative. We have introduced and optimized four generations of FRET sensors for cAMP, based on the effector molecule Epac1, including variants for either ratio imaging or FLIM detection. Recently, Massengill and colleagues introduced additional mutations that improve cytosolic localization in these sensors, focusing on constructs optimized for ratio imaging. Here we present and briefly characterize these mutations in our dedicated FLIM sensors, finding they enhance cytosolic localization while maintaining performance comparable to original constructs.</p>","PeriodicalId":12142,"journal":{"name":"FEBS Letters","volume":"599 7","pages":"1075-1085"},"PeriodicalIF":3.5,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/1873-3468.15093","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142906815","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":"Cell cycle-dependent regulation of CRISPR-Cas9 repetitive activation by anti-CRISPR and Cdt1 fusion in the CRISPRa system","authors":"Kanae Kishi, Kiyomi Nigorikawa, Yuki Hasegawa, Yusaku Ohta, Erina Matsugi, Daisuke Matsumoto, Wataru Nomura","doi":"10.1002/1873-3468.15090","DOIUrl":"10.1002/1873-3468.15090","url":null,"abstract":"<p>CRISPR-Cas9 is a widely used genome-editing tool. We previously developed a method with improved homology-directed repair efficiency and reduced off-target effects by utilizing a fusion protein of AcrIIA4, a Cas9 inhibitor, and Cdt1, which accumulates in the G1 phase and activates Cas9 only in the S/G2 phase. However, it is unknown whether Cas9 inhibition by AcrIIA4 + Cdt1 occurs repeatedly in the G1 phase as the cell cycle progresses. In this study, we used the CRISPRa system to monitor changes in the interaction between Cas9 and AcrIIA4 + Cdt1 at single-cell resolution and in real time. Our findings are among the few examples of successful detection of fluctuating protein–protein interactions that oscillate over time.</p>","PeriodicalId":12142,"journal":{"name":"FEBS Letters","volume":"599 6","pages":"828-837"},"PeriodicalIF":3.5,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142909443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
FEBS LettersPub Date : 2024-12-30DOI: 10.1002/1873-3468.15088
Dawn M. Maynard, Bernadette R. Gochuico, Hadass Pri Chen, Christopher K. E. Bleck, Patricia M. Zerfas, Wendy J. Introne, William A. Gahl, May C. V. Malicdan
{"title":"Insights into the renal pathophysiology in Hermansky-Pudlak syndrome-1 from urinary extracellular vesicle proteomics and a new mouse model","authors":"Dawn M. Maynard, Bernadette R. Gochuico, Hadass Pri Chen, Christopher K. E. Bleck, Patricia M. Zerfas, Wendy J. Introne, William A. Gahl, May C. V. Malicdan","doi":"10.1002/1873-3468.15088","DOIUrl":"10.1002/1873-3468.15088","url":null,"abstract":"<p>Hermansky-Pudlak syndrome type 1 (HPS-1) is a rare, autosomal recessive disorder caused by defects in the biogenesis of lysosome-related organelles complex-3 (BLOC-3). Impaired kidney function is among its clinical manifestations. To investigate HPS-1 renal involvement, we employed 1D-gel-LC–MS/MS and compared the protein composition of urinary extracellular vesicles (uEVs) from HPS-1 patients to normal control individuals. We identified 1029 proteins, 149 of which were altered in HPS-1 uEVs. Ingenuity Pathway Analysis revealed disruptions in mitochondrial function and the LXR/RXR pathway that regulates lipid metabolism, which is supported by our novel <i>Hps1</i> knockout mouse. Serum concentration of the LXR/RXR pathway protein ApoA1 in our patient cohort was positively correlated with kidney function (with the estimated glomerular filtration rate or eGFR). uEVs can be used to study epithelial cell protein trafficking in HPS-1 and may provide outcome measures for HPS-1 therapeutic interventions.</p>","PeriodicalId":12142,"journal":{"name":"FEBS Letters","volume":"599 7","pages":"1055-1074"},"PeriodicalIF":3.5,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/1873-3468.15088","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142909453","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}
FEBS LettersPub Date : 2024-12-30DOI: 10.1002/1873-3468.15092
Stefan Pieter Hendrik van den Berg, Adja Zoumaro-Djayoon, Flora Yang, Gregory Bokinsky
{"title":"Exogenous fatty acids inhibit fatty acid synthesis by competing with endogenously generated substrates for phospholipid synthesis in Escherichia coli","authors":"Stefan Pieter Hendrik van den Berg, Adja Zoumaro-Djayoon, Flora Yang, Gregory Bokinsky","doi":"10.1002/1873-3468.15092","DOIUrl":"10.1002/1873-3468.15092","url":null,"abstract":"<p>Exogenous fatty acids are directly incorporated into bacterial membranes, heavily influencing cell envelope properties, antibiotic susceptibility, and bacterial ecology. Here, we quantify fatty acid biosynthesis metabolites and enzymes of the fatty acid synthesis pathway to determine how exogenous fatty acids inhibit fatty acid synthesis in <i>Escherichia coli.</i> We find that acyl-CoA synthesized from exogenous fatty acids rapidly increases concentrations of long-chain acyl-acyl carrier protein (acyl-ACP), which inhibits fatty acid synthesis initiation. Accumulation of long-chain acyl-ACP is caused by competition with acyl-CoA for phospholipid synthesis enzymes. Furthermore, we find that transcriptional regulation rebalances saturated and unsaturated acyl-ACP while maintaining overall expression levels of fatty acid synthesis enzymes. Rapid feedback inhibition of fatty acid synthesis by exogenous fatty acids thus allows <i>E. coli</i> to benefit from exogenous fatty acids while maintaining fatty acid synthesis capacity. We hypothesize that this indirect feedback mechanism is ubiquitous across bacterial species.</p>","PeriodicalId":12142,"journal":{"name":"FEBS Letters","volume":"599 5","pages":"667-681"},"PeriodicalIF":3.5,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/1873-3468.15092","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142909450","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}
FEBS LettersPub Date : 2024-12-29DOI: 10.1002/1873-3468.15086
Tadashi Nakaya
{"title":"Release of FUS into the extracellular space is regulated by its amino-terminal prion-like domain","authors":"Tadashi Nakaya","doi":"10.1002/1873-3468.15086","DOIUrl":"10.1002/1873-3468.15086","url":null,"abstract":"<p>Fused in sarcoma (FUS) is a causative factor of amyotrophic lateral sclerosis (ALS) and is believed to propagate pathologically by transmission from cell to cell. However, the mechanism underlying FUS release from cells, which is a critical step for the propagation system, remains poorly understood. This study conducted an analysis of the release of human and mouse FUS from neurons, revealing that human FUS is significantly released into the media compared to its mouse counterpart. Further study using chimeric FUS proteins identified the amino-terminal region of human FUS as essential for its release. These findings indicate that human FUS is released directly from neurons and underscore the novel functional role of its amino-terminal region in this process.</p>","PeriodicalId":12142,"journal":{"name":"FEBS Letters","volume":"599 7","pages":"1046-1054"},"PeriodicalIF":3.5,"publicationDate":"2024-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142906818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Violaceoid F induces nuclear translocation of FOXO3a by inhibiting CRM1 via a novel mechanism and suppresses HeLa cell growth","authors":"Nobumoto Watanabe, Emiko Sanada, Akiko Okano, Toshihiko Nogawa, Ngit Shin Lai, Yui Mazaki, Makoto Muroi, Yoko Yashiroda, Minoru Yoshida, Hiroyuki Osada","doi":"10.1002/1873-3468.15085","DOIUrl":"10.1002/1873-3468.15085","url":null,"abstract":"<p>FOXO3a is a transcription factor involved in cell growth inhibition and apoptosis. FOXO3a is localized in the cytoplasm in cancer cells, and its nuclear translocation by small molecules is expected to prevent cancer cell growth. In this study, we screened a fungal broth library in HeLa cells using fluorescently labeled FOXO3a and an AI-based imaging system. We identified violaceoid F, which translocates FOXO3a into the nucleus by inhibiting CRM1, which is responsible for nuclear protein export. Violaceoid F was observed to target the reactive cysteine of CRM1 through its α, β-epoxyketone. However, because violaceoid F did not inhibit Crm1 in fission yeast cells, it seems to target cysteine residue(s) other than Cys528 of human CRM1 which are not targeted by other known CRM1 inhibitors, indicating that violaceoid F inhibits CRM1 <i>via</i> a novel mechanism.</p>","PeriodicalId":12142,"journal":{"name":"FEBS Letters","volume":"599 5","pages":"755-765"},"PeriodicalIF":3.5,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142893249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
FEBS LettersPub Date : 2024-12-23DOI: 10.1002/1873-3468.15066
Duncan E. Wright
{"title":"The FEBS 60th anniversary writing contest—blueprints for the scientific society of tomorrow","authors":"Duncan E. Wright","doi":"10.1002/1873-3468.15066","DOIUrl":"10.1002/1873-3468.15066","url":null,"abstract":"<p>The Federation of European Biochemical Societies (FEBS) celebrated its 60th anniversary in 2024, and <i>FEBS Letters</i> marked the occasion with a writing contest on the future of scientific societies. This editorial introduces the winning article by Yussuf Ali and presents an overview of the predominant themes that emerged during the contest, which included AI, interdisciplinarity, diversity and sustainability.</p>","PeriodicalId":12142,"journal":{"name":"FEBS Letters","volume":"598 24","pages":"2943-2945"},"PeriodicalIF":3.5,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/1873-3468.15066","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142881670","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":"Membrane structure-responsive lipid scramblase activity of the TMEM63/OSCA family","authors":"Yugo Miyata, Megumi Nishimura, Aya Nagata, Xu Jing, Cheryl S. Sultan, Risa Kuribayashi, Katsuya Takahashi, Yongchan Lee, Tomohiro Nishizawa, Katsumori Segawa","doi":"10.1002/1873-3468.15084","DOIUrl":"10.1002/1873-3468.15084","url":null,"abstract":"<p>Phospholipids are asymmetrically distributed in the plasma membrane (PM), and scramblases disrupt this asymmetry by shuffling phospholipids. We recently identified mouse Tmem63b as a membrane structure-responsive scramblase. Tmem63b belongs to the TMEM63/OSCA family of ion channels; however, the conservation of the scramblase activity within this family remains unclear. We expressed human TMEM63 paralogs, TMEM63B orthologs, and plant OSCA1.1 in <i>Tmem63b</i>-deficient mouse pro-B cells and found that vertebrate TMEM63B orthologs exhibit scramblase activity at the PM. Previously, ten pathogenic human TMEM63B variants were identified, some of which exhibited constitutive scramblase activity. Upon expressing all variants, we found that nine variants displayed constitutive scramblase activity. These results suggest that membrane structure-responsive scramblase activity at the PM is conserved among vertebrate TMEM63B orthologs.</p>","PeriodicalId":12142,"journal":{"name":"FEBS Letters","volume":"599 5","pages":"656-666"},"PeriodicalIF":3.5,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142881655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
FEBS LettersPub Date : 2024-12-23DOI: 10.1002/1873-3468.15082
I-Ting Lee, Yu Takahashi, Takashi Sasaki, Yoshio Yamauchi, Ryuichiro Sato
{"title":"Human colon organoid differentiation from induced pluripotent stem cells using an improved method","authors":"I-Ting Lee, Yu Takahashi, Takashi Sasaki, Yoshio Yamauchi, Ryuichiro Sato","doi":"10.1002/1873-3468.15082","DOIUrl":"10.1002/1873-3468.15082","url":null,"abstract":"<p>The colonic epithelium plays a crucial role in gastrointestinal homeostasis, and colon organoids enable investigation into the molecular mechanisms underlying colonic physiology. However, the method for differentiating induced pluripotent stem cells (iPSCs) into human colon organoids (HCOs) is not necessarily standardized, and studies using HCOs are limited. This study refines the differentiation of HCOs by comparing two protocols reported in <i>Cell Stem Cell</i> and <i>Nature Medicine</i> journals. The former protocol, which uses transient bone morphogenetic protein 2 (BMP2) signaling activation, demonstrated superior efficacy in upregulating colon-specific markers. Additionally, adenovirus-mediated transduction of the transcription factors HOXD13 or SATB2 during hindgut endoderm development, together with BMP2 treatment, enhanced colonic identity, suggesting improved colonic maturation. This optimized protocol advances the generation of mature HCOs, offering a better model for investigating colonic epithelial biology and pathology.</p>","PeriodicalId":12142,"journal":{"name":"FEBS Letters","volume":"599 6","pages":"912-924"},"PeriodicalIF":3.5,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/1873-3468.15082","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142881628","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}
FEBS LettersPub Date : 2024-12-20DOI: 10.1002/1873-3468.15074
Laura Gardano, Jordan Ferreira, Christine Le Roy, Dominique Ledoux, Nadine Varin-Blank
{"title":"The survival grip-how cell adhesion promotes tumor maintenance within the microenvironment.","authors":"Laura Gardano, Jordan Ferreira, Christine Le Roy, Dominique Ledoux, Nadine Varin-Blank","doi":"10.1002/1873-3468.15074","DOIUrl":"https://doi.org/10.1002/1873-3468.15074","url":null,"abstract":"<p><p>Cell adhesion is warranted by proteins that are crucial for the maintenance of tissue integrity and homeostasis. Most of these proteins behave as receptors to link adhesion to the control of cell survival and their expression or regulation are often altered in cancers. B-cell malignancies do not evade this principle as they are sustained in relapsed niches by interacting with the microenvironment that includes cells and their secreted factors. Focusing on chronic lymphocytic leukemia and mantle cell lymphoma, this Review delves with the molecules involved in the dialog between the adhesion platforms and signaling pathways known to regulate both cell adhesion and survival. Current therapeutic strategies disrupt adhesive structures and compromise the microenvironment support to tumor cells, rendering them sensitive to immune recognition. The development of organ-on-chip and 3D culture systems, such as spheroids, have revealed the importance of mechanical cues in regulating signaling pathways to organize cell adhesion and survival. All these elements contribute to the elaboration of the crosstalk of lymphoma cells with the microenvironment and the education processes that allow the establishment of the supportive niche.</p>","PeriodicalId":12142,"journal":{"name":"FEBS Letters","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142863877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}