BACKGROUND Anal fistula is increasingly prevalent due to modern lifestyle factors,and surgery remains the primary treatment.However,the rising incidence of antibiotic resistance,particularly to cefuroxime,complicates ...BACKGROUND Anal fistula is increasingly prevalent due to modern lifestyle factors,and surgery remains the primary treatment.However,the rising incidence of antibiotic resistance,particularly to cefuroxime,complicates perioperative management.The role of gut microbiota in influencing this resistance is not well understood.AIM To investigate the relationship between gut microbiota composition and cefuroxime resistance in anal fistula patients and to assess probiotic intervention impact.METHODS This study included 30 anal fistula patients categorized into cefuroxime-sensitive(Cefur-S)and cefuroxime-resistant(Cefur-NS)groups.Gut microbiota samples were collected during colonoscopy,and 16S ribosomal DNA sequencing was performed to analyze microbial diversity.Patients in the Cefur-NS group received a 7-day course of Clostridium butyricum tablets.Post-intervention,microbial composition and cefuroxime resistance were reassessed.RESULTS Alpha and beta diversity analyses showed no significant differences in microbial diversity between the Cefur-S and Cefur-NS groups.However,effect size analysis identified Roseburia and Butyricicoccus as dominant genera in the Cefur-S group,with higher butyrate production potentially protecting against cefuroxime resistance.Post-intervention,the Cefur-NS group showed a significant reduction in cefuroxime resistance,improved stool consistency,and reduced bowel movement frequency.CONCLUSION This study suggests that specific gut microbiota,particularly Butyricicoccus and Roseburia,may mitigate cefuroxime resistance in anal fistula patients by increasing butyrate production.Probiotic intervention targeting gut microbiota composition presents a promising strategy for reducing antibiotic resistance and improving clinical outcomes.展开更多
Objective The nucleolar protein PES1(Pescadillo homolog 1)plays critical roles in ribosome biogenesis and cell cycle regulation,yet its involvement in cellular senescence remains poorly understood.This study aimed to ...Objective The nucleolar protein PES1(Pescadillo homolog 1)plays critical roles in ribosome biogenesis and cell cycle regulation,yet its involvement in cellular senescence remains poorly understood.This study aimed to comprehensively investigate the functional consequences of PES1 suppression in cellular senescence and elucidate the molecular mechanisms underlying its regulatory role.Methods Initially,we assessed PES1 expression patterns in two distinct senescence models:replicative senescent mouse embryonic fibroblasts(MEFs)and doxorubicin-induced senescent human hepatocellular carcinoma HepG2 cells.Subsequently,PES1 expression was specifically downregulated using siRNA-mediated knockdown in these cell lines as well as additional relevant cell types.Cellular proliferation and senescence were assessed by EdU incorporation and SA-β-gal staining assays,respectively.The expression of senescence-associated proteins(p53,p21,and Rb)and SASP factors(IL-6,IL-1β,and IL-8)were analyzed by Western blot or qPCR.Furthermore,Northern blot and immunofluorescence were employed to evaluate pre-rRNA processing and nucleolar morphology.Results PES1 expression was significantly downregulated in senescent MEFs and HepG2 cells.PES1 knockdown resulted in decreased EdU-positive cells and increased SA-β-gal-positive cells,indicating proliferation inhibition and senescence induction.Mechanistically,PES1 suppression activated the p53-p21 pathway without affecting Rb expression,while upregulating IL-6,IL-1β,and IL-8 production.Notably,PES1 depletion impaired pre-rRNA maturation and induced nucleolar stress,as evidenced by aberrant nucleolar morphology.Conclusion Our findings demonstrate that PES1 deficiency triggers nucleolar stress and promotes p53-dependent(but Rb-independent)cellular senescence,highlighting its crucial role in maintaining nucleolar homeostasis and regulating senescence-associated pathways.展开更多
Background:The study aimed to explore the clinical value of mitochondrial ribosomal protein L18(MRPL18)in breast cancer.Methods:Multiple databases were used to validate the expression of MRPL18.The prognostic impact a...Background:The study aimed to explore the clinical value of mitochondrial ribosomal protein L18(MRPL18)in breast cancer.Methods:Multiple databases were used to validate the expression of MRPL18.The prognostic impact and predictive value of MRPL18 were evaluated by using predictive models.Protein-protein interaction(PPI)networks were constructed by using GeneMANIA.Enrichment analysis is used to explore the signaling pathway regulated by MRPL18.Cell counting kit-8(CCK-8)assays,colony formation,migration assays,flow cytometry,and xenograft models were employed to evaluate the role of MRPL18 in tumor progression.The immune response of MRPL18 was examined using correlation analysis.Results:High levels of MRPL18 are considered a risk factor in breast cancer.In vitro and in vivo studies demonstrated that MRPL18 promotes proliferation and migration in breast cancer.Besides,results found that MRPL18 promotes tumor growth through the activation of phosphatidylinositol 3-kinase(PI3K).Furthermore,high MRPL18 expression was linked to reduced immunotherapy efficacy,as indicated by correlations with immune checkpoints and immune-infiltrating patterns.Conclusion:MRPL18 promotes the progression of breast cancer.展开更多
BACKGROUND Gastric cancer(GC)and head and neck squamous cell carcinoma(HNSCC)are common malignancies with high morbidity and mortality rates.Traditional treatments often yield limited efficacy,especially in advanced c...BACKGROUND Gastric cancer(GC)and head and neck squamous cell carcinoma(HNSCC)are common malignancies with high morbidity and mortality rates.Traditional treatments often yield limited efficacy,especially in advanced cases.Recent advancements in immunotherapy,particularly immune checkpoint inhibitors targeting programmed death-ligand 1(PD-L1),have shown promise.However,the expression and interaction of pescadillo ribosomal biogenesis factor 1(PES1)and PD-L1 in these cancers remain unclear.Understanding their roles could provide new insights into tumor biology and improve therapeutic strategies.AIM To investigate the expression levels of PES1 and PD-L1 in tumor tissues of patients with GC and HNSCC.METHODS A total of 58 cases of GC and HNSCC undergoing surgical resection were selected from January 2022 to January 2024.Paraffin specimens of GC and HNSCC tissues were taken from the patients,and the sections were subjected to staining with immunohistochemistry and hematoxylin-eosin staining,and the protein expression of PES1 and PD-L1 was observed microscopically.RESULTS Among 58 GC and HNSCC tissues,30 cases were positive and 28 cases were negative for PES1 expression,and 34 cases were positive and 24 cases were negative for PD-L1 expression.The positive expression rates of PES1 and PDL1 were 51.72% and 58.62%,respectively.PES1 expression was correlated with the TNM stage,lymph node metastasis,and the depth of infiltration(P<0.05),and PD-L1 expression was correlated with the differentiation degree,lymph node metastasis,and infiltration depth(P<0.05).CONCLUSION PES1 and PD-L1 were positively expressed in GC and HNSCC tissues and correlated with clinical features.They may serve as potential biomarkers for immune-targeted therapies.展开更多
High expression of pescadillo ribosomal biogenesis factor 1(PES1)has been re-ported across multiple cancer types and is significantly associated with poor prog-nosis.Hu et al in their recent paper described their inve...High expression of pescadillo ribosomal biogenesis factor 1(PES1)has been re-ported across multiple cancer types and is significantly associated with poor prog-nosis.Hu et al in their recent paper described their investigation of PES1 in gastric cancer and head and neck squamous cell carcinoma,demonstrating positive cor-relations between PES1 and programmed death-ligand 1(PD-L1)expression(51.72%for PES1 and 58.62%for PD-L1),as well as associations with lymph node metastasis and tumor invasion depth.However,the relationship between PES1 and PD-L1 remains incompletely defined.To further address this gap,we ana-lyzed The Cancer Genome Atlas gastric adenocarcinoma dataset and found a negative correlation between PES1 expression and CD8+T cell infiltration,along-side a positive correlation with PD-L1 expression.Based on prior findings,we hypothesize that PES1 may regulate PD-L1 through the phosphatidylinositol 3-kinase/protein kinase B pathway or cellular Myc-mediated mechanisms.While these pathways require experimental validation,our observations highlight PES1 as a potential regulator of immune evasion and a promising target for cancer immunotherapy.展开更多
Ribosomally synthesized and post-translationally modified peptides(RiPPs)constitute a vast and diverse family of bioactive peptides.These peptides,synthesized by ribosomes and subsequently modified by various tailorin...Ribosomally synthesized and post-translationally modified peptides(RiPPs)constitute a vast and diverse family of bioactive peptides.These peptides,synthesized by ribosomes and subsequently modified by various tailoring enzymes,possess a wide chemical space.Among these modifications,radical S-adenosylmethionine(rSAM)enzymes employ unique radical chemistry to introduce a variety of novel peptide structures,which are crucial for their activity.This review examines the major types of modifications in RiPPs catalyzed by rSAM enzymes,incorporating recent advancements in protein structure analysis techniques and computational methods.Additionally,it elucidates the diverse catalytic mechanisms and substrate selectivity of these enzymes through an analysis of the latest crystal structures.展开更多
Protein biosynthesis by the ribosome is a fundamental biological process in living systems.Recent studies suggest that ribosomal subunits also play essential roles in cell growth and differentiation beyond their roles...Protein biosynthesis by the ribosome is a fundamental biological process in living systems.Recent studies suggest that ribosomal subunits also play essential roles in cell growth and differentiation beyond their roles in protein translation.The ribosomal subunit RPS6 has been studied for more than 50 years in various organisms,but little is known about its specific roles in certain signaling pathways.In this study,we focused on the functions of Arabidopsis RPS6A in auxin-related root growth and development.The rps6a mutant presented a series of auxin-deficient phenotypes,such as shortened primary roots,reduced lateral root numbers,and defective vasculatures.Treatment of the rps6a mutant with various concentrations of auxin and its analogs did not restore the root defect phenotypes,suggesting a defect in the auxin signaling pathway.Further cell biological and global transcriptome analyses revealed that auxin signaling was weakened in the rps6a mutant and that there was a reduced abundance of PIN-FORMED(PIN)auxin transporters.Our work provides insights into the role of the protein biosynthesis pathway involved in auxin signaling.展开更多
The conventional theory of concerted evolution has been used to explain the lack of sequence variation in ribosomal RNA(rRNA)genes across diverse eukaryotic species.However,recent investigations into rRNA genes in fla...The conventional theory of concerted evolution has been used to explain the lack of sequence variation in ribosomal RNA(rRNA)genes across diverse eukaryotic species.However,recent investigations into rRNA genes in flatfish genome have resulted in controversial findings.This study focuses on 18S rRNA genes of the widely distributed tongue sole,Cynoglossus abbreviatus(Pleuronectiformes:Cynoglossidae),aiming to explore sequence polymorphism.Five distinct 18S rDNA sequence types(Type A,B,R1,R2,and R3)were identified,suggesting a departure from concerted evolution.A combination of general criteria and variations in highly conserved regions were employed to detect pseudogenes.The results pinpointed Type A sequences as potential pseudogenes due to significant sequence variations and deviations in secondary structure within highly conserved regions.Three types(Type R1,R2,and R3)were identified as recombinants between Type A and B sequences,with simple crossing over and gene conversion as the most likely recombination mechanisms.These findings not only contribute to rRNA pseudogene identification but also shed light on the evolutionary dynamics of rRNA genes in teleost genomes.展开更多
Objective:To determine the genetic diversity of Plasmodium(P.)knowlesi isolates from Sabah,Malaysian Borneo and Peninsular Malaysia,targeting the S-type SSU rRNA gene and including aspects of natural selection and hap...Objective:To determine the genetic diversity of Plasmodium(P.)knowlesi isolates from Sabah,Malaysian Borneo and Peninsular Malaysia,targeting the S-type SSU rRNA gene and including aspects of natural selection and haplotype.Methods:Thirty-nine blood samples infected with P.knowlesi were collected in Sabah,Malaysian Borneo and Peninsular Malaysia.The S-type SSU rRNA gene was amplified using polymerase chain reaction,cloned into a vector,and sequenced.The natural selection and haplotype of the S-type SSU rRNA gene sequences were determined using DnaSP v6 and illustrated using NETWORK v10.This study's 39 S-type SSU rRNA sequences and eight sequences from the Genbank database were subjected to phylogenetic analysis using MEGA 11.Results:Overall,the phylogenetic analysis showed no evidence of a geographical cluster of P.knowlesi isolates from different areas in Malaysia based on the S-type SSU rRNA gene sequences.The S-type SSU rRNA gene sequences were relatively conserved and with a purifying effect.Haplotype sharing of the S-type SSU rRNA gene was observed between the P.knowlesi isolates in Sabah,Malaysian Borneo,but not between Sabah,Malaysian Borneo and Peninsular Malaysia.Conclusions:This study suggests that the S-type SSU rRNA gene of P.knowlesi isolates in Sabah,Malaysian Borneo,and Peninsular Malaysia has fewer polymorphic sites,representing the conservation of the gene.These features make the S-type SSU rRNA gene suitable for comparative studies,such as determining the evolutionary relationships and common ancestry among P.knowlesi species.展开更多
Objectives To identify the 5'untranslated region of Zika virus(ZIKV 5'UTR)RNA-binding proteins and to investigate the impact of the binding protein on the activity of internal ribosomal entry site(IRES)located...Objectives To identify the 5'untranslated region of Zika virus(ZIKV 5'UTR)RNA-binding proteins and to investigate the impact of the binding protein on the activity of internal ribosomal entry site(IRES)located in ZIKV 5'UTR and virus production.Methods Interacting proteins in U251 cells were captured using tRSA-tagged ZIKV 5'UTR RNA and tRSA-ZIKV 5'UTR RNA-binding proteins were visualized by SDS-PAGE silver staining,Subsequently,liquid chromatographytandem mass spectrometry(LC-MS/MS),bioinformatics analysis,and Western blot were used to identify the candidate proteins binding to ZIKV 5'UTR.Dicistronic expression assay and plaque forming assay were performed to analyze the effect of the binding protein on ZIKV IRES activity and ZIKV production,respecitvely.Results tRSA RNA pull-down assay,LC-MS/MS,and Western blot analysis showed that polypyrimidine tractbinding protein(PTB)bound to the ZIKV 5'UTR.Furthermore,dual luciferase reporter assay revealed that overexpression of PTB significantly enhanced the IRES activity of ZIKV(t=10.220,P<0.001),while PTB knockdown had the opposite effect(t=4.897,P<0.01).Additionally,virus plaque forming assay demonstrated that up-regulation of PTB expression significantly enhanced viral titer(t=6.400,P<0.01),whereas reducing PTB expression level weakened virus infectivity(t=5.055,P<0.01).Conclusion PTB positively interacts with the ZIKV 5'UTR and enhances IRES activity and virus production.展开更多
This study investigated the mechanism underlying electroacupuncture therapy for vascular dementia through electroacupuncture at the acupoints of Baihui （DU20）, Dazhui （DU14）, and bilateral Shenshu （BL23） in a ra...This study investigated the mechanism underlying electroacupuncture therapy for vascular dementia through electroacupuncture at the acupoints of Baihui （DU20）, Dazhui （DU14）, and bilateral Shenshu （BL23） in a rat model of vascular dementia produced by bilateral middle cerebral artery occlusion. Morris water maze test showed that electroacupuncture improved the learning ability of vascular dementia rats. Western blot assay revealed that the expression of p70 ribosomal protein S6 kinase and ribosomal protein S6 in vascular dementia rats was significantly increased after electroacupuncture, compared with the model group that was not treated with acupuncture. The average escape latency was also shortened after electroacupuncture, and escape strategies in the spatial probe test improved from edge and random searches, to linear and trending swim pathways. The experimental findings indicate that electroacupuncture improves learning and memory ability by up-regulating expression of p70 ribosomal protein S6 kinase and ribosomal protein S6 in the hippocampus of vascular dementia rats.展开更多
Filamentous Bangia,which are distributed extensively throughout the world,have simple and similar morphological characteristics.Scientists can classify these organisms using molecular markers in combination with morph...Filamentous Bangia,which are distributed extensively throughout the world,have simple and similar morphological characteristics.Scientists can classify these organisms using molecular markers in combination with morphology.We successfully sequenced the complete nuclear ribosomal DNA.approximately 13 kb in length,from a marine Bangia population.We further analyzed the small subunit ribosomal DNA gene(nrSSU) and the internal transcribed spacer(ITS) sequence regions along with nine other marine,and two freshwater Bangia samples from China.Pairwise distances of the nrSSU and 5.8S ribosomal DNA gene sequences show the marine samples grouping together with low divergences(0-0.003;0-0.006,respectively) from each other,but high divergences(0.123-0.126;0.198,respectively) from freshwater samples.An exception is the marine sample collected from Weihai,which shows high divergence from both other marine samples(0.063-0.065;0.129,respectively) and the freshwater samples(0.097;0.120,respectively).A maximum likelihood phylogenetic tree based on a combined SSU-ITS dataset with maximum likelihood method shows the samples divided into three clades,with the two marine sample clades containing Bangia spp.from North America,Europe,Asia,and Australia;and one freshwater clade,containing Bangia atropurpurea from North America and China.展开更多
[Objective] ＂Tapping panel dryness （TPD）＂, a syndrome known as tapping incision blocked partly or entirely during latex exploiting, has become the most important factor causing great losses for rubber production. ...[Objective] ＂Tapping panel dryness （TPD）＂, a syndrome known as tapping incision blocked partly or entirely during latex exploiting, has become the most important factor causing great losses for rubber production. Aiming to elucidate the molecular mechanism of tapping panel dryness occurrence, this study carried out molecular cloning and bioinformatical analysis of a mRPL21 cDNA sequence, a gene associated with TPD. [Method] In a preliminary study, an expressed sequence tag （EST） encoding a deduced protein homologous to mitochondrial 50S ribosomal protein L21 （mRPL21）, which showed to be down-regulated in the latex of TPD-affected rubber trees, was isolated by suppression subtractive hybridization （SSH）. After ESTs assembling and RT-PCR validation, an 853 bp cDNA sequence with an open reading frame （ORF） was cloned, which was named as HbmRPL21 under GenBank accession number of HM230670. [Result] Bioinformatical analysis suggests that HbmRPL21 encodes a deduced polypeptide of 271 amino acids with a theoretical molecular weight （Mw） of 30.52 kDa and isolectric point （pI） of 8.40, and HbmRPL21 is a mitochondrion-targeted protein with a conserved domain of Ribosomal_L21p involving translation. Homology analysis reveals high amino acid sequence identity of mRPL21 from plants, while diversity of that between plant and animal kingdom. [Conclusion] This study laid the basis for further revealing the biological functions of mRPL21 in TPD-affected rubber trees.展开更多
Chromatin structure is important for controlling gene expression, but mechanisms underlying chromatin remodel- ing are not fully understood. Here we report that an FKBP （FK506 binding protein） type immunophilin, AtF...Chromatin structure is important for controlling gene expression, but mechanisms underlying chromatin remodel- ing are not fully understood. Here we report that an FKBP （FK506 binding protein） type immunophilin, AtFKBP53, possesses histone chaperone activity and is required for repressing ribosomal gene expression in Arabidopsis. The At- FKBP53 protein is a multidomain FKBP with a typical peptidylprolyl isomerase （PPIase） domain and several highly charged domains. Using nucleosome assembly assays, we showed that AtFKBP53 has histone chaperone activity and the charged acidic domains are sufficient for the activity. We show that AtFKBP53 interacts with histone H3 through the acidic domains, whereas the PPIase domain is dispensable for histone chaperone activity or histone binding. Ri- bosomal RNA gene （18S rDNA） is overexpressed when AtFKBP53 activity is reduced or eliminated in Arabidopsis plants. Chromatin immunoprecipitation assay showed that AtFKBP53 is associated with the 18S rDNA gene chro- matin, implicating that AtFKBP53 represses rRNA genes at the chromatin level. This study identifies a new histone chaperone in plants that functions in chromatin remodeling and regulation of transcription.展开更多
Fargesia,the largest genus within the temperate bamboo tribe Arundinarieae,has more than 90 species mainly distributed in the mountains of Southwest China.The Fargesia bamboos are important components of the subalpine...Fargesia,the largest genus within the temperate bamboo tribe Arundinarieae,has more than 90 species mainly distributed in the mountains of Southwest China.The Fargesia bamboos are important components of the subalpine forest ecosystems that provide food and habitat for many endangered animals,including the giant panda.However,species-level identification of Fargesia is difficult.Moreover,the rapid radiation and slow molecular evolutionary rate of Fargesia pose a significant challenge to using DNA barcoding with standard plant barcodes(rbcL,matK,and ITS) in bamboos.With progress in the sequencing technologies,complete plastid genomes(plastomes) and nuclear ribosomal DNA(nrDNA)sequences have been proposed as organelle barcodes for species identification;however,these have not been tested in bamboos.We collected 196 individuals representing 62 species of Fargesia to comprehensively evaluate the discriminatory power of plastomes and nrDNA sequences compared to standard barcodes.Our analysis indicates that complete plastomes have substantially higher discriminatory power(28.6%) than standard barcodes(5.7%),whereas nrDNA sequences show a moderate improvement(65.4%) compared to ITS(47.2%).We also found that nuclear markers performed better than plastid markers,and ITS alone had higher discriminatory power than complete plastomes.The study also demonstrated that plastomes and nrDNA sequences can contribute to intrageneric phylogenetic resolution in Fargesia.However,neither of these sequences were able to discriminate all the sampled species,and therefore,more nuclear markers need to be identified.展开更多
The 18S ribosomal DNA gene （18S rDNA） sequences （approxtmately 1300 bp in length） were amplified from the DNA extracted from the free-living marine nematodes collected from the inter-tidal sediment of Qingdao coas...The 18S ribosomal DNA gene （18S rDNA） sequences （approxtmately 1300 bp in length） were amplified from the DNA extracted from the free-living marine nematodes collected from the inter-tidal sediment of Qingdao coast in bulk with nematode specific primers. The PCR products were cloned, re-amplified, digested with Rsa I and Hin61 restriction endonucleases and separated in agarose gel. Among 17 restriction fragment length types, types 1, 2 and 6 covered 61.2%, 14.4% and 9.3% of the clones analyzed, respectively, while the remaining 14 only covered 21 clones, which accounted for 15.1% of the total. Twenty-four representative clones were sequenced and phylogenetically analyzed by referring to those currently available in RDP and GenBank databases. Although it was hard to assign these sequences to known species or genera due to the lack of the 18S rDNA sequence data of known marine free-living nematodes, the obtained sequences were assigned to the nematodes of Adenophorea. Among them, twelve sequences were close to Pontonema vulgate and Adoncholaimus sp., four to Daptonema procerus and two （identical） to Enoplus brews. Our results showed that free-living marine nematode diversities could be determined by PCR retrieving and analysis of the 18S rDNA sequences and an 18S rDNA sequence could be assigned to a species or a genus only if the 18S rDNA sequences of the free-living marine nematodes were accumulated to some extent.展开更多
Ribosomes are abundant,large RNA-protein complexes that are the sites of all protein synthesis in cells.Defects in ribosomal proteins(RPs),including proteoforms arising from genetic variations,alternative splicing of ...Ribosomes are abundant,large RNA-protein complexes that are the sites of all protein synthesis in cells.Defects in ribosomal proteins(RPs),including proteoforms arising from genetic variations,alternative splicing of RNA transcripts,post-translational modifications and alterations of protein expression level,have been linked to a diverse range of diseases,including cancer and aging.Comprehensive characterization of ribosomal proteoforms is challenging but important for the discovery of potential disease biomarkers or protein targets.In the present work,using E.coli 70S RPs as an example,we first developed a top-down proteomics approach on a Waters Synapt G2 Si mass spectrometry(MS)system,and then applied it to the HeLa 80S ribosome.The results were complemented by a bottom-up approach.In total,50 out of 55 RPs were identified using the top-down approach.Among these,more than 30 RPs were found to have their N-terminal methionine removed.Additional modifications such as methylation,acetylation,and hydroxylation were also observed,and the modification sites were identified by bottomup MS.In a HeLa 80S ribosomal sample,we identified 98 ribosomal proteoforms,among which multiple truncated 80S ribosomal proteoforms were observed,the type of information which is often overlooked by bottom-up experiments.Although their relevance to diseases is not yet known,the integration of topdown and bottom-up proteomics approaches paves the way for the discovery of proteoform-specific disease biomarkers or targets.展开更多
基金Supported by the Jiaxing Science and Technology Project,No.2023AD11016 and No.2023AD31028.
文摘BACKGROUND Anal fistula is increasingly prevalent due to modern lifestyle factors,and surgery remains the primary treatment.However,the rising incidence of antibiotic resistance,particularly to cefuroxime,complicates perioperative management.The role of gut microbiota in influencing this resistance is not well understood.AIM To investigate the relationship between gut microbiota composition and cefuroxime resistance in anal fistula patients and to assess probiotic intervention impact.METHODS This study included 30 anal fistula patients categorized into cefuroxime-sensitive(Cefur-S)and cefuroxime-resistant(Cefur-NS)groups.Gut microbiota samples were collected during colonoscopy,and 16S ribosomal DNA sequencing was performed to analyze microbial diversity.Patients in the Cefur-NS group received a 7-day course of Clostridium butyricum tablets.Post-intervention,microbial composition and cefuroxime resistance were reassessed.RESULTS Alpha and beta diversity analyses showed no significant differences in microbial diversity between the Cefur-S and Cefur-NS groups.However,effect size analysis identified Roseburia and Butyricicoccus as dominant genera in the Cefur-S group,with higher butyrate production potentially protecting against cefuroxime resistance.Post-intervention,the Cefur-NS group showed a significant reduction in cefuroxime resistance,improved stool consistency,and reduced bowel movement frequency.CONCLUSION This study suggests that specific gut microbiota,particularly Butyricicoccus and Roseburia,may mitigate cefuroxime resistance in anal fistula patients by increasing butyrate production.Probiotic intervention targeting gut microbiota composition presents a promising strategy for reducing antibiotic resistance and improving clinical outcomes.
文摘Objective The nucleolar protein PES1(Pescadillo homolog 1)plays critical roles in ribosome biogenesis and cell cycle regulation,yet its involvement in cellular senescence remains poorly understood.This study aimed to comprehensively investigate the functional consequences of PES1 suppression in cellular senescence and elucidate the molecular mechanisms underlying its regulatory role.Methods Initially,we assessed PES1 expression patterns in two distinct senescence models:replicative senescent mouse embryonic fibroblasts(MEFs)and doxorubicin-induced senescent human hepatocellular carcinoma HepG2 cells.Subsequently,PES1 expression was specifically downregulated using siRNA-mediated knockdown in these cell lines as well as additional relevant cell types.Cellular proliferation and senescence were assessed by EdU incorporation and SA-β-gal staining assays,respectively.The expression of senescence-associated proteins(p53,p21,and Rb)and SASP factors(IL-6,IL-1β,and IL-8)were analyzed by Western blot or qPCR.Furthermore,Northern blot and immunofluorescence were employed to evaluate pre-rRNA processing and nucleolar morphology.Results PES1 expression was significantly downregulated in senescent MEFs and HepG2 cells.PES1 knockdown resulted in decreased EdU-positive cells and increased SA-β-gal-positive cells,indicating proliferation inhibition and senescence induction.Mechanistically,PES1 suppression activated the p53-p21 pathway without affecting Rb expression,while upregulating IL-6,IL-1β,and IL-8 production.Notably,PES1 depletion impaired pre-rRNA maturation and induced nucleolar stress,as evidenced by aberrant nucleolar morphology.Conclusion Our findings demonstrate that PES1 deficiency triggers nucleolar stress and promotes p53-dependent(but Rb-independent)cellular senescence,highlighting its crucial role in maintaining nucleolar homeostasis and regulating senescence-associated pathways.
基金supported by grants from the Key Project of Scientific Research Plan of Hunan Provincial Health Commission(C202301047982,Wei Du)Changde City Science and Technology Innovation Guidance Plan Project(2022ZD39,Wei Du)+1 种基金the Wings Scientific and Technological Foundation of The First People’s Hospital of Changde City(2022ZZ05,Wei Du,2024ZC02,Rong Xu,Z2025ZC04,Hailong Li)The Science and Technology Innovation Program of Changde City(2024ZD248,Rong Xu,2024ZD200,Yun Peng).
文摘Background:The study aimed to explore the clinical value of mitochondrial ribosomal protein L18(MRPL18)in breast cancer.Methods:Multiple databases were used to validate the expression of MRPL18.The prognostic impact and predictive value of MRPL18 were evaluated by using predictive models.Protein-protein interaction(PPI)networks were constructed by using GeneMANIA.Enrichment analysis is used to explore the signaling pathway regulated by MRPL18.Cell counting kit-8(CCK-8)assays,colony formation,migration assays,flow cytometry,and xenograft models were employed to evaluate the role of MRPL18 in tumor progression.The immune response of MRPL18 was examined using correlation analysis.Results:High levels of MRPL18 are considered a risk factor in breast cancer.In vitro and in vivo studies demonstrated that MRPL18 promotes proliferation and migration in breast cancer.Besides,results found that MRPL18 promotes tumor growth through the activation of phosphatidylinositol 3-kinase(PI3K).Furthermore,high MRPL18 expression was linked to reduced immunotherapy efficacy,as indicated by correlations with immune checkpoints and immune-infiltrating patterns.Conclusion:MRPL18 promotes the progression of breast cancer.
文摘BACKGROUND Gastric cancer(GC)and head and neck squamous cell carcinoma(HNSCC)are common malignancies with high morbidity and mortality rates.Traditional treatments often yield limited efficacy,especially in advanced cases.Recent advancements in immunotherapy,particularly immune checkpoint inhibitors targeting programmed death-ligand 1(PD-L1),have shown promise.However,the expression and interaction of pescadillo ribosomal biogenesis factor 1(PES1)and PD-L1 in these cancers remain unclear.Understanding their roles could provide new insights into tumor biology and improve therapeutic strategies.AIM To investigate the expression levels of PES1 and PD-L1 in tumor tissues of patients with GC and HNSCC.METHODS A total of 58 cases of GC and HNSCC undergoing surgical resection were selected from January 2022 to January 2024.Paraffin specimens of GC and HNSCC tissues were taken from the patients,and the sections were subjected to staining with immunohistochemistry and hematoxylin-eosin staining,and the protein expression of PES1 and PD-L1 was observed microscopically.RESULTS Among 58 GC and HNSCC tissues,30 cases were positive and 28 cases were negative for PES1 expression,and 34 cases were positive and 24 cases were negative for PD-L1 expression.The positive expression rates of PES1 and PDL1 were 51.72% and 58.62%,respectively.PES1 expression was correlated with the TNM stage,lymph node metastasis,and the depth of infiltration(P<0.05),and PD-L1 expression was correlated with the differentiation degree,lymph node metastasis,and infiltration depth(P<0.05).CONCLUSION PES1 and PD-L1 were positively expressed in GC and HNSCC tissues and correlated with clinical features.They may serve as potential biomarkers for immune-targeted therapies.
文摘High expression of pescadillo ribosomal biogenesis factor 1(PES1)has been re-ported across multiple cancer types and is significantly associated with poor prog-nosis.Hu et al in their recent paper described their investigation of PES1 in gastric cancer and head and neck squamous cell carcinoma,demonstrating positive cor-relations between PES1 and programmed death-ligand 1(PD-L1)expression(51.72%for PES1 and 58.62%for PD-L1),as well as associations with lymph node metastasis and tumor invasion depth.However,the relationship between PES1 and PD-L1 remains incompletely defined.To further address this gap,we ana-lyzed The Cancer Genome Atlas gastric adenocarcinoma dataset and found a negative correlation between PES1 expression and CD8+T cell infiltration,along-side a positive correlation with PD-L1 expression.Based on prior findings,we hypothesize that PES1 may regulate PD-L1 through the phosphatidylinositol 3-kinase/protein kinase B pathway or cellular Myc-mediated mechanisms.While these pathways require experimental validation,our observations highlight PES1 as a potential regulator of immune evasion and a promising target for cancer immunotherapy.
基金supported by the National Key Research and Development Program of China(No.2023YFA0916000)the National Natural Science Foundation of China(No.32371324)the High-level Talent Startup Fund provided by China Pharmaceutical University.
文摘Ribosomally synthesized and post-translationally modified peptides(RiPPs)constitute a vast and diverse family of bioactive peptides.These peptides,synthesized by ribosomes and subsequently modified by various tailoring enzymes,possess a wide chemical space.Among these modifications,radical S-adenosylmethionine(rSAM)enzymes employ unique radical chemistry to introduce a variety of novel peptide structures,which are crucial for their activity.This review examines the major types of modifications in RiPPs catalyzed by rSAM enzymes,incorporating recent advancements in protein structure analysis techniques and computational methods.Additionally,it elucidates the diverse catalytic mechanisms and substrate selectivity of these enzymes through an analysis of the latest crystal structures.
基金supported by the National Natural Science Foundation of China(32321001)the Forestry Bureau of Anhui Province(AHLYJBGS-2024-01)+3 种基金the Center for Advanced Interdisciplinary Science and Biomedicine of IHM,the Division of Life Sciences and Medicine,the University of Science and Technology of China(QYPY20220012)the USTC Research Funds of the Double First-Class Initiative(YD9100002016)start-up funding from the University of Science and Technology of China and the Chinese Academy of Sciences(GG9100007007,KY9100000026,KY9100000051,KJ2070000079)the Fundamental Research Funds for the Central Universities(WK9100000021)。
文摘Protein biosynthesis by the ribosome is a fundamental biological process in living systems.Recent studies suggest that ribosomal subunits also play essential roles in cell growth and differentiation beyond their roles in protein translation.The ribosomal subunit RPS6 has been studied for more than 50 years in various organisms,but little is known about its specific roles in certain signaling pathways.In this study,we focused on the functions of Arabidopsis RPS6A in auxin-related root growth and development.The rps6a mutant presented a series of auxin-deficient phenotypes,such as shortened primary roots,reduced lateral root numbers,and defective vasculatures.Treatment of the rps6a mutant with various concentrations of auxin and its analogs did not restore the root defect phenotypes,suggesting a defect in the auxin signaling pathway.Further cell biological and global transcriptome analyses revealed that auxin signaling was weakened in the rps6a mutant and that there was a reduced abundance of PIN-FORMED(PIN)auxin transporters.Our work provides insights into the role of the protein biosynthesis pathway involved in auxin signaling.
基金The Basic Scientific Research Operating Expenses of Zhejiang Provincial Universities under contract 2021JZ003the Zhoushan Science and Technology Bureau under contract No.2021C21007+1 种基金the Natural Science Foundation of Zhejiang Province under contract Y21C190023the National Natural Science Foundation of China under contract 31272273.
文摘The conventional theory of concerted evolution has been used to explain the lack of sequence variation in ribosomal RNA(rRNA)genes across diverse eukaryotic species.However,recent investigations into rRNA genes in flatfish genome have resulted in controversial findings.This study focuses on 18S rRNA genes of the widely distributed tongue sole,Cynoglossus abbreviatus(Pleuronectiformes:Cynoglossidae),aiming to explore sequence polymorphism.Five distinct 18S rDNA sequence types(Type A,B,R1,R2,and R3)were identified,suggesting a departure from concerted evolution.A combination of general criteria and variations in highly conserved regions were employed to detect pseudogenes.The results pinpointed Type A sequences as potential pseudogenes due to significant sequence variations and deviations in secondary structure within highly conserved regions.Three types(Type R1,R2,and R3)were identified as recombinants between Type A and B sequences,with simple crossing over and gene conversion as the most likely recombination mechanisms.These findings not only contribute to rRNA pseudogene identification but also shed light on the evolutionary dynamics of rRNA genes in teleost genomes.
基金This study was supported by the Ministry of Higher Education,Malaysia(FRGS0322-SG-1/2013)Universiti Malaysia Sabah(GUG0521-2/2020).
文摘Objective:To determine the genetic diversity of Plasmodium(P.)knowlesi isolates from Sabah,Malaysian Borneo and Peninsular Malaysia,targeting the S-type SSU rRNA gene and including aspects of natural selection and haplotype.Methods:Thirty-nine blood samples infected with P.knowlesi were collected in Sabah,Malaysian Borneo and Peninsular Malaysia.The S-type SSU rRNA gene was amplified using polymerase chain reaction,cloned into a vector,and sequenced.The natural selection and haplotype of the S-type SSU rRNA gene sequences were determined using DnaSP v6 and illustrated using NETWORK v10.This study's 39 S-type SSU rRNA sequences and eight sequences from the Genbank database were subjected to phylogenetic analysis using MEGA 11.Results:Overall,the phylogenetic analysis showed no evidence of a geographical cluster of P.knowlesi isolates from different areas in Malaysia based on the S-type SSU rRNA gene sequences.The S-type SSU rRNA gene sequences were relatively conserved and with a purifying effect.Haplotype sharing of the S-type SSU rRNA gene was observed between the P.knowlesi isolates in Sabah,Malaysian Borneo,but not between Sabah,Malaysian Borneo and Peninsular Malaysia.Conclusions:This study suggests that the S-type SSU rRNA gene of P.knowlesi isolates in Sabah,Malaysian Borneo,and Peninsular Malaysia has fewer polymorphic sites,representing the conservation of the gene.These features make the S-type SSU rRNA gene suitable for comparative studies,such as determining the evolutionary relationships and common ancestry among P.knowlesi species.
文摘Objectives To identify the 5'untranslated region of Zika virus(ZIKV 5'UTR)RNA-binding proteins and to investigate the impact of the binding protein on the activity of internal ribosomal entry site(IRES)located in ZIKV 5'UTR and virus production.Methods Interacting proteins in U251 cells were captured using tRSA-tagged ZIKV 5'UTR RNA and tRSA-ZIKV 5'UTR RNA-binding proteins were visualized by SDS-PAGE silver staining,Subsequently,liquid chromatographytandem mass spectrometry(LC-MS/MS),bioinformatics analysis,and Western blot were used to identify the candidate proteins binding to ZIKV 5'UTR.Dicistronic expression assay and plaque forming assay were performed to analyze the effect of the binding protein on ZIKV IRES activity and ZIKV production,respecitvely.Results tRSA RNA pull-down assay,LC-MS/MS,and Western blot analysis showed that polypyrimidine tractbinding protein(PTB)bound to the ZIKV 5'UTR.Furthermore,dual luciferase reporter assay revealed that overexpression of PTB significantly enhanced the IRES activity of ZIKV(t=10.220,P<0.001),while PTB knockdown had the opposite effect(t=4.897,P<0.01).Additionally,virus plaque forming assay demonstrated that up-regulation of PTB expression significantly enhanced viral titer(t=6.400,P<0.01),whereas reducing PTB expression level weakened virus infectivity(t=5.055,P<0.01).Conclusion PTB positively interacts with the ZIKV 5'UTR and enhances IRES activity and virus production.
基金supported by the National Natural Science Foundation of China, No. 81001541
文摘This study investigated the mechanism underlying electroacupuncture therapy for vascular dementia through electroacupuncture at the acupoints of Baihui （DU20）, Dazhui （DU14）, and bilateral Shenshu （BL23） in a rat model of vascular dementia produced by bilateral middle cerebral artery occlusion. Morris water maze test showed that electroacupuncture improved the learning ability of vascular dementia rats. Western blot assay revealed that the expression of p70 ribosomal protein S6 kinase and ribosomal protein S6 in vascular dementia rats was significantly increased after electroacupuncture, compared with the model group that was not treated with acupuncture. The average escape latency was also shortened after electroacupuncture, and escape strategies in the spatial probe test improved from edge and random searches, to linear and trending swim pathways. The experimental findings indicate that electroacupuncture improves learning and memory ability by up-regulating expression of p70 ribosomal protein S6 kinase and ribosomal protein S6 in the hippocampus of vascular dementia rats.
基金Supported by the National Natural Science Foundation of China(Nos.31270256,41276134)the National High Technology Research and Development Program of China(863 Program)(No.2012AA10A406-6)
文摘Filamentous Bangia,which are distributed extensively throughout the world,have simple and similar morphological characteristics.Scientists can classify these organisms using molecular markers in combination with morphology.We successfully sequenced the complete nuclear ribosomal DNA.approximately 13 kb in length,from a marine Bangia population.We further analyzed the small subunit ribosomal DNA gene(nrSSU) and the internal transcribed spacer(ITS) sequence regions along with nine other marine,and two freshwater Bangia samples from China.Pairwise distances of the nrSSU and 5.8S ribosomal DNA gene sequences show the marine samples grouping together with low divergences(0-0.003;0-0.006,respectively) from each other,but high divergences(0.123-0.126;0.198,respectively) from freshwater samples.An exception is the marine sample collected from Weihai,which shows high divergence from both other marine samples(0.063-0.065;0.129,respectively) and the freshwater samples(0.097;0.120,respectively).A maximum likelihood phylogenetic tree based on a combined SSU-ITS dataset with maximum likelihood method shows the samples divided into three clades,with the two marine sample clades containing Bangia spp.from North America,Europe,Asia,and Australia;and one freshwater clade,containing Bangia atropurpurea from North America and China.
基金Supported by the Fundamental Research Funds for Rubber Research Institute, CATAS (1630022011014)Key Science and Technology Project of Hainan Province (90107)+1 种基金Basic Scientific Research Operational Fund for Central-level Public-interest Research Institutes (YWFZX2010-9)Special Fund for Science and Technology Research of Public Welfare Trades ( nyhyzx07-033-1)~~
文摘[Objective] ＂Tapping panel dryness （TPD）＂, a syndrome known as tapping incision blocked partly or entirely during latex exploiting, has become the most important factor causing great losses for rubber production. Aiming to elucidate the molecular mechanism of tapping panel dryness occurrence, this study carried out molecular cloning and bioinformatical analysis of a mRPL21 cDNA sequence, a gene associated with TPD. [Method] In a preliminary study, an expressed sequence tag （EST） encoding a deduced protein homologous to mitochondrial 50S ribosomal protein L21 （mRPL21）, which showed to be down-regulated in the latex of TPD-affected rubber trees, was isolated by suppression subtractive hybridization （SSH）. After ESTs assembling and RT-PCR validation, an 853 bp cDNA sequence with an open reading frame （ORF） was cloned, which was named as HbmRPL21 under GenBank accession number of HM230670. [Result] Bioinformatical analysis suggests that HbmRPL21 encodes a deduced polypeptide of 271 amino acids with a theoretical molecular weight （Mw） of 30.52 kDa and isolectric point （pI） of 8.40, and HbmRPL21 is a mitochondrion-targeted protein with a conserved domain of Ribosomal_L21p involving translation. Homology analysis reveals high amino acid sequence identity of mRPL21 from plants, while diversity of that between plant and animal kingdom. [Conclusion] This study laid the basis for further revealing the biological functions of mRPL21 in TPD-affected rubber trees.
基金We thank Veder Garcia （University of California, Berkeley, USA） for critically reading the paper, Zengyong He for providing the AtFKBP53：：GUS transgenic line and Masami Horikoshi （The University of Tokyo, Japan） for the pET-6His-SpFkbp39P plasmid. This work was supported by grants from the National Science Foundation and US Department of Energy （toSL）.
文摘Chromatin structure is important for controlling gene expression, but mechanisms underlying chromatin remodel- ing are not fully understood. Here we report that an FKBP （FK506 binding protein） type immunophilin, AtFKBP53, possesses histone chaperone activity and is required for repressing ribosomal gene expression in Arabidopsis. The At- FKBP53 protein is a multidomain FKBP with a typical peptidylprolyl isomerase （PPIase） domain and several highly charged domains. Using nucleosome assembly assays, we showed that AtFKBP53 has histone chaperone activity and the charged acidic domains are sufficient for the activity. We show that AtFKBP53 interacts with histone H3 through the acidic domains, whereas the PPIase domain is dispensable for histone chaperone activity or histone binding. Ri- bosomal RNA gene （18S rDNA） is overexpressed when AtFKBP53 activity is reduced or eliminated in Arabidopsis plants. Chromatin immunoprecipitation assay showed that AtFKBP53 is associated with the 18S rDNA gene chro- matin, implicating that AtFKBP53 represses rRNA genes at the chromatin level. This study identifies a new histone chaperone in plants that functions in chromatin remodeling and regulation of transcription.
基金supported by grants from CAS' Largescale Scientific Facilities (Grant No.2017-LSF-GBOWS-02)the Key R & D Program of Yunnan Province,China (Grant No.20210 3AC100003)Ten Thousand Talent Program of Yunnan Province (Grant No.YNWR-QNBJ-2020-297)。
文摘Fargesia,the largest genus within the temperate bamboo tribe Arundinarieae,has more than 90 species mainly distributed in the mountains of Southwest China.The Fargesia bamboos are important components of the subalpine forest ecosystems that provide food and habitat for many endangered animals,including the giant panda.However,species-level identification of Fargesia is difficult.Moreover,the rapid radiation and slow molecular evolutionary rate of Fargesia pose a significant challenge to using DNA barcoding with standard plant barcodes(rbcL,matK,and ITS) in bamboos.With progress in the sequencing technologies,complete plastid genomes(plastomes) and nuclear ribosomal DNA(nrDNA)sequences have been proposed as organelle barcodes for species identification;however,these have not been tested in bamboos.We collected 196 individuals representing 62 species of Fargesia to comprehensively evaluate the discriminatory power of plastomes and nrDNA sequences compared to standard barcodes.Our analysis indicates that complete plastomes have substantially higher discriminatory power(28.6%) than standard barcodes(5.7%),whereas nrDNA sequences show a moderate improvement(65.4%) compared to ITS(47.2%).We also found that nuclear markers performed better than plastid markers,and ITS alone had higher discriminatory power than complete plastomes.The study also demonstrated that plastomes and nrDNA sequences can contribute to intrageneric phylogenetic resolution in Fargesia.However,neither of these sequences were able to discriminate all the sampled species,and therefore,more nuclear markers need to be identified.
基金This study was supported financially by the National Natural Science Foundation of China （No. 40176028）.
文摘The 18S ribosomal DNA gene （18S rDNA） sequences （approxtmately 1300 bp in length） were amplified from the DNA extracted from the free-living marine nematodes collected from the inter-tidal sediment of Qingdao coast in bulk with nematode specific primers. The PCR products were cloned, re-amplified, digested with Rsa I and Hin61 restriction endonucleases and separated in agarose gel. Among 17 restriction fragment length types, types 1, 2 and 6 covered 61.2%, 14.4% and 9.3% of the clones analyzed, respectively, while the remaining 14 only covered 21 clones, which accounted for 15.1% of the total. Twenty-four representative clones were sequenced and phylogenetically analyzed by referring to those currently available in RDP and GenBank databases. Although it was hard to assign these sequences to known species or genera due to the lack of the 18S rDNA sequence data of known marine free-living nematodes, the obtained sequences were assigned to the nematodes of Adenophorea. Among them, twelve sequences were close to Pontonema vulgate and Adoncholaimus sp., four to Daptonema procerus and two （identical） to Enoplus brews. Our results showed that free-living marine nematode diversities could be determined by PCR retrieving and analysis of the 18S rDNA sequences and an 18S rDNA sequence could be assigned to a species or a genus only if the 18S rDNA sequences of the free-living marine nematodes were accumulated to some extent.
基金supported in part by the National Natural Science Foundation of China(Grant Nos.:91953102 and 81872836)Natural Science Foundation of Guangdong Province,China(Grant Nos.:2019A1515011265 and 2022A1515010965)+1 种基金the Fundamental Research Funds for Sun Yat-sen University,China(Grant No.:19ykzd26)Open Project Funding of the State Key Laboratory of Crop Stress Adaptation and Improvement(Grant No.:2020KF05).Huilin Li would like to thank the Pearl River Talent Recruitment Program for support.
文摘Ribosomes are abundant,large RNA-protein complexes that are the sites of all protein synthesis in cells.Defects in ribosomal proteins(RPs),including proteoforms arising from genetic variations,alternative splicing of RNA transcripts,post-translational modifications and alterations of protein expression level,have been linked to a diverse range of diseases,including cancer and aging.Comprehensive characterization of ribosomal proteoforms is challenging but important for the discovery of potential disease biomarkers or protein targets.In the present work,using E.coli 70S RPs as an example,we first developed a top-down proteomics approach on a Waters Synapt G2 Si mass spectrometry(MS)system,and then applied it to the HeLa 80S ribosome.The results were complemented by a bottom-up approach.In total,50 out of 55 RPs were identified using the top-down approach.Among these,more than 30 RPs were found to have their N-terminal methionine removed.Additional modifications such as methylation,acetylation,and hydroxylation were also observed,and the modification sites were identified by bottomup MS.In a HeLa 80S ribosomal sample,we identified 98 ribosomal proteoforms,among which multiple truncated 80S ribosomal proteoforms were observed,the type of information which is often overlooked by bottom-up experiments.Although their relevance to diseases is not yet known,the integration of topdown and bottom-up proteomics approaches paves the way for the discovery of proteoform-specific disease biomarkers or targets.
