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Half a century after their discovery:Structural insights into exonuclease and annealase proteins catalyzing recombineering

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Engineering Microbiology 2024年第1期4卷 39-54页

作者： Lucy J.Fitschen Timothy P.Newing Nikolas P.Johnston Charles E.Bell Gökhan Tolun School of Chemistry and molecular Bioscience and Molecular HorizonsUniversity of WollongongWollongongNSWAustralia The ARC Training Centre for Cryo-electron Microscopy of Membrane Proteins University of WollongongWollongongNSWAustralia Faculty of Science University of Technology SydneyUltimoNSW 2007Australia department of Biological Chemistry and pharmacology The Ohio State University College of MedicineColumbusOH 43210

Recombineering is an essential tool for molecular biologists,allowing for the facile and efficient manipulation of bacterial genomes directly in cells without the need for costly and laborious in vitro manipulations involving restriction *** main workhorses behind recombineering are bacteriophage proteins that promote the single-strand annealing(SSA)homologous recombination pathway to repair double-stranded DNA *** there have been several reviews examining recombineering methods and applications,comparatively few have focused on the mechanisms of the proteins that are the key players in the SSA pathway:a 5′→3′exonuclease and a single-strand annealing protein(SSAP or“annealase”).This review dives into the structures and functions of the two SSA recombination systems that were the first to be developed for recombineering in ***:the RecET system from *** Rac prophage and the𝜆Red system from bacteriophageλ.By comparing the structures of the RecT and Red𝛽annealases,and the RecE and𝜆Exo exonucleases,we provide new insights into how the structures of these proteins dictate their *** the sequence conservation of the𝜆λExo and RecE exonucleases gives more profound insights into their critical functional ***,as recombineering accelerates and evolves in the laboratory,a better understanding of the mechanisms of the proteins behind this powerful technique will drive the development of improved and expanded capabilities in the future.

关键词： Recombineering Redβ λExo RecE RecT Protein structure Annealase Exonuclease

Structural basis for polyuridine tract recognition by SARS-CoV-2 Nsp15

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Protein & Cell 2024年第7期15卷 547-552页

作者： Fumiaki Ito Hanjing Yang Z.Hong Zhou Xiaojiang S.Chen molecular and Computational Biology Department of Biological SciencesUniversity of Southern CaliforniaLos AngelesCA 90089United States department of Microbiology Immunology and Molecular GeneticsUniversity of CaliforniaLos AngelesCA 90095United States California NanoSystems Institute University of CaliforniaLos AngelesCA90095United States Genetic Molecular and Cellular Biology ProgramKeck School of MedicineUniversity of Southern CaliforniaLos AngelesCA 90089United States Norris Comprehensive Cancer Center University of Southern CaliforniaLos AngelesCA 90089United States Center of Excellence in NanoBiophysics University of Southern CaliforniaLos AngelesCA 90089United States

Dear Editor,Coronaviruses have evolved a wide array of tactics to evade host antiviral *** host cells detect invading foreign nucleic acids including viral genome and viral replication intermediates,they activate interferon(IFN)signaling via cytoplasmic pattern recognition receptors(Kang et al.,2002;Kato et al.,2006).Remarkable stealth activities exhibited by coronaviruses are facilitated by a series of non-structural proteins(Nsps),such as Nsp15(Deng and Baker,2018;Deng et al.,2019;Hackbart et al.,2020),which is a uridine-specific endoribonuclease that mediates evasion of host detection of viral double-stranded RNA(dsRNA)(Bhardwaj et al.,2004;Deng et al.,2017;Frazier et al.,2021;Ivanov et al.,2004).Nsp15 targets a polyuridine[poly(U)]tract on the coronavirus negative strand RNA(Hackbart et al.,2020).Nsp15 limits the abundance and length of poly(U)within the negative strand RNA 5ʹ-extension by trimming down the initially synthesized poly(U)lead sequence to the optimal length that can suppress dsRNA formation but still serves as a template for poly(A)tail of the positive strand genome of the coronaviruses(Hofmann and Brian,1991).

关键词： p15 interferon template

A multi-platform analysis of human gingival crevicular fluid reveals ferroptosis as a relevant regulated cell death mechanism during the clinical progression of periodontitis

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International Journal of Oral Science 2024年第2期16卷 265-279页

作者： Alfredo Torres M.Angélica Michea Ákos Végvári Marion Arce Valentina Pérez Marcela Alcota Alicia Morales Rolando Vernal Mauricio Budini Roman A.Zubarev Fermín E.González Laboratory of Experimental Immunology&Cancer Faculty of DentistryUniversity of ChileSantiagoChile department of Conservative Dentistry Faculty of DentistryUniversity of ChileSantiagoChile Division of Chemistry I Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden Periodontal Biology Laboratory Faculty of DentistryUniversidad de ChileSantiagoChile Laboratory of cellular and molecular Pathology Institute for Research in Dental SciencesFaculty of DentistryUniversity of ChileSantiagoChile

Ferroptosis is implicated in the pathogenesis of numerous chronic-inflammatory diseases,yet its association with progressive periodontitis remains *** investigate the involvement and significance of ferroptosis in periodontitis progression,we assessed sixteen periodontitis-diagnosed *** progression was clinically monitored over twelve weeks via weekly clinical evaluations and gingival crevicular fluid(GCF)collection was performed for further *** metrics,proteomic data,in silico methods,and bioinformatics tools were combined to identify protein profiles linked to periodontitis progression and to explore their potential connection with *** western blot analyses validated key ***,a single-cell RNA sequencing(scRNA-seq)dataset(GSE164241)for gingival tissues was analyzed to elucidate cellular dynamics during periodontitis *** progression was identified as occurring at a faster rate than traditionally *** samples from progressing and non-progressing periodontal sites showed quantitative and qualitatively distinct proteomic *** addition,specific biological processes and molecular functions during progressive periodontitis were revealed and a set of hub proteins,including SNCA,CA1,HBB,SLC4A1,and ANK1 was strongly associated with the clinical progression status of ***,we found specific proteins-drivers or suppressors-associated with ferroptosis(SNCA,FTH1,HSPB1,CD44,and GCLC),revealing the co-occurrence of this specific type of regulated cell death during the clinical progression of ***,the integration of quantitative proteomic data with scRNA-seq analysis suggested the susceptibility of fibroblasts to *** analyses reveal proteins and processes linked to ferroptosis for the first time in periodontal patients,which offer new insights into the molecular mechanisms of progressive periodontal *** findings may le

关键词： finding progression faster

The effect of celastrol in combination with 5-fluorouracil on proliferation and apoptosis of gastric cancer cell lines

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Oncology Research 2024年第7期32卷 1231-1237页

作者： MOHAMMAD-TAGHI MORADI DHIYA ALTEMEMY MAJID ASADI-SAMANI PEGAH KHOSRAVIAN MARZIYEH SOLTANI LEILA HASHEMI AZADEH SAMIEI-SEFAT Medical Plants Research Center Basic Health Sciences InstituteShahrekord University of Medical SciencesShahrekordIran department of Pharmaceutics College of PharmacyAl-Zahraa University for WomenKarbalaIraq cellular and molecular Research Center Basic Health Sciences InstituteShahrekord University of Medical SciencesShahrekordIran

Background:Despite the availability of chemotherapy drugs such as 5-ﬂuorouracil(5-FU),the treatment of some cancers such as gastric cancer remains challenging due to drug resistance and side *** study aimed to investigate the effect of celastrol in combination with the chemotherapy drug 5-FU on proliferation and induction of apoptosis in human gastric cancer cell lines(AGS and EPG85-257).Materials and Methods:In this in vitro study,AGS and EPG85-257 cells were treated with different concentrations of celastrol,5-FU,and their *** proliferation was assessed using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide(MTT)*** synergistic effect of 5-FU and celastrol was studied using Compusyn *** DNA content at different phases of the cell cycle and apoptosis rate was measured usingﬂow ***:Co-treatment with low concentrations(10%inhibitory concentration(IC10))of celastrol and 5-FU signiﬁcantly reduced IC50(p<0.05)so that 48 h after treatment,IC50 was calculated at 3.77 and 6.9μM for celastrol,20.7 and 11.6μM for 5-FU,and 5.03 and 4.57μM for their combination for AGS and EPG85-257 cells,*** mean percentage of apoptosis for AGS cells treated with celastrol,5-FU,and their combination was obtained 23.9,41.2,and 61.9,and for EPG85-257 cells 5.65,46.9,and 55.7,*** addition,the 5-FU and celastrol-5-FU combination induced cell cycle arrest in the synthesis ***:Although celastrol could decrease the concentration of 5-ﬂuorouracil that sufﬁced to suppress gastric cancer cells,additional studies are required to arrive at conclusive evidence on the anticancer effects of celastrol.

关键词： Gastric cancer Celastrol Terpenoid Cell cycle regulation Apoptosis Synergism

Agmatine ameliorates diabetes type 2-induced nephropathy in rats

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Asian Pacific Journal of Tropical Biomedicine 2024年第1期14卷 8-16页

作者： Fatemah O.Kamel Ohoud Shagroud Mai AAlim A.Sattar Ahmad Gamal S Abd El-Aziz Abdulhadi S.Burzangi Duaa Bakhshwin Maha Jamal Shahid Karim department of Clinical pharmacology Faculty of MedicineKing Abdulaziz UniversityJeddah 21589Saudi Arabia department of Anatomy Faculty of MedicineKing Abdulaziz UniversityJeddah 21589Saudi Arabia

Objective:To assess the nephroprotective potential of agmatine in a rat model of streptozotocin-induced diabetic ***:A single dose of streptozotocin(40 mg/kg)coupled with a fructose diet induced diabetes in Wistar ***(40 and 80 mg/kg)was administered to rats for 12 *** body weight and fasting blood glucose were measured *** level,urine output,total protein,albumin,blood urea nitrogen,creatinine,and cystatin-C were also determined at the end of the ***,superoxide dismutase,glutathione,interleukin-1β,interleukin-6,and tumor necrosis factor-alpha were evaluated in kidney *** study was also performed using hematoxylin and eosin ***:Agmatine at both doses significantly increased final body weight,and lowered fasting blood glucose,urine output,insulin,total protein,albumin,blood urea nitrogen,creatinine,and cystatin-C levels compared with the diabetic group(Pmolecular mechanisms of its nephroprotective actions need to be investigated in future study.

关键词： Agmatine Type 2 diabetes Nephropathy Oxidative stress Nephroprotection

Presepsin as a biomarker of bacterial translocation and an indicator for the prescription of probiotics in cirrhosis

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World Journal of Hepatology 2024年第5期16卷 822-831页

作者： Irina Efremova Roman Maslennikov Elena Poluektova Oleg Medvedev Anna Kudryavtseva George Krasnov Maria Fedorova Filipp Romanikhin Maria Zharkova Oxana Zolnikova Gyunay Bagieva Vladimir Ivashkin department of Internal Medicine Gastroenterology and HepatologySechenov UniversityMoscow 119435Russia department of Scientific Scientific Community for the Promotion of the Clinical Study of the Human MicrobiomeMoscow 119435Russia department of pharmacology Lomonosov Moscow State UniversityMoscow 119192Russia department of Post-Genomic Research Laboratory Engelhardt Institute of Molecular BiologyRussian Academy of SciencesMoscow 119991Russia

BACKGROUND The gut–liver axis and bacterial translocation are important in cirrhosis,but there is no available universal biomarker of cellular bacterial translocation,for which presepsin may be a *** To evaluate the relationship of the blood presepsin levels with the state of the gut microbiota in cirrhosis in the absence of obvious *** This study included 48 patients with Child–Pugh cirrhosis classes B and C and 15 healthy *** fecal microbiome was assessed using 16S rRNA gene *** levels of presepsin were measured.A total of 22 patients received a probiotic(Saccharomyces boulardii)for 3 *** Presepsin levels were higher in patients with cirrhosis than in healthy individuals[342(91-2875)vs 120(102-141)pg/mL;P=0.048].Patients with elevated presepsin levels accounted for 56.3%of all included *** had lower levels of serum albumin and higher levels of serum total bilirubin and overall severity of cirrhosis as assessed using the Child–Pugh *** with elevated presepsin levels had an increased abundance of the main taxa responsible for bacterial translocation,namely Bacilli and Proteobacteria(including the main class Gammaproteobacteria and the minor taxa Xanthobacteraceae and Stenotrophomonas),and a low abundance of bacteria from the family Lachnospiraceae(including the minor genus Fusicatenibacter),which produce short-chain fatty acids that have a positive effect on intestinal barrier *** presepsin level directly correlated with the relative abundance of Bacilli,Proteobacteria,and inversely correlated with the abundance of Lachnospiraceae and *** 3 months of taking the probiotic,the severity of cirrhosis on the Child–Pugh scale decreased significantly only in the group with elevated presepsin levels[from 9(8-11)to 7(6-9);P=0.004],while there were no significant changes in the group with normal presepsin levels[from 8(7-8)to 7(6-8);P=0.123].A high level of presepsin

关键词： Dysbiosis Gut Intestinal permeability Leaky gut Gut-liver axis Liver Microbiota

MicroRNAs in thyroid cancer with focus on medullary thyroid carcinoma:potential therapeutic targets and diagnostic/prognostic markers and web based tools

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Oncology Research 2024年第6期32卷 1011-1019页

作者： ELHAM SHAKIBA SETI BOROOMAND SIMA KHERADMAND KIA MEHDI HEDAYATI department of Biochemistry Faculty of Biological SciencesNorth Tehran BranchIslamic Azad UniversityTehran***Iran department of Pathology and Laboratory Medicine Vancouver General HospitalVancouverV5Z 1M9Canada department of Blood Cell Research Laboratory for Red Blood Cell DiagnosticsSanquinAmsterdam1006 ANThe Netherlands cellular and molecular Endocrine Research Center Research Institute for Endocrine SciencesShahid Beheshti University of Medical SciencesTehran***Iran

This review aimed to describe the inculpation of microRNAs(miRNAs)in thyroid cancer(TC)and its subtypes,mainly medullary thyroid carcinoma(MTC),and to outline web-based tools and databases for bioinformatics analysis of miRNAs in ***,the capacity of miRNAs to serve as therapeutic targets and biomarkers in TC management will be *** review is based on a literature search of relevant articles on the role of miRNAs in TC and its subtypes,mainly ***,web-based tools and databases for bioinformatics analysis of miRNAs in TC were identified and *** can perform as oncomiRs or antioncoges,relying on the target mRNAs they *** replacement therapy using miRNA mimics or antimiRs that aim to suppress the function of certain miRNAs can be applied to correct miRNAs aberrantly expressed in diseases,particularly in *** are involved in the modulation of fundamental pathways related to cancer,resembling cell cycle checkpoints and DNA repair *** are also rather stable and can reliably be detected in different types of biological materials,rendering them favorable diagnosis and prognosis biomarkers as *** have emerged as promising tools for evaluating medical outcomes in TC and as possible therapeutic *** contribution of miRNAs in thyroid cancer,particularly MTC,is an active area of research,and the utility of web applications and databases for the biological data analysis of miRNAs in TC is becoming increasingly important.

关键词： Thyroid cancer MicroRNAs Biomarker Bioinformatics analysis Medullary thyroid carcinoma(MTC) OncomiRs Antioncoges

Sciadopitysin exerts anticancer effects on HepG2 hepatocellular carcinoma cells by regulating reactive oxygen species-mediated signaling pathways

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BIOCELL 2024年第7期48卷 1055-1069页

作者： YAN-NAN LI YUN-HONG XIU YAN-JUN TANG JING-LONG CAO WEN-SHUANG HOU AN-QI WANG TIAN-ZHU LI CHENG-HAO JIN department of Biochemistry and molecular Biology Heilongjiang Bayi Agricultural UniversityDaqingChina Hemodialysis Center Daqing Oilfield General HospitalDaqingChina department of Food Science and Engineering Heilongjiang Bayi Agricultural UniversityDaqingChina department of molecular Biology Chifeng UniversityChifengChina National Coarse Cereals Engineering Research Center DaqingChina

Objectives:Sciadopitysin(SP)is aﬂavonoid in Ginkgo biloba that exhibits various pharmacological *** study aimed to investigate its antitumor effects and the underlying molecular mechanism of SP in hepatocellular carcinoma(HCC)***:Network pharmacology was used for target prediction *** Counting Kit-8(CCK-8)assay was used to test the cell *** cytometry was used to test the cell cycle distribution,apoptosis status,and reactive oxygen species(ROS)*** and wound-healing assay was used to test the migration effect of SP on HepG2 *** Blot assay was used to test the expression levels of ***:Network pharmacology analysis results showed that the mitogen-activated protein kinase(MAPK)and other signaling pathways are involved in the SP anti-HCC biological ***-8 assay results demonstrated that SP showed an obvious killing effect on three types of HCC cells and low cytotoxic effect on normal *** Blot andﬂow cytometry results showed that SP regulated MAPK/signal transducer and activator of transcription 3(STAT3)/nuclear factor kappa-B(NF-κB)signaling pathway to induce mitochondrion-dependent apoptosis in HepG2 ***,SP can arrest the G0/G1 phase cell cycle via the protein kinase B(AKT)/p21/p27/cyclin-dependent kinase(CDK)/Cyclin signaling *** healing and transwell assays showed that SP inhibited cell motility and invasion through the AKT/glycogen synthase kinase3β(GSK-3β)/vimentin/β-catenin signaling ***:Theseﬁndings demonstrated that SP induced mitochondrion-dependent apoptosis,arrested cell cycle in the G0/G1 phase,and inhibited cell migration by regulating the ROS-mediated signaling pathway in HepG2 ***,SP could serve as a therapeutic agent for the treatment of human HCC.

关键词： Sciadopitysin Hepatocellular carcinoma Apoptosis Cell cycle Cell migration

Ce6 nanoassemblies:molecular mechanism and strategies for combinational anticancer therapy Special Collection:Aggregation-Induced Processes and Functions

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Aggregate

Aggregate 2024年第1期5卷 130-147页

作者： Yuwei Liu Shuting Xu Qingyang Lyu Yi Huang Weiping Wang State Key Laboratory of Pharmaceutical Biotechnology The University of Hong KongHong KongChina department of pharmacology and Pharmacy Li Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina Laboratory of molecular Engineering and Nanomedicine Dr.Li Dak-Sum Research CentreThe University of Hong KongHong KongChina

Nowadays,cancer has become the leading cause of death worldwide,driving the need for effective therapeutics to improve patient *** therapy(PDT)has been widely applied as an antitumor modality,owing to its minimal invasiveness,localized tumor damage,and high safety ***,its efficacy is limited by poor stability of photosensitizers,inadequate tumor accumulation,and a complex tumor *** overcome these challenges,extensive endeavors have been made to explore the co-assembly of the widely used photosensitizer chlorin e6(Ce6)with various functional small molecules to enhance pharmacodynamic *** review provides a comprehensive overview of current studies on Ce6-based nanoparticles for effective PDT and precise delivery of functional *** self-assembly mechanism will be discussed in detail,with a focus on potential strategies for combinational therapy with PDT.

关键词： cancer treatment carrier-free chlorin e6(Ce6) light nanomedicine photodynamic therapy(PDT) selfassembly