Advances in biological regulation最新文献

{"title":"IP8: A quantitatively minor inositol pyrophosphate signaling molecule that punches above its weight","authors":"Chunfang Gu ,&nbsp;Xingyao Li ,&nbsp;Guangning Zong ,&nbsp;Huanchen Wang ,&nbsp;Stephen B. Shears","doi":"10.1016/j.jbior.2023.101002","DOIUrl":"https://doi.org/10.1016/j.jbior.2023.101002","url":null,"abstract":"<div><p><span>The inositol<span> pyrophosphates (PP-IPs) are specialized members of the wider inositol phosphate signaling family that possess functionally significant diphosphate groups. The PP-IPs exhibit remarkable functionally versatility throughout the eukaryotic kingdoms. However, a quantitatively minor PP-IP – 1,5 bisdiphosphoinositol tetrakisphosphate (1,5-IP</span></span>₈<span>) – has received considerably less attention from the cell signalling community. The main purpose of this review is to summarize recently-published data which have now brought 1,5-IP</span>₈<span> into the spotlight, by expanding insight into the molecular mechanisms by which this polyphosphate regulates many fundamental biological processes.</span></p></div>","PeriodicalId":7214,"journal":{"name":"Advances in biological regulation","volume":"91 ","pages":"Article 101002"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138557336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural basis for the conserved roles of PI4KA and its regulatory partners and their misregulation in disease","authors":"Sushant Suresh ,&nbsp;John E. Burke","doi":"10.1016/j.jbior.2023.100996","DOIUrl":"https://doi.org/10.1016/j.jbior.2023.100996","url":null,"abstract":"<div><p>The type III Phosphatidylinositol<span><span> 4-kinase alpha (PI4KA) is an essential lipid kinase that is a master regulator of </span>phosphoinositide<span><span> signalling at the plasma membrane (PM). It produces the predominant pool of phosphatidylinositol 4-phosphate (PI4P) at the PM, with this being essential in lipid transport and in regulating the PLC and PI3K </span>signalling pathways<span>. PI4KA is essential and is highly conserved in all eukaryotes. In yeast, the PI4KA ortholog stt4 predominantly exists as a heterodimer with its regulatory partner ypp1. In higher eukaryotes, PI4KA instead primarily forms a heterotrimer with a TTC7 subunit (ortholog of ypp1) and a FAM126 subunit. In all eukaryotes PI4KA is recruited to the plasma membrane by the protein EFR3, which does not directly bind PI4KA, but instead binds to the TTC7/ypp1 regulatory partner. Misregulation in PI4KA or its regulatory partners is involved in myriad human diseases, including loss of function mutations in neurodevelopmental and inflammatory intestinal disorders and gain of function in human cancers. This review describes an in-depth analysis of the structure function of PI4KA and its regulatory partners, with a major focus on comparing and contrasting the differences in regulation of PI4KA throughout evolution.</span></span></span></p></div>","PeriodicalId":7214,"journal":{"name":"Advances in biological regulation","volume":"90 ","pages":"Article 100996"},"PeriodicalIF":0.0,"publicationDate":"2023-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134652434","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Site-specific crosslinking reveals Phosphofructokinase-L inhibition drives self-assembly and attenuation of protein interactions","authors":"Athira Sivadas ,&nbsp;Eli Fritz McDonald ,&nbsp;Sydney O. Shuster ,&nbsp;Caitlin M. Davis ,&nbsp;Lars Plate","doi":"10.1016/j.jbior.2023.100987","DOIUrl":"10.1016/j.jbior.2023.100987","url":null,"abstract":"<div><p>Phosphofructokinase is the central enzyme in glycolysis and constitutes a highly regulated step. The liver isoform (PFKL) compartmentalizes during activation and inhibition <em>in vitro</em> and <em>in vivo,</em> respectively. Compartmentalized PFKL is hypothesized to modulate metabolic flux consistent with its central role as the rate limiting step in glycolysis. PFKL tetramers self-assemble at two interfaces in the monomer (interface 1 and 2), yet how these interfaces contribute to PFKL compartmentalization and drive protein interactions remains unclear. Here, we used site-specific incorporation of noncanonical photocrosslinking amino acids to identify PFKL interactors at interface 1, 2, and the active site. Tandem mass tag-based quantitative interactomics reveals interface 2 as a hotspot for PFKL interactions, particularly with cytoskeletal, glycolytic, and carbohydrate derivative metabolic proteins. Furthermore, PFKL compartmentalization into puncta was observed in human cells using citrate inhibition. Puncta formation attenuated crosslinked protein-protein interactions with the cytoskeleton at interface 2. This result suggests that PFKL compartmentalization sequesters interface 2, but not interface 1, and may modulate associated protein assemblies with the cytoskeleton.</p></div>","PeriodicalId":7214,"journal":{"name":"Advances in biological regulation","volume":"90 ","pages":"Article 100987"},"PeriodicalIF":0.0,"publicationDate":"2023-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41113652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phosphorylation impacts GLE1 nuclear localization and association with DDX1","authors":"Manisha Sharma ,&nbsp;Aaron C. Mason ,&nbsp;T. Renee Dawson ,&nbsp;Susan R. Wente","doi":"10.1016/j.jbior.2023.100990","DOIUrl":"10.1016/j.jbior.2023.100990","url":null,"abstract":"<div><p>Gle1 regulates gene expression at multiple steps from transcription to mRNA export to translation under stressed and non-stressed conditions. To better understand Gle1 function in stressed human cells, specific antibodies were generated that recognized the phosphorylation of threonine residue 102 (T102) in Gle1. A series of <em>in vitro</em> kinase assays indicated that T102 phosphorylation serves as a priming event for further phosphorylation in Gle1's N-terminal low complexity cluster. Indirect immunofluorescence microscopy with the anti-Gle1-pT102 antibodies revealed that basally phosphorylated Gle1 was pre-dominantly nuclear with punctate distribution; however, under sodium arsenite-induced stress, more cytoplasmic localization was detected. Immunoprecipitation with the anti-Gle1-pT102 antibody resulted in co-isolation of Gle1-pT102 with the DEAD-box protein DDX1 in a phosphatase sensitive manner. This suggested Gle1 phosphorylation might be linked to its role in regulating DDX1 during transcription termination. Notably, whereas the total Gle1-DDX1 association was decreased when Gle1 nucleocytoplasmic shuttling was disrupted, co-isolation of Gle1-pT102 and DDX1 increased under the same conditions. Taken together, these studies demonstrated that Gle1 phosphorylation impacts its cellular distribution and potentially drives nuclear Gle1 functions in transcription termination. We propose a model wherein phosphorylation of Gle1 either reduces its nucleocytoplasmic shuttling capacity or increases its binding affinity with nuclear interaction partners.</p></div>","PeriodicalId":7214,"journal":{"name":"Advances in biological regulation","volume":"90 ","pages":"Article 100990"},"PeriodicalIF":0.0,"publicationDate":"2023-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41106548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chromatin conformations of HSP12 during transcriptional activation in the Saccharomyces cerevisiae stationary phase","authors":"Yuri D'Alessio,&nbsp;Anna D'Alfonso,&nbsp;Giorgio Camilloni","doi":"10.1016/j.jbior.2023.100986","DOIUrl":"10.1016/j.jbior.2023.100986","url":null,"abstract":"<div><p>During evolution, living cells have developed sophisticated molecular and physiological processes to cope with a variety of stressors. These mechanisms, which collectively constitute the Environmental Stress Response, involve the activation/repression of hundreds of genes that are regulated to respond rapidly and effectively to protect the cell. The main stressors include sudden increases in environmental temperature and osmolarity, exposure to heavy metals, nutrient limitation, ROS accumulation, and protein-damaging events. The growth stages of the yeast <em>S. cerevisiae</em> proceed from the exponential to the diauxic phase, finally reaching the stationary phase. It is in this latter phase that the main stressor events are more active. In the present work, we aim to understand whether the responses evoked by the sudden onset of a stressor, like what happens to cells going through the stationary phase, would be different or similar to those induced by a gradual increase in the same stimulus. To this aim, we studied the expression of the <em>HSP12</em> gene of the HSP family of proteins, typically induced by stress conditions, with a focus on the role of chromatin in this regulation. Analyses of nucleosome occupancy and three-dimensional chromatin conformation suggest the activation of a different response pathway upon a sudden vs a gradual onset of a stress stimulus. Here we show that it is the three-dimensional chromatin structure of <em>HSP12</em>, rather than nucleosome remodeling, that becomes altered in <em>HSP12</em> transcription during the stationary phase.</p></div>","PeriodicalId":7214,"journal":{"name":"Advances in biological regulation","volume":"90 ","pages":"Article 100986"},"PeriodicalIF":0.0,"publicationDate":"2023-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41099909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolism configures immune response across multi-systems: Lessons from COVID-19","authors":"Tinku Gupta ,&nbsp;Najumuddin ,&nbsp;Dhanya Rajendran ,&nbsp;Akash Gujral ,&nbsp;Ashok Jangra","doi":"10.1016/j.jbior.2023.100977","DOIUrl":"10.1016/j.jbior.2023.100977","url":null,"abstract":"<div><p>Several studies over the last decade demonstrate the recruitment of immune cells, increased inflammatory cytokines, and chemokine in patients with metabolic diseases, including heart failure, parenchymal inflammation, obesity, tuberculosis, and diabetes mellitus. Metabolic rewiring of immune cells is associated with the severity and prevalence of these diseases. The risk of developing COVID-19/SARS-CoV-2 infection increases in patients with metabolic dysfunction (heart failure, diabetes mellitus, and obesity). Several etiologies, including fatigue, dyspnea, and dizziness, persist even months after COVID-19 infection, commonly known as Post-Acute Sequelae of CoV-2 (PASC) or long COVID. A chronic inflammatory state and metabolic dysfunction are the factors that contribute to long COVID. Here, this study explores the potential link between pathogenic metabolic and immune alterations across different organ systems that could underlie COVID-19 and PASC. These interactions could be utilized for targeted future therapeutic approaches.</p></div>","PeriodicalId":7214,"journal":{"name":"Advances in biological regulation","volume":"90 ","pages":"Article 100977"},"PeriodicalIF":0.0,"publicationDate":"2023-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10256594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A possible role for G-quadruplexes formation and DNA methylation at IMOOD gene promoter in Obsessive Compulsive Disorder","authors":"Annalaura Sabatucci ,&nbsp;Antonio Girella ,&nbsp;Martina Di Bartolomeo ,&nbsp;Mariangela Pucci ,&nbsp;Matteo Vismara ,&nbsp;Beatrice Benatti ,&nbsp;Isobel Alice Blacksell ,&nbsp;Dianne Cooper ,&nbsp;Enrico Dainese ,&nbsp;Fulvio D'Acquisto ,&nbsp;Bernardo Dell’Osso ,&nbsp;Claudio D'Addario","doi":"10.1016/j.jbior.2023.100976","DOIUrl":"10.1016/j.jbior.2023.100976","url":null,"abstract":"<div><p>Obsessive Compulsive Disorder (OCD) is a mental health condition still classified and diagnosed with subjective interview-based assessments and which molecular clues have not completely been elucidated. We have recently identified a new regulator of anxiety and OCD-like behavior called Immuno-moodulin (IMOOD) and, here, we report that <em>IMOOD</em> gene promoter is differentially methylated in OCD subjects when compared to genomic material collected from healthy controls and this alteration is significantly correlated with the increased expression of the gene in OCD. We also demonstrated that <em>IMOOD</em> promoter can form G-quadruplexes and we suggest that, in homeostatic conditions, these structures could evoke DNA-methylation silencing the gene, whereas in pathological conditions, like OCD, could induce gene expression making the promoter more accessible to transcriptional factors. We here thus further suggest <em>IMOOD</em> as a new biomarker for OCD and also hypothesize new mechanisms of gene regulation.</p></div>","PeriodicalId":7214,"journal":{"name":"Advances in biological regulation","volume":"89 ","pages":"Article 100976"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10565633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improved efficacy of quizartinib in combination therapy with PI3K inhibition in primary FLT3-ITD AML cells","authors":"Salihanur Darici ,&nbsp;Heather G. Jørgensen ,&nbsp;Xu Huang ,&nbsp;Valentina Serafin ,&nbsp;Ludovica Antolini ,&nbsp;Patrizia Barozzi ,&nbsp;Mario Luppi ,&nbsp;Fabio Forghieri ,&nbsp;Sandra Marmiroli ,&nbsp;Manuela Zavatti","doi":"10.1016/j.jbior.2023.100974","DOIUrl":"10.1016/j.jbior.2023.100974","url":null,"abstract":"<div><p>Acute myeloid leukemia is a heterogeneous hematopoietic malignancy, characterized by uncontrolled clonal proliferation of abnormal myeloid progenitor cells, with poor outcomes.</p><p>The internal tandem duplication (ITD) mutation of the Fms-like receptor tyrosine kinase 3 (FLT3) (FLT3-ITD) represents the most common genetic alteration in AML, detected in approximately 30% of AML patients, and is associated with high leukemic burden and poor prognosis. Therefore, this kinase has been regarded as an attractive druggable target for the treatment of FLT3-ITD AML, and selective small molecule inhibitors, such as quizartinib, have been identified and trialled. However, clinical outcomes have been disappointing so far due to poor remission rates, also because of acquired resistance. A strategy to overcome resistance is to combine FLT3 inhibitors with other targeted therapies. In this study, we investigated the preclinical efficacy of the combination of quizartinib with the pan PI3K inhibitor BAY-806946 in FLT3-ITD cell lines and primary cells from AML patients. We show here that BAY-806946 enhanced quizartinib cytotoxicity and, most importantly, that this combination increases the ability of quizartinib to kill CD34⁺ CD38⁻leukemia stem cells, whilst sparing normal hematopoietic stem cells. Because constitutively active FLT3 receptor tyrosine kinase is known to boost aberrant PI3K signaling, the increased sensitivity of primary cells to the above combination can be the mechanistic results of the disruption of signaling by vertical inhibition.</p></div>","PeriodicalId":7214,"journal":{"name":"Advances in biological regulation","volume":"89 ","pages":"Article 100974"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10190931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Circulating ACE2 level and zinc/albumin ratio as potential biomarkers for a precision medicine approach to COVID-19","authors":"Serena Benedetti ,&nbsp;Davide Sisti ,&nbsp;Daniela Vandini ,&nbsp;Simone Barocci ,&nbsp;Maurizio Sudano ,&nbsp;Eugenio Carlotti ,&nbsp;Jade Lee Lee Teng ,&nbsp;Loris Zamai","doi":"10.1016/j.jbior.2023.100973","DOIUrl":"10.1016/j.jbior.2023.100973","url":null,"abstract":"<div><p>Highly mutable influenza is successfully countered based on individual susceptibility and similar precision-like medicine approach should be effective against SARS-COV-2. Among predictive markers to bring precision medicine to COVID-19, circulating ACE2 has potential features being upregulated in both severe COVID-19 and predisposing comorbidities. Spike SARS-CoVs were shown to induce ADAM17-mediated shedding of enzymatic active ACE2, thus accounting for its increased activity that has also been suggested to induce positive feedback loops leading to COVID-19-like manifestations. For this reason, pre-existing ACE2 activity and inhibition of ACE2/ADAM17 zinc-metalloproteases through zinc chelating agents have been proposed to predict COVID-19 outcome before infection and to protect from COVID-19, respectively. Since most diagnostic laboratories are not equipped for enzymatic activity determination, other potential predictive markers of disease progression exploitable by diagnostic laboratories were explored.</p><p>Concentrations of circulating albumin, zinc, ACE2 protein and its activity were investigated in healthy, diabetic (COVID-19-susceptible) and SARS-CoV-2-negative COVID-19 individuals.</p><p>ACE2 both protein levels and activity significantly increased in COVID-19 and diabetic patients. Abnormal high levels of ACE2 characterised a subgroup (16–19%) of diabetics, while COVID-19 patients were characterised by significantly higher zinc/albumin ratios, pointing to a relative increase of albumin-unbound zinc species, such as free zinc ones.</p><p>Data on circulating ACE2 levels are in line with the hypothesis that they can drive susceptibility to COVID-19 and elevated zinc/albumin ratios support the therapeutic use of zinc chelating inhibitors of ACE2/ADAM17 zinc-metalloproteases in a targeted therapy for COVID-19.</p></div>","PeriodicalId":7214,"journal":{"name":"Advances in biological regulation","volume":"89 ","pages":"Article 100973"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10202900/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10194087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A motif in the 5′untranslated region of messenger RNAs regulates protein synthesis in a S6 kinase-dependent manner","authors":"Hyun-Chul Shin ,&nbsp;Yury A. Bochkov ,&nbsp;Kangsan Kim ,&nbsp;James E. Gern ,&nbsp;Nizar N. Jarjour ,&nbsp;Stephane Esnault","doi":"10.1016/j.jbior.2023.100975","DOIUrl":"10.1016/j.jbior.2023.100975","url":null,"abstract":"<div><p>The 5′ untranslated regions (UTRs) in messenger RNAs (mRNAs) play an important role in the regulation of protein synthesis. We had previously identified a group of mRNAs that includes human semaphorin 7A (SEMA7A) whose translation is upregulated by the Erk/p90S6K pathway in human eosinophils, with a potential negative impact in asthma and airway inflammation. In the current study, we aimed to find a common 5′UTR regulatory cis-element, and determine its impact on protein synthesis. We identified a common and conserved 5′UTR motif GGCTG—[(C/G)T(C/G)]_n—GCC that was present in this group of mRNAs. Mutations of the first two GG bases in this motif in SEMA7A 5′UTR led to a complete loss of S6K activity dependence for maximal translation. In conclusion, the newly identified 5′UTR motif present in SEMA7A has a critical role in regulating S6K-dependent protein synthesis.</p></div>","PeriodicalId":7214,"journal":{"name":"Advances in biological regulation","volume":"89 ","pages":"Article 100975"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10196148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}