BACKGROUND In recent years,many studies have shown that proteasome 26S subunit non-ATPase 6(PSMD6)plays an important role in the occurrence and development of malignant tumours.Unfortunately,there are no reports on th...BACKGROUND In recent years,many studies have shown that proteasome 26S subunit non-ATPase 6(PSMD6)plays an important role in the occurrence and development of malignant tumours.Unfortunately,there are no reports on the evaluation of the potential role of PSMD6 in hepatocellular carcinoma(HCC).AIM To comprehensively evaluate the overexpression pattern and clinical significance of PSMD6 in HCC tissues.METHODS This study integrated PSMD6 mRNA expression profiles from 4672 HCC and 3667 non-HCC tissues,along with immunohistochemical scores from 383 HCC and adjacent tissues,to assess PSMD6 overexpression in HCC.Clustered regularly interspaced short palindromic repeats knockout technology evaluated PSMD6’s essential role in HCC cell growth.Functional enrichment analysis explored the molecular mechanism of PSMD6 abnormalities in HCC.Drug sensitivity analysis and molecular docking analysed the effect of abnormal expression of PSMD6 on the drug sensitivity of HCC cells.RESULTS The results of 41 external and two internal datasets showed that PSMD6 mRNA(SMD=0.26,95%CI:0.09-0.42,P<0.05)and protein(SMD=2.85,95%CI:1.19-4.50,P<0.05)were significantly overexpressed in HCC tissues.The integrated analysis results showed that PSMD6 had a significant overexpression pattern in HCC tissues(SMD=0.40,95%CI:0.15-0.66,P<0.05).PSMD6 knockout inhibited HCC cell growth(chronos scores<-1).Functional enrichment implicated ribosome biogenesis and RNA splicing.Significant enrichment of signalling pathways such as RNA degradation,ribosomes,and chemical carcinogenesis—reactive oxygen species.Drug sensitivity analysis and a molecular docking model showed that high expression of PSMD6 was associated with the tolerance of HCC cells to drugs such as ML323,sepantronium bromide,and GDC0810.Overexpressed PSMD6 effectively distinguished HCC tissues(AUC=0.75,95%CI:0.71-0.79).CONCLUSION This study was the first to discover that PSMD6 was overexpressed in HCC tissues.PSMD6 is essential for the growth of HCC cells and may be involved in ribosome biogenesis and RNA splicing.展开更多
Elucidating protein translational regulation is crucial for understanding cellular function and drug development.A key molecule in protein translation is ribosome,which is a super-molecular complex extensively studied...Elucidating protein translational regulation is crucial for understanding cellular function and drug development.A key molecule in protein translation is ribosome,which is a super-molecular complex extensively studied for more than a half century.The structure and dynamics of ribosome complexes were resolved recently thanks to the development of X-ray crystallography,Cryo-EM,and single molecule biophysics.Current studies of the ribosome have shown multiple functional states,each with a unique conformation.In this study,we analyzed the RNA-protein distances of ribosome(2.5 MDa)complexes and compared these changes among different ribosome complexes.We found that the RNA-protein distance is significantly correlated with the ribosomal functional state.Thus,the analysis of RNA-protein binding distances at important functional sites can distinguish ribosomal functional states and help understand ribosome functions.In particular,the mechanism of translational attenuation by nascent peptides and antibiotics was revealed by the conformational changes of local functional sites.展开更多
Ribosome biogenesis,which takes place mainly in the nucleolus,involves coordinated expression of preribosomal RNAs(pre-rRNAs)and ribosomal proteins,pre-rRNA processing,and subunit assembly with the aid of numerous ass...Ribosome biogenesis,which takes place mainly in the nucleolus,involves coordinated expression of preribosomal RNAs(pre-rRNAs)and ribosomal proteins,pre-rRNA processing,and subunit assembly with the aid of numerous assembly factors.Our previous study showed that the Arabidopsis thaliana protein arginine methyltransferase AtPRMT3 regulates pre-rRNA processing;however,the underlying molecular mechanism remains unknown.Here,we report that AtPRMT3 interacts with Ribosomal Protein S2(RPS2),facilitating processing of the 90S/Small Subunit(SSU)processome and repressing nucleolar stress.We isolated an intragenic suppressor of atprmt3-2,which rescues the developmental defects of atprmt3-2 while produces a putative truncated AtPRMT3 protein bearing the entire N-terminus but lacking an intact enzymatic activity domain We further identified RPS2 as an interacting partner of AtPRMT3,and found that loss-of-function rps2a2b mutants were phenotypically reminiscent of atprmt3,showing pleiotropic developmental defects and aberrant pre-rRNA processing.RPS2B binds directly to pre-rRNAs in the nucleus,and such binding is enhanced in atprmt3-2.Consistently,multiple components of the 90S/SSU processome were more enriched by RPS2B in atprmt3-2,which accounts for early pre-rRNA processing defects and results in nucleolar stress.Collectively,our study uncovered a novel mechanism by which AtPRMT3 cooperates with RPS2B to facilitate the dynamic assembly/disassembly of the 90S/SSU processome during ribosome biogenesis and repress nucleolar stress.展开更多
Elongation factor 4(EF4) is one of the highly conserved translational GTPases, whose functions are largely unknown. Structures of EF4 bound ribosomal PRE-translocation and POST-translocation complexes have both been...Elongation factor 4(EF4) is one of the highly conserved translational GTPases, whose functions are largely unknown. Structures of EF4 bound ribosomal PRE-translocation and POST-translocation complexes have both been visualized. On top of cellular, structural, and biochemical studies, several controversial models have been raised to rationalize functions of EF4. However, how EF4 modulates elongation through its interactions with ribosomes has not been revealed. Here, using single-molecule fluorescence resonance energy transfer assays, we directly captured short-lived EF4·GTP bound ribosomal PRE and POST translocation complexes, which may adopt slightly different conformations from structures prepared using GDP, GDPNP, or GDPCP. Furthermore, we revealed that EF4·GTP severely impairs delivery of aminoacyl-tRNA into the A-site of the ribosome and moderately accelerates translocation. We proposed that functions of EF4 are to slow overall elongation and to stall majority of ribosomes in POST states under stress conditions.展开更多
Background:Axonal degeneration and defects in neuromuscular neurotransmission represent a pathological hall-mark in spinal muscular atrophy(SMA)and other forms of motoneuron disease.These pathological changes do not o...Background:Axonal degeneration and defects in neuromuscular neurotransmission represent a pathological hall-mark in spinal muscular atrophy(SMA)and other forms of motoneuron disease.These pathological changes do not only base on altered axonal and presynaptic architecture,but also on alterations in dynamic movements of organelles and subcellular structures that are not necessarily reflected by static histopathological changes.The dynamic inter-play between the axonal endoplasmic reticulum(ER)and ribosomes is essential for stimulus-induced local translation in motor axons and presynaptic terminals.However,it remains enigmatic whether the ER and ribosome crosstalk is impaired in the presynaptic compartment of motoneurons with Smn(survival of motor neuron)deficiency that could contribute to axonopathy and presynaptic dysfunction in SMA.Methods:Using super-resolution microscopy,proximity ligation assay(PLA)and live imaging of cultured motoneu-rons from a mouse model of SMA,we investigated the dynamics of the axonal ER and ribosome distribution and activation.Results:We observed that the dynamic remodeling of ER was impaired in axon terminals of Smn-deficient motoneu-rons.In addition,in axon terminals of Smn-deficient motoneurons,ribosomes failed to respond to the brain-derived neurotrophic factor stimulation,and did not undergo rapid association with the axonal ER in response to extracellular stimuli.Conclusions:These findings implicate impaired dynamic interplay between the ribosomes and ER in axon terminals of motoneurons as a contributor to the pathophysiology of SMA and possibly also other motoneuron diseases.展开更多
Ribosome-like particles have been found in the proplastids in young cotyledon cells of lotus (%Nelumbo nucifera Gaertn% L.). Following the development of young embryo, some lamellar structures and tubular complex occu...Ribosome-like particles have been found in the proplastids in young cotyledon cells of lotus (%Nelumbo nucifera Gaertn% L.). Following the development of young embryo, some lamellar structures and tubular complex occurred in the plastids in young cotyledon cells, and some ribosome-like particles appeared in the loose region of these membrane system and stroma. About 15- 20 d after fertilization, with the further development of plastid, a large number of starch and DNA were synthesized in the plastids, and the plastids contained abundant and clear morphologically ribosomes, some of which presented spiral structure. About 16-18 d after fertilization, amyloplasts were isolated and purified from cotyledon of lotus, and ribosomes bands were obtained by use of sucrose density gradient centrifugation of ribosomes isolated from amyloplasts. RNA and protein contents of ribosomes have also been determined.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
Ribosomopathies encompass a spectrum of disorders arising from impaired ribosome biogenesis and reduced functionality.Mutation or dysexpression of the genes that disturb any finely regulated steps of ribosome biogenes...Ribosomopathies encompass a spectrum of disorders arising from impaired ribosome biogenesis and reduced functionality.Mutation or dysexpression of the genes that disturb any finely regulated steps of ribosome biogenesis can result in different types of ribosomopathies in clinic,collectively known as ribosomopathy genes.Emerging data suggest that ribosomopathy patients exhibit a significantly heightened susceptibility to cancer.Abnormal ribosome biogenesis and dysregulation of some ribosomopathy genes have also been found to be intimately associated with cancer development.The correlation between ribosome biogenesis or ribosomopathy and the development of malignancies has been well established.This work aims to review the recent advances in the research of ribosomopathy genes among human cancers and meanwhile,to excavate the potential role of these genes,which have not or rarely been reported in cancer,in the disease development across cancers.We plan to establish a theoretical framework between the ribosomopathy gene and cancer development,to further facilitate the potential of these genes as diagnostic biomarker as well as pharmaceutical targets for cancer treatment.展开更多
Chaetoceros Ehrenberg is one of the most diverse genera of planktonic diatoms.The species in section Chaetoceros are characterized by cells and setae having numerous chloroplasts and being widely distributed.However,t...Chaetoceros Ehrenberg is one of the most diverse genera of planktonic diatoms.The species in section Chaetoceros are characterized by cells and setae having numerous chloroplasts and being widely distributed.However,the delimitations of some species are problematic because of limited morphological information in the classical descriptions.Monoclonal strains of the section Chaetoceros were established,morphological features were studied using light and electron microscopy,and the hypervariable D 1-D 3 region of the nuclear ribosomal large subunit gene was sequenced to address phylogenetic relationships.Fifteen species belonging to the section Chaetoceros were recorded,including two new species,C.hainanensis sp.nov.and C.tridiscus sp.nov.Chaetoceros hainanensis was characterized by straight chains,narrowly lanceolate to hexagonal apertures,sibling setae diverging in nearly right angles,stipule-shaped spines on terminal setae and arrowhead-shaped spines on intercalary setae.C.tridiscus had short straight chains,narrowly lanceolate apertures,arrowhead-shaped spines and circular poroids arranged in a grid pattern on terminal and intercalary setae.The phylogenetic analyses revealed six groups formed by 19 species within the section Chaetoceros,which was found to be monophyletic.The subdivision of the section is still not well understood.The morphological characters within each group varied considerably and molecular information on more species are needed to enrich the phylogenetic profiling.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
Eukaryotic chromatin consisting of nucleosomes connected by linker DNA is organized into higher order structures,which is facilitated by linker histone H1.Formation of chromatin compacts and protects the genome,but al...Eukaryotic chromatin consisting of nucleosomes connected by linker DNA is organized into higher order structures,which is facilitated by linker histone H1.Formation of chromatin compacts and protects the genome,but also hinders DNA transactions.Cells have evolved mechanisms to modify/remodel chromatin resulting in chromatin states suitable for genome functions.The high mobility group box(HMGB)proteins are non-histone chromatin architectural factors characterized by one or more HMGB motifs that bind DNA in a sequence nonspecific fashion.They play a major role in chromatin dynamics.The Saccharomyces cerevisiae(yeast hereafter)HMGB protein Hmo1 contains two HMGB motifs.However,unlike a canonical HMGB protein that has an acidic C-terminus,Hmo1 ends with a lysine rich,basic,C-terminus,resembling linker histone H1.Hmo1 exhibits characteristics of both HMGB proteins and linker histones in its multiple functions.For instance,Hmo1 promotes transcription by RNA polymerases I and II like canonical HMGB proteins but makes chromatin more compact/stable like linker histones.Recent studies have demonstrated that Hmo1 destabilizes/disrupts nucleosome similarly as other HMGB proteins in vitro and acts to maintain a common topological architecture of genes in yeast genome.This minireview reviews the functions of Hmo1 and the underlying mechanisms,highlighting recent discoveries.展开更多
A study was conducted on the identifications of the degraded samples of sika deer (Cervus nippon) and red deer (Cervus elaphus) by phylogenetic and nucleotide distance analysis of partial Cytb and 12s rRNA genes s...A study was conducted on the identifications of the degraded samples of sika deer (Cervus nippon) and red deer (Cervus elaphus) by phylogenetic and nucleotide distance analysis of partial Cytb and 12s rRNA genes sequences. 402 bp Cytb genes were achieved by PCR-sequencing using DNA extracted from 8 case samples, and contrasted with 27 sequences of Cytb gene downloaded from GenBank database. The values of three nucleotide distance between three suspected samples and sika deer were identical (0.026±0.006), which was smaller than the smallest nucleotide distance between eastern red deer and sika deer (0.036). Furthermore, phylogenetic analysis of sika deer and red deer indicated that the evidences located within the same cluster as sika deer. The evidences were sika deer materials. As the same way, other three suspected samples were derived from red deer. The results were further confirmed by phylogenetic and nucleotide distance analysis of 387 bp 12s rRNA gene. The method was powerful and less time-consuming and helpful to reduce the related cases with wildlife.展开更多
In this study, non radioactive Digoxigenin labeled ribosomal DNA(rDNA) probes were used for Southern blotting analysis to study the molecular phylogeny of the giant panda and related species. Restriction maps in the ...In this study, non radioactive Digoxigenin labeled ribosomal DNA(rDNA) probes were used for Southern blotting analysis to study the molecular phylogeny of the giant panda and related species. Restriction maps in the regions of rDNA spacers were compared between giant panda( Ailuropoda melanoleuca ), lesser panda( Ailurus fulgens ), Asiatic black bear( Selenarctos thibetanus ), sun bear( Helarctos malayanus ), raccoon( Procyon lotor ) and lynx( Felis lynx ). Phylogenetic trees for these species were constructed using maximum likelihood and parsimony method. The results show that in respect to rDNA RFLPs, the giant panda is more closely related to bear than to lesser panda; while the lesser panda is slightly related to the raccoon.展开更多
背景与目的:研究发现核糖体蛋白L8(ribosomal protein L8,RPL8)在黑色素瘤中表达能激活黑色素瘤患者外周血单个核细胞增殖并产生白细胞介素2,提示RPL8可能参与抗肿瘤免疫应答,有望成为抗肿瘤治疗的靶点。本研究通过RPL8蛋白负载树突状细...背景与目的:研究发现核糖体蛋白L8(ribosomal protein L8,RPL8)在黑色素瘤中表达能激活黑色素瘤患者外周血单个核细胞增殖并产生白细胞介素2,提示RPL8可能参与抗肿瘤免疫应答,有望成为抗肿瘤治疗的靶点。本研究通过RPL8蛋白负载树突状细胞(dentritic cell,DC),探讨负载RPL8蛋白的DC对黑色素瘤的免疫效应。方法:原核表达RPL8蛋白,纯化后致敏小鼠骨髓来源DC,流式细胞仪检测DC表面标志,MTT法检测细胞毒性T淋巴细胞对小鼠黑色素瘤细胞的杀伤作用;负载RPL8蛋白DC免疫治疗小鼠后,观察肿瘤体积变化及小鼠生存时间。结果:纯化蛋白经蛋白质印迹法(Western blot)分析见约28×103大小的特异性条带;DC经RPL8及细菌脂多糖(Lipoplysaccharide,LPS)诱导成熟后细胞表面CD11c、CD80、MHC-Ⅰ类、MHC-Ⅱ类分子表达增高,能激活T淋巴细胞,对B16细胞有抑制作用,RPL8-DC组的抑制率在效靶比为30∶1时高达70%,较PBS组和DC组明显增高;负载RPL8蛋白DC免疫治疗小鼠后,肿瘤体积缩小,小鼠的生存期明显延长。结论:负载RPL8的DC对黑色素瘤有生长抑制作用。展开更多
A cDNA library was successfully constructed from Anip973, a human lung adenocarcinoma cell line with high metastatic potential. NIH3T3 cells were stably transfected using this cDNA library and screened for morphologic...A cDNA library was successfully constructed from Anip973, a human lung adenocarcinoma cell line with high metastatic potential. NIH3T3 cells were stably transfected using this cDNA library and screened for morphological changes in a soft agar assay. Genomic DNA was isolated from putative clones and the integrated sequence was retrieved by PCR and sequencing. Three known genes, ribosomal protein L23, hypothetical protein FLJ22104, and serine protease inhibitor, kazal type 6 and a number of 5'-terminally truncated sequences were identified. Furthermore, cells transfected with ribosomal protein L23 was highly invasive compared with the empty vector as control (P 〈 0.02). These results indicate that the expression cloning of cDNA libraries in NIH3T3 cells and subsequent screening for loss of contact inhibition in soft agar is a viable tool for identifying tumor-related genes and ribosomal protein L23 gene plays a role in cell movement and metastasis.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
In the present experiments the changes in levels of ribosome,polysome and 3H-leucine incorporation rate in liver post-mitochondrial supernatant (PM-supernatant) were investigated in Sedericient and Se-supplented rats....In the present experiments the changes in levels of ribosome,polysome and 3H-leucine incorporation rate in liver post-mitochondrial supernatant (PM-supernatant) were investigated in Sedericient and Se-supplented rats.The results demonstrated that the amounts of ribosome and polysome as well as the ratio of polysome to ribosome in liver PM-supernatant from the Se-deficient rats were all remarkahly decreased.In the meantime,the rate of protein synthesis expressed as radioactivity or 3H-leucine incorporated into protein in the PM-supernatant system also decreased significantly.The results suggest that the decreases of ribosomes and proportion of ribosomal aggregates in PM-supernatant may be responsible for the decrease of the protein synthesis activity in liver of the Se-deficient animals.展开更多
基金Supported by National Natural Science Foundation of China,No.82160762Guangxi Zhuang Autonomous Region Administration of Traditional Chinese Medicine Scientific Research Project,No.GXZYA20230267+2 种基金China Undergraduate Innovation and Entrepreneurship Training Program,No.S202410598060XChina Undergraduate Innovation and Entrepreneurship Training Program,No.X202410598360Future Academic Star of Guangxi Medical University,No.WLXSZX24074.
文摘BACKGROUND In recent years,many studies have shown that proteasome 26S subunit non-ATPase 6(PSMD6)plays an important role in the occurrence and development of malignant tumours.Unfortunately,there are no reports on the evaluation of the potential role of PSMD6 in hepatocellular carcinoma(HCC).AIM To comprehensively evaluate the overexpression pattern and clinical significance of PSMD6 in HCC tissues.METHODS This study integrated PSMD6 mRNA expression profiles from 4672 HCC and 3667 non-HCC tissues,along with immunohistochemical scores from 383 HCC and adjacent tissues,to assess PSMD6 overexpression in HCC.Clustered regularly interspaced short palindromic repeats knockout technology evaluated PSMD6’s essential role in HCC cell growth.Functional enrichment analysis explored the molecular mechanism of PSMD6 abnormalities in HCC.Drug sensitivity analysis and molecular docking analysed the effect of abnormal expression of PSMD6 on the drug sensitivity of HCC cells.RESULTS The results of 41 external and two internal datasets showed that PSMD6 mRNA(SMD=0.26,95%CI:0.09-0.42,P<0.05)and protein(SMD=2.85,95%CI:1.19-4.50,P<0.05)were significantly overexpressed in HCC tissues.The integrated analysis results showed that PSMD6 had a significant overexpression pattern in HCC tissues(SMD=0.40,95%CI:0.15-0.66,P<0.05).PSMD6 knockout inhibited HCC cell growth(chronos scores<-1).Functional enrichment implicated ribosome biogenesis and RNA splicing.Significant enrichment of signalling pathways such as RNA degradation,ribosomes,and chemical carcinogenesis—reactive oxygen species.Drug sensitivity analysis and a molecular docking model showed that high expression of PSMD6 was associated with the tolerance of HCC cells to drugs such as ML323,sepantronium bromide,and GDC0810.Overexpressed PSMD6 effectively distinguished HCC tissues(AUC=0.75,95%CI:0.71-0.79).CONCLUSION This study was the first to discover that PSMD6 was overexpressed in HCC tissues.PSMD6 is essential for the growth of HCC cells and may be involved in ribosome biogenesis and RNA splicing.
基金partially supported by National Institute of Health(R21/R33-GM078601 and R01-GM100701)National Science Foundation(MCB-1151343)in the US
文摘Elucidating protein translational regulation is crucial for understanding cellular function and drug development.A key molecule in protein translation is ribosome,which is a super-molecular complex extensively studied for more than a half century.The structure and dynamics of ribosome complexes were resolved recently thanks to the development of X-ray crystallography,Cryo-EM,and single molecule biophysics.Current studies of the ribosome have shown multiple functional states,each with a unique conformation.In this study,we analyzed the RNA-protein distances of ribosome(2.5 MDa)complexes and compared these changes among different ribosome complexes.We found that the RNA-protein distance is significantly correlated with the ribosomal functional state.Thus,the analysis of RNA-protein binding distances at important functional sites can distinguish ribosomal functional states and help understand ribosome functions.In particular,the mechanism of translational attenuation by nascent peptides and antibiotics was revealed by the conformational changes of local functional sites.
基金This work was supported by grants from the National Natural Science Foundation of China(31788103 and 91540203 to X.Cao,31770874 to C.L.,31900932 to R.H.,and 31701096 to J.S.),Chinathe Strategic Priority Research Program of Chinese Academy of Sciences(XDB27030201 to X.Cao),China+1 种基金the Key Research Program of Frontier Sciences of Chinese Academy of Sciences(QYZDY-SSW-SMC022 to X.Cao),Chinathe State Key Laboratory of Plant Genomics,China.
文摘Ribosome biogenesis,which takes place mainly in the nucleolus,involves coordinated expression of preribosomal RNAs(pre-rRNAs)and ribosomal proteins,pre-rRNA processing,and subunit assembly with the aid of numerous assembly factors.Our previous study showed that the Arabidopsis thaliana protein arginine methyltransferase AtPRMT3 regulates pre-rRNA processing;however,the underlying molecular mechanism remains unknown.Here,we report that AtPRMT3 interacts with Ribosomal Protein S2(RPS2),facilitating processing of the 90S/Small Subunit(SSU)processome and repressing nucleolar stress.We isolated an intragenic suppressor of atprmt3-2,which rescues the developmental defects of atprmt3-2 while produces a putative truncated AtPRMT3 protein bearing the entire N-terminus but lacking an intact enzymatic activity domain We further identified RPS2 as an interacting partner of AtPRMT3,and found that loss-of-function rps2a2b mutants were phenotypically reminiscent of atprmt3,showing pleiotropic developmental defects and aberrant pre-rRNA processing.RPS2B binds directly to pre-rRNAs in the nucleus,and such binding is enhanced in atprmt3-2.Consistently,multiple components of the 90S/SSU processome were more enriched by RPS2B in atprmt3-2,which accounts for early pre-rRNA processing defects and results in nucleolar stress.Collectively,our study uncovered a novel mechanism by which AtPRMT3 cooperates with RPS2B to facilitate the dynamic assembly/disassembly of the 90S/SSU processome during ribosome biogenesis and repress nucleolar stress.
基金supported by funds from the National Natural Science Foundation of China (No. 31570754)Tsinghua-Peking Joint Center for Life Sciences and Beijing Advanced Innovation Center for Structural Biology to C. ChenLab Innovation Funding from Lab and Instrument Department, Tsinghua University to W. Wang
文摘Elongation factor 4(EF4) is one of the highly conserved translational GTPases, whose functions are largely unknown. Structures of EF4 bound ribosomal PRE-translocation and POST-translocation complexes have both been visualized. On top of cellular, structural, and biochemical studies, several controversial models have been raised to rationalize functions of EF4. However, how EF4 modulates elongation through its interactions with ribosomes has not been revealed. Here, using single-molecule fluorescence resonance energy transfer assays, we directly captured short-lived EF4·GTP bound ribosomal PRE and POST translocation complexes, which may adopt slightly different conformations from structures prepared using GDP, GDPNP, or GDPCP. Furthermore, we revealed that EF4·GTP severely impairs delivery of aminoacyl-tRNA into the A-site of the ribosome and moderately accelerates translocation. We proposed that functions of EF4 are to slow overall elongation and to stall majority of ribosomes in POST states under stress conditions.
基金Open Access funding enabled and organized by Projekt DEAL.Chunchu Deng was funded by PicoQuant and the Deutsche Forschungsgemeinschaft(DFG)Grant Se697/7-1,Project Number 405988308,DFG Grant JA1823/3-1 for SJ and Cure SMA for SJ,Grant JAB1920.PicoQuant did not influence project design,conduction of experiments or data analyses.
文摘Background:Axonal degeneration and defects in neuromuscular neurotransmission represent a pathological hall-mark in spinal muscular atrophy(SMA)and other forms of motoneuron disease.These pathological changes do not only base on altered axonal and presynaptic architecture,but also on alterations in dynamic movements of organelles and subcellular structures that are not necessarily reflected by static histopathological changes.The dynamic inter-play between the axonal endoplasmic reticulum(ER)and ribosomes is essential for stimulus-induced local translation in motor axons and presynaptic terminals.However,it remains enigmatic whether the ER and ribosome crosstalk is impaired in the presynaptic compartment of motoneurons with Smn(survival of motor neuron)deficiency that could contribute to axonopathy and presynaptic dysfunction in SMA.Methods:Using super-resolution microscopy,proximity ligation assay(PLA)and live imaging of cultured motoneu-rons from a mouse model of SMA,we investigated the dynamics of the axonal ER and ribosome distribution and activation.Results:We observed that the dynamic remodeling of ER was impaired in axon terminals of Smn-deficient motoneu-rons.In addition,in axon terminals of Smn-deficient motoneurons,ribosomes failed to respond to the brain-derived neurotrophic factor stimulation,and did not undergo rapid association with the axonal ER in response to extracellular stimuli.Conclusions:These findings implicate impaired dynamic interplay between the ribosomes and ER in axon terminals of motoneurons as a contributor to the pathophysiology of SMA and possibly also other motoneuron diseases.
文摘Ribosome-like particles have been found in the proplastids in young cotyledon cells of lotus (%Nelumbo nucifera Gaertn% L.). Following the development of young embryo, some lamellar structures and tubular complex occurred in the plastids in young cotyledon cells, and some ribosome-like particles appeared in the loose region of these membrane system and stroma. About 15- 20 d after fertilization, with the further development of plastid, a large number of starch and DNA were synthesized in the plastids, and the plastids contained abundant and clear morphologically ribosomes, some of which presented spiral structure. About 16-18 d after fertilization, amyloplasts were isolated and purified from cotyledon of lotus, and ribosomes bands were obtained by use of sucrose density gradient centrifugation of ribosomes isolated from amyloplasts. RNA and protein contents of ribosomes have also been determined.
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the National Natural Science Foundation of China(Grant No.:82360542)Jiangxi Provincial Natural Science Foundation,China(Grant Nos.:20224BAB214030 and 20224BAB216072)+2 种基金Doctoral Startup Fund of Gannan Medical University,China(Grant Nos.:QD202136 and QD202132)Science and Technology Planning Projects of Fuzhou,China(Grant No.:2021FZR0101)the Natural Science Foundation of Fujian Province,China(Grant No.:2022YZ0104).
文摘Ribosomopathies encompass a spectrum of disorders arising from impaired ribosome biogenesis and reduced functionality.Mutation or dysexpression of the genes that disturb any finely regulated steps of ribosome biogenesis can result in different types of ribosomopathies in clinic,collectively known as ribosomopathy genes.Emerging data suggest that ribosomopathy patients exhibit a significantly heightened susceptibility to cancer.Abnormal ribosome biogenesis and dysregulation of some ribosomopathy genes have also been found to be intimately associated with cancer development.The correlation between ribosome biogenesis or ribosomopathy and the development of malignancies has been well established.This work aims to review the recent advances in the research of ribosomopathy genes among human cancers and meanwhile,to excavate the potential role of these genes,which have not or rarely been reported in cancer,in the disease development across cancers.We plan to establish a theoretical framework between the ribosomopathy gene and cancer development,to further facilitate the potential of these genes as diagnostic biomarker as well as pharmaceutical targets for cancer treatment.
基金Supported by the Joint Fund of National Natural Science Foundation of China and Chinese Shandong Province(No.U 2106205)the National Natural Science Foundation of China(No.32170206)the National Key Research and Development Program of China(No.2022YFC3105201)。
文摘Chaetoceros Ehrenberg is one of the most diverse genera of planktonic diatoms.The species in section Chaetoceros are characterized by cells and setae having numerous chloroplasts and being widely distributed.However,the delimitations of some species are problematic because of limited morphological information in the classical descriptions.Monoclonal strains of the section Chaetoceros were established,morphological features were studied using light and electron microscopy,and the hypervariable D 1-D 3 region of the nuclear ribosomal large subunit gene was sequenced to address phylogenetic relationships.Fifteen species belonging to the section Chaetoceros were recorded,including two new species,C.hainanensis sp.nov.and C.tridiscus sp.nov.Chaetoceros hainanensis was characterized by straight chains,narrowly lanceolate to hexagonal apertures,sibling setae diverging in nearly right angles,stipule-shaped spines on terminal setae and arrowhead-shaped spines on intercalary setae.C.tridiscus had short straight chains,narrowly lanceolate apertures,arrowhead-shaped spines and circular poroids arranged in a grid pattern on terminal and intercalary setae.The phylogenetic analyses revealed six groups formed by 19 species within the section Chaetoceros,which was found to be monophyletic.The subdivision of the section is still not well understood.The morphological characters within each group varied considerably and molecular information on more species are needed to enrich the phylogenetic profiling.
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.
文摘Eukaryotic chromatin consisting of nucleosomes connected by linker DNA is organized into higher order structures,which is facilitated by linker histone H1.Formation of chromatin compacts and protects the genome,but also hinders DNA transactions.Cells have evolved mechanisms to modify/remodel chromatin resulting in chromatin states suitable for genome functions.The high mobility group box(HMGB)proteins are non-histone chromatin architectural factors characterized by one or more HMGB motifs that bind DNA in a sequence nonspecific fashion.They play a major role in chromatin dynamics.The Saccharomyces cerevisiae(yeast hereafter)HMGB protein Hmo1 contains two HMGB motifs.However,unlike a canonical HMGB protein that has an acidic C-terminus,Hmo1 ends with a lysine rich,basic,C-terminus,resembling linker histone H1.Hmo1 exhibits characteristics of both HMGB proteins and linker histones in its multiple functions.For instance,Hmo1 promotes transcription by RNA polymerases I and II like canonical HMGB proteins but makes chromatin more compact/stable like linker histones.Recent studies have demonstrated that Hmo1 destabilizes/disrupts nucleosome similarly as other HMGB proteins in vitro and acts to maintain a common topological architecture of genes in yeast genome.This minireview reviews the functions of Hmo1 and the underlying mechanisms,highlighting recent discoveries.
文摘A study was conducted on the identifications of the degraded samples of sika deer (Cervus nippon) and red deer (Cervus elaphus) by phylogenetic and nucleotide distance analysis of partial Cytb and 12s rRNA genes sequences. 402 bp Cytb genes were achieved by PCR-sequencing using DNA extracted from 8 case samples, and contrasted with 27 sequences of Cytb gene downloaded from GenBank database. The values of three nucleotide distance between three suspected samples and sika deer were identical (0.026±0.006), which was smaller than the smallest nucleotide distance between eastern red deer and sika deer (0.036). Furthermore, phylogenetic analysis of sika deer and red deer indicated that the evidences located within the same cluster as sika deer. The evidences were sika deer materials. As the same way, other three suspected samples were derived from red deer. The results were further confirmed by phylogenetic and nucleotide distance analysis of 387 bp 12s rRNA gene. The method was powerful and less time-consuming and helpful to reduce the related cases with wildlife.
文摘In this study, non radioactive Digoxigenin labeled ribosomal DNA(rDNA) probes were used for Southern blotting analysis to study the molecular phylogeny of the giant panda and related species. Restriction maps in the regions of rDNA spacers were compared between giant panda( Ailuropoda melanoleuca ), lesser panda( Ailurus fulgens ), Asiatic black bear( Selenarctos thibetanus ), sun bear( Helarctos malayanus ), raccoon( Procyon lotor ) and lynx( Felis lynx ). Phylogenetic trees for these species were constructed using maximum likelihood and parsimony method. The results show that in respect to rDNA RFLPs, the giant panda is more closely related to bear than to lesser panda; while the lesser panda is slightly related to the raccoon.
文摘背景与目的:研究发现核糖体蛋白L8(ribosomal protein L8,RPL8)在黑色素瘤中表达能激活黑色素瘤患者外周血单个核细胞增殖并产生白细胞介素2,提示RPL8可能参与抗肿瘤免疫应答,有望成为抗肿瘤治疗的靶点。本研究通过RPL8蛋白负载树突状细胞(dentritic cell,DC),探讨负载RPL8蛋白的DC对黑色素瘤的免疫效应。方法:原核表达RPL8蛋白,纯化后致敏小鼠骨髓来源DC,流式细胞仪检测DC表面标志,MTT法检测细胞毒性T淋巴细胞对小鼠黑色素瘤细胞的杀伤作用;负载RPL8蛋白DC免疫治疗小鼠后,观察肿瘤体积变化及小鼠生存时间。结果:纯化蛋白经蛋白质印迹法(Western blot)分析见约28×103大小的特异性条带;DC经RPL8及细菌脂多糖(Lipoplysaccharide,LPS)诱导成熟后细胞表面CD11c、CD80、MHC-Ⅰ类、MHC-Ⅱ类分子表达增高,能激活T淋巴细胞,对B16细胞有抑制作用,RPL8-DC组的抑制率在效靶比为30∶1时高达70%,较PBS组和DC组明显增高;负载RPL8蛋白DC免疫治疗小鼠后,肿瘤体积缩小,小鼠的生存期明显延长。结论:负载RPL8的DC对黑色素瘤有生长抑制作用。
基金This work was supported by Returning Scholars Fund of Heilongjiang Province (No. LC04C02) the Department of Education Overseas Researcher Fund of Heilongjiang Province (No. 1054HZ013).
文摘A cDNA library was successfully constructed from Anip973, a human lung adenocarcinoma cell line with high metastatic potential. NIH3T3 cells were stably transfected using this cDNA library and screened for morphological changes in a soft agar assay. Genomic DNA was isolated from putative clones and the integrated sequence was retrieved by PCR and sequencing. Three known genes, ribosomal protein L23, hypothetical protein FLJ22104, and serine protease inhibitor, kazal type 6 and a number of 5'-terminally truncated sequences were identified. Furthermore, cells transfected with ribosomal protein L23 was highly invasive compared with the empty vector as control (P 〈 0.02). These results indicate that the expression cloning of cDNA libraries in NIH3T3 cells and subsequent screening for loss of contact inhibition in soft agar is a viable tool for identifying tumor-related genes and ribosomal protein L23 gene plays a role in cell movement and metastasis.
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.
文摘In the present experiments the changes in levels of ribosome,polysome and 3H-leucine incorporation rate in liver post-mitochondrial supernatant (PM-supernatant) were investigated in Sedericient and Se-supplented rats.The results demonstrated that the amounts of ribosome and polysome as well as the ratio of polysome to ribosome in liver PM-supernatant from the Se-deficient rats were all remarkahly decreased.In the meantime,the rate of protein synthesis expressed as radioactivity or 3H-leucine incorporated into protein in the PM-supernatant system also decreased significantly.The results suggest that the decreases of ribosomes and proportion of ribosomal aggregates in PM-supernatant may be responsible for the decrease of the protein synthesis activity in liver of the Se-deficient animals.