HCLS1-associated protein X-1(HAX1)is a multifunctional mitochondrial protein involved in the regulation of apoptosis,a crucial process of programmed cell death,and mRNA processing.Despite its significance,limited stru...HCLS1-associated protein X-1(HAX1)is a multifunctional mitochondrial protein involved in the regulation of apoptosis,a crucial process of programmed cell death,and mRNA processing.Despite its significance,limited structural data is available for HAX1,hindering a comprehensive understanding of its biological function.Notably,the caseinolytic mitochondrial matrix peptidase chaperone subunit B(CLPB)has been identified as an interacting partner of HAX1,yet the biophysical properties and binding affinity governing their interaction remain poorly defined.In this study,we present a thorough biophysical characterization of full-length human HAX1 and CLPB,accomplished through recombinant expression and purification.By employing size exclusion chromatography,dynamic light scattering,and circular dichroism spectroscopy,we successfully established their biophysical properties,revealing contrasting structural features,with CLPB displaying a-helical content and HAX1 exhibiting a disordered nature.Moreover,we employed solutionstate nuclear magnetic resonance(NMR)spectroscopy to probe their binding affinity.Our findings demonstrate the formation of stable multimeric complexes between HAX1 and CLPB,and we quantified a dissociation constant in the low range of micro-molar for their high affinity interaction.These results lay the foundation for further in-depth investigations into the dynamics and energetics governing the HAX1-CLPB interaction,ultimately contributing to a comprehensive understanding of their functional mechanisms.展开更多
Melon(Cucumis melo)is an economically important horticultural crop cultivated worldwide.NAC(NAM/ATAC/CUC)transcription factors play crucial roles in the transcriptional regulation of various developmental stages in pl...Melon(Cucumis melo)is an economically important horticultural crop cultivated worldwide.NAC(NAM/ATAC/CUC)transcription factors play crucial roles in the transcriptional regulation of various developmental stages in plant growth and fruit development,but their gene functions in melon remain largely unknown.Here,we identified 78 CmNAC family genes with an integrated and conserved no apical meristem(NAM)domain in the melon genome by performing genome-wide identification and bioinformatics analysis.Transcriptome data analysis and qRTPCR results showed that most CmNACs are specifically enriched in either the vegetative or reproductive organs of melon.Through genetic transformation,we found that overexpression of CmNAC34 in melons led to early ripening fruits,suggesting its positive role in promoting fruit maturation.Using yeast two-hybrid and bimolecular fluorescence complementation assays,we verified the direct protein interaction between CmNAC34 and CmNACNOR.The expression patterns of CmNAC34 and CmNAC-NOR were similar in melon tissues,and subcellular localization revealed their nuclear protein characteristics.We transformed CmNAC-NOR in melon and found that its overexpression resulted in early ripening fruits.Then,the yeast one-hybrid and dual luciferase reporter gene assays showed that the CmNAC34 protein can bind to the promoters of two glyoxalase(GLY)genes,which are involved in the abscisic acid signal pathway and associated with fruit regulation.These findings revealed the molecular characteristics,expression profiles,and functional patterns of the NAC family genes and provide new insights into the molecular mechanism by which CmNAC34 regulates climacteric fruit ripening.展开更多
The yeast two\|hybrid system is a molecular genetic approach for protein interaction and it is widely used to screen for proteins that interact with a protein of interest in recent years.This process includes,construc...The yeast two\|hybrid system is a molecular genetic approach for protein interaction and it is widely used to screen for proteins that interact with a protein of interest in recent years.This process includes,construction and testing of the bait plasmid,screening a plasmid library for interacting fusion protein,elimination of false positives and delection analysis of true positives.This procedure is designed to allow investigators to identify proteins and their encoding cDNAs that have a biologically significant interaction with a protein of interest.More and more studies have demonstrated that the two\|hybrid system is a powerful and sensitive technique for the identification of genes that code for proteins that interact in a biologically significant fashion with a protein of interest in higher plants.This method has been used to identify new interaction protein in many laboratories.The recently reported yeast tri\|brid system,should allow the investigation of more complex protein\|protein interactions.The aim of this review is to outline the recent progress made in protein interactions by using yeast two\|hybrid system.展开更多
The B-box(BBX)family of proteins consists of zinc-finger transcription factors with one or two highly conserved B-box motifs at their N-termini.BBX proteins play crucial roles in various aspects of plant growth and de...The B-box(BBX)family of proteins consists of zinc-finger transcription factors with one or two highly conserved B-box motifs at their N-termini.BBX proteins play crucial roles in various aspects of plant growth and development,including seedling photomorphogenesis,shade avoidance,flowering time,and biotic and abiotic stress responses.Previous studies have identified many different BBXs from several plant species,although the BBX family members in maize are largely unknown.Genome-wide identification and comprehensive analysis of maize BBX(ZmBBX)expression and interaction networks would therefore provide valuable information for understanding their functions.In this study,36 maize BBXs in three major clades were identified.The ZmBBXs within a given clade were found to share similar domains,motifs,and genomic structures.Gene duplication analyses revealed that the expansion of BBX proteins in maize has mainly occurred by segmental duplication.The expression levels of ZmBBXs were analyzed in various organs and tissues,and under different abiotic stress conditions.Protein–protein interaction networks of ZmBBXs were established using bioinformatic tools and verified by bimolecular fluorescence complementation(BiFC)assays.Our findings can facilitate a greater understanding of the complexity of the ZmBBX family and provide novel clues for unravelling ZmBBX protein functions.展开更多
The mechanism and interaction among Rb/p16, Rb/E2F1 and HDAC1 proteins in gallbladder carcinoma were investigated. By using the immunoprecipitation method, the interactions among Rb, p16, E2F1, HDAC1 proteins in gallb...The mechanism and interaction among Rb/p16, Rb/E2F1 and HDAC1 proteins in gallbladder carcinoma were investigated. By using the immunoprecipitation method, the interactions among Rb, p16, E2F1, HDAC1 proteins in gallbladder carcinoma cell line （Mz-ChA-1） were studied. It was found that there were Rb and E2F1 proteins in the precipitates with anti-HDAC1, and there were HDAC1 and E2F1 proteins in the precipitate with anti-Rb. It was concluded that there are specific interactions among Rb, HDAC1 and E2F1 proteins in gallbladder carcinoma, indicating the existence of the direct Rb/E2F1/HDAC1 signal transduction pathway. There is no direct relationship between p16 proteins with Rb, HDAC1, and E2F1 proteins.展开更多
Hot pepper(Capsicum annuum var.conoides)is a significant vegetable that is widely cultivated around the world.Currently,global climate change has caused frequent severe weather events,and waterlogging stress harms the...Hot pepper(Capsicum annuum var.conoides)is a significant vegetable that is widely cultivated around the world.Currently,global climate change has caused frequent severe weather events,and waterlogging stress harms the pepper industry by affecting the planting period,growth conditions,and disease susceptibility.The gene CaABI3/VP1-1 could improve pepper waterlogging tolerance.In order to explore the upstream regulatory mechanism of CaABI3/VP1-1,a high-quality standardized yeast hybrid library was successfully constructed for yeast one-,two-,and threehybrid screening using pepper‘ZHC2’as the experimental material,with a library recombinant efficiency of up to 100%.The length of inserted fragments varied from 650 to 5000 bp,the library titer was 5.18×10^(6)colony-forming units(CFU)·mL-1,and the library capacity was 1.04×10^(7)CFU of cDNA inserts.The recombinant bait plasmid was used to successfully identify 78 different proteins through the yeast one-hybrid system,including one transcription factor within the ethylene-responsive factor family and the other within the growth-regulating factor family.The interaction happened between LOC124895848 and CaABI3/VP1-1 promoter by point-to-point yeast one-hybrid experiment.The expression level of the 12 selected protein-coding genes was then evaluated by quantitative real-time polymerase chain reaction.Results indicated the protein coding genes showed different responses to waterlogging stress and that the activity of the CaABI3/VP1-1 promoter could be inhibited or activated by up-regulating or down-regulating gene expression,respectively.The identification of these proteins interacting with the promoter provides a new perspective for understanding the gene regulatory network of hot pepper operating under waterlogging stress and provides theoretical support for further analysis of the complex regulatory relationship between transcription factors and promoters.展开更多
Essential proteins are inseparable in cell growth and survival. The study of essential proteins is important for understanding cellular functions and biological mechanisms. Therefore, various computable methods have b...Essential proteins are inseparable in cell growth and survival. The study of essential proteins is important for understanding cellular functions and biological mechanisms. Therefore, various computable methods have been proposed to identify essential proteins. Unfortunately, most methods based on network topology only consider the interactions between a protein and its neighboring proteins, and not the interactions with its higher-order distance proteins. In this paper, we propose the DSEP algorithm in which we integrated network topology properties and subcellular localization information in protein–protein interaction(PPI) networks based on four-order distances, and then used random walks to identify the essential proteins. We also propose a method to calculate the finite-order distance of the network, which can greatly reduce the time complexity of our algorithm. We conducted a comprehensive comparison of the DSEP algorithm with 11 existing classical algorithms to identify essential proteins with multiple evaluation methods. The results show that DSEP is superior to these 11 methods.展开更多
The E3 ubiquitin ligase,carboxyl terminus of heat shock protein 70(Hsp70)interacting protein(CHIP),also functions as a co-chaperone and plays a crucial role in the protein quality control system.In this study,we aimed...The E3 ubiquitin ligase,carboxyl terminus of heat shock protein 70(Hsp70)interacting protein(CHIP),also functions as a co-chaperone and plays a crucial role in the protein quality control system.In this study,we aimed to investigate the neuroprotective effect of overexpressed CHIP on Alzheimer’s disease.We used an adeno-associated virus vector that can cross the blood-brain barrier to mediate CHIP overexpression in APP/PS1 mouse brain.CHIP overexpression significantly ameliorated the performance of APP/PS1 mice in the Morris water maze and nest building tests,reduced amyloid-βplaques,and decreased the expression of both amyloid-βand phosphorylated tau.CHIP also alleviated the concentration of microglia and astrocytes around plaques.In APP/PS1 mice of a younger age,CHIP overexpression promoted an increase in ADAM10 expression and inhibitedβ-site APP cleaving enzyme 1,insulin degrading enzyme,and neprilysin expression.Levels of HSP70 and HSP40,which have functional relevance to CHIP,were also increased.Single nuclei transcriptome sequencing in the hippocampus of CHIP overexpressed mice showed that the lysosomal pathway and oligodendrocyte-related biological processes were up-regulated,which may also reflect a potential mechanism for the neuroprotective effect of CHIP.Our research shows that CHIP effectively reduces the behavior and pathological manifestations of APP/PS1 mice.Indeed,overexpression of CHIP could be a beneficial approach for the treatment of Alzheimer’s disease.展开更多
Objective ZW10 interacting kinetochore protein(ZWINT)has been demonstrated to play a pivotal role in the growth,invasion,and migration of cancers.Nevertheless,whether the expression levels of ZWINT are significantly c...Objective ZW10 interacting kinetochore protein(ZWINT)has been demonstrated to play a pivotal role in the growth,invasion,and migration of cancers.Nevertheless,whether the expression levels of ZWINT are significantly correlated with clinicopathological characteristics and prognostic outcomes of patients with breast cancer remains elusive.This study systematically investigated the clinical significance of ZWINT expression in breast cancer through integrated molecular subtyping and survival analysis.Methods We systematically characterized the spatial expression pattern of ZWINT across various breast cancer subtypes and assessed its prognostic significance using an integrated bioinformatics approach that involved multi-omics analysis.The approach included the Breast Cancer Gene-Expression Miner v5.1(bc-GenExMiner v5.1),TNMplot,MuTarget,PrognoScan database,and Database for Annotation,Visualization,and Integrated Discovery(DAVID).Results Our analysis revealed consistent upregulation of ZWINT mRNA and protein expression across distinct clinicopathological subtypes of breast cancer.ZWINT overexpression demonstrated significant co-occurrence with truncating mutations in cadherin 1(CDH1)and tumor protein p53(TP53),suggesting potential functional crosstalk in tumor progression pathways.The overexpression of ZWINT correlated with adverse clinical outcomes,showing 48%increased mortality risk(overall survival:HR 1.48,95%CI 1.23–1.79),66%higher recurrence probability(relapse-free survival:1.66,95%CI 1.50–1.84),and 63%elevated metastasis risk(distant metastasis-free survival:HR 1.63,95%CI 1.39–1.90).Multivariate Cox regression incorporating TNM staging and molecular subtypes confirmed ZWINT as an independent prognostic determinant(P<0.001,Harrell’s C-index=0.7827),which was validated through bootstrap resampling(1000 iterations).Conclusion ZWINT may serve as a potential biomarker for prognosis and a possible therapeutic target alongside TP53/CDH1 in breast cancer.展开更多
FCS-like zinc finger(FLZ)gene family members are C2-C2 zinc finger proteins that take part in seed dormancy,resistance to Myzus persicae 1,sucrose signaling and abiotic stresse tolerance.However,their functions,especi...FCS-like zinc finger(FLZ)gene family members are C2-C2 zinc finger proteins that take part in seed dormancy,resistance to Myzus persicae 1,sucrose signaling and abiotic stresse tolerance.However,their functions,especially the molecular mechanism through which FLZs function,are not well understood.In this study,we characterized 120FLZs in wheat and revealed the function and mechanism of TaFLZ54D increasing salt stress tolerance in transgenic wheat.Expression analysis demonstrated that TaFLZ54D can be induced by NaCl treatment and it had the highest expression level under NaCl treatment among the 120 FLZs.Over-expression of TaFLZ54D increased wheat salt stress tolerance and the transgenic plants had higher levels of superoxide dismutase(SOD)and peroxidase(POD)activities and soluble sugar content,but a lower Na^(+)/K^(+)ratio and malondialdehyde(MDA)content than the wild type(WT)plants.Potassium ion transmembrane transporters and serine/threonine kinase inhibitor proteins showed differential expression between Ta FLZ54D transgenic wheat and the WT.Yeast two hybrid and luciferase complementation assays revealed that TaSGT1 and TaPP2C are the proteins that interact directly with TaFLZ54D.In summary,TaFLZ54D enhances salt stress tolerance through interaction with TaSGT1 and TaPP2C to reduce Na^(+)absorption and mitigate oxidative stress.The interaction between TaFLZ54D and TaSGT1,as well as TaPP2C indicated a link between salt stress tolerance of TaFLZ54D and the ubiquitin-mediated degradation of negative regulatory proteins.展开更多
Objective Oral squamous cell carcinoma(OSCC)is an aggressive cancer with a high mortality rate.San-Zhong-Kui-Jian-Tang(SZKJT),a Chinese herbal formula,has long been used as an adjuvant therapy in cancer clinical pract...Objective Oral squamous cell carcinoma(OSCC)is an aggressive cancer with a high mortality rate.San-Zhong-Kui-Jian-Tang(SZKJT),a Chinese herbal formula,has long been used as an adjuvant therapy in cancer clinical practice.Although its therapeutic effects and molecular mechanisms in OSCC have been previously elucidated,the potential interactions and mechanisms between the active phytochemicals and their therapeutic targets are still lacking.Methods The present study employed network pharmacology and topology approaches to establish a“herbal ingredients–active phytochemicals–target interaction”network to explore the potential therapeutic targets of SZKJT-active phytochemicals in the treatment of OSCC.The role of the target proteins in oncogenesis was assessed via GO and KEGG enrichment analyses,and their interactions with the active phytochemicals of SZKJT were calculated via molecular docking and dynamic simulations.The pharmacokinetic properties and toxicity of the active phytochemicals were also predicted.Results A total of 171 active phytochemicals of SZKJT fulfilled the bioavailability and drug-likeness screening criteria,with the flavonoids quercetin,kaempferol,and naringenin having the greatest potential.The 4 crucial targets of these active phytochemicals are PTGS2,TNF,BCL2,and CASP3,which encode cyclooxygenase-2,tumor necrosis factor(TNF),BCL-2 apoptosis regulator,and caspase-3,respectively.The interactions between phytochemicals and target proteins were predicted to be thermodynamically feasible and stable via molecular docking and dynamics simulations.Finally,the results revealed that the IL-6/JAK/STAT3 pathway and TNF signaling via NF-κB are the two prominent pathways targeted by SZKJT.Conclusion In summary,this study provides computational data for in-depth exploration of the mechanism by which SZKJT activates phytochemicals to treat OSCC.展开更多
Pumpkin is of great economic importance not only as food resources but also as the most widely used rootstock to graft cucurbit crops.Pumpkin rootstock improves salt tolerance of cucumber scion through respiratory bur...Pumpkin is of great economic importance not only as food resources but also as the most widely used rootstock to graft cucurbit crops.Pumpkin rootstock improves salt tolerance of cucumber scion through respiratory burst oxidase homolog protein D(CmRbohD)-mediated reactive oxygen species(ROS)burst,which further enhances Na^(+)export and K^(+)uptake.Rboh D activation requires calcium signaling.However,the underlying mechanism remains largely unknown.In this study,we discovered two Rboh D members from pumpkin involved in the ROS burst at the early stage of salt stress.CmRbohD1 and CmRbohD2 were functionally redundant and double mutation significantly impaired salt tolerance in pumpkin.Overexpression of CmRbohD1 and CmRbohD2 mitigated salinity-induced damage and maintained a relatively low Na+content and high K+content.We screened the potential calcineurin B-like interacting protein kinases(Cm CIPKs)which could bind with CmRbohD1 and CmRbohD2.Our results revealed that two Rboh Ds formed complexes specifically with CmCIPK1,thereby bursting ROS production.Overexpression of CmCIPK1 promoted the early ROS burst under salt stress condition and maintained a relatively balanced Na+/K+homeostasis.Altogether,we proposed a CmCIPK1-CmRbohD1/D2 complex for pumpkin salt stress signaling transduction,which regulates the ROS burst and Na+/K+homeostasis.Our findings offer unprecedented insights into the general mechanism of pumpkin salt tolerance.展开更多
Stilbenes,a natural plant phytoalexin,are involved in the plant's response to various biotic and abiotic stresses in its environment.STILBENE SYNTHASE(STS)is the key enzyme regulating resveratrol synthesis in grap...Stilbenes,a natural plant phytoalexin,are involved in the plant's response to various biotic and abiotic stresses in its environment.STILBENE SYNTHASE(STS)is the key enzyme regulating resveratrol synthesis in grapevine.However,the regulatory mechanism of STS gene expression remains unclear.In this study,we reported a NAC transcription factor,VqNAC17,in Vitis quinquangularis,which can improve plant resistance to salt stress,drought stress,and Pseudomonas syringae pv.Tomato DC3000(Pst DC3000)in transgenic Arabidopsis thaliana.Additionally,the interaction between the transcription factors VqNAC17 and VqMYB15 was confrmed using yeast two-hybrid and BiFC.In transgenic A.thaliana,VqNAC17 participates in plant immunity through interaction with VqMYB15 to affect the stilbene synthesis.Furthermore,the experimental results of the yeast one-hybrid assay and LUC transient expression assay found that VqNAC17 can also bind to the promoter of VqMYB15.These results indicate that VqNAC17 is a key regulator that can promote the expression of STS by interacting with VqMYB15.展开更多
Three-dimensional(3D)bio-printing is an emerging tissue engineering technology,and its printing parameters have been upgraded to enable in-depth application in cell-cultured meat.However,excellent printable and edible...Three-dimensional(3D)bio-printing is an emerging tissue engineering technology,and its printing parameters have been upgraded to enable in-depth application in cell-cultured meat.However,excellent printable and edible bio-inks for cell-cultured meat are in urgent need of development.Therefore,a low-cost bio-ink based on albumin and gelatin was developed.At first,suitable printability of the bio-ink was determined by rheology analysis,excellent mechanical stability,and excellent mechanical stability of the printed scaffold was also proved by water absorption and degradation rate.Next,the biocompatibility of the scaffold and its interaction with cells were clarified through cell proliferation culture,cell status research and omics analysis.Notably,AG7 demonstrated better printability and AGS7 provided better conditions for cell attachment,proliferation and migration,S-shaped exponential growth curve further revealed the significant advantages of AGS7 scaffolds in cell culture.More importantly,the tissue culture process of muscle cells was simulated to organoid culture,which elucidated the interaction information between cells and scaffolds.This work has filled the vacancy in the industry and provides a novel strategy for the development of production of cell cultured meat.展开更多
The velvet protein family serves as a crucial factor in coordinating development and secondary metabolism in numerous pathogenic fungi.However,no previous research has examined the function of the velvet protein famil...The velvet protein family serves as a crucial factor in coordinating development and secondary metabolism in numerous pathogenic fungi.However,no previous research has examined the function of the velvet protein family in Fusarium oxysporum f.sp.niveum(FON),a pathogen causing a highly destructive disease in watermelon.In this study,∆fovel1 and∆folae1 deletion mutants and∆fovel1-C and∆folae1-C corresponding complementation mutants of FON were validated.Additionally,the phenotypic,biochemical,and virulence effects of the deletion mutants were investigated.Compared to the wild-type strains,the∆fovel1 and∆folae1 mutants exhibited altered mycelial phenotype,reduced conidiation,and decreased production of bikaverin and fusaric acid.Furthermore,their virulence on watermelon plant roots significantly decreased.All these alterations in mutants were restored in corresponding complementation strains.Notably,yeast two-hybrid results demonstrated an interaction between FoVel1 and FoLae1.This study reveals that FoVEL1 and FoLAE1 play essential roles in secondary metabolism,conidiation,and virulence in FON.These findings enhance our understanding of the genetic and functional roles of VEL1 and LAE1 in pathogenic fungi.展开更多
AIM:To understand the complex reaction of gastric inflammation induced by Helicobacter pylori(H pylori) in a systematic manner using a protein interaction network. METHODS:The expression of genes significantly changed...AIM:To understand the complex reaction of gastric inflammation induced by Helicobacter pylori(H pylori) in a systematic manner using a protein interaction network. METHODS:The expression of genes significantly changed on microarray during H pylori infection was scanned from the web literary database and translated into proteins.A network of protein interactions was constructed by searching the primary interactions of selected proteins.The constructed network was mathematically analyzed and its biological function was examined.In addition,the nodes on the network were checked to determine if they had any further functional importance or relation to other proteins by extending them. RESULTS:The scale-free network showing the relationship between inflammation and carcinogenesis was constructed.Mathematical analysis showed hub and bottleneck proteins,and these proteins were mostly related to immune response.The network contained pathways and proteins related to H pylori infection,such as the JAK-STAT pathway triggered by interleukins.Activation of nuclear factor (NF)-κB,TLR4,and other proteins known to function as core proteins of immune response were also found. These immune-related proteins interacted on the network with pathways and proteins related to the cell cycle,cell maintenance and proliferation,andtranscription regulators such as BRCA1,FOS,REL,and zinc finger proteins.The extension of nodes showed interactions of the immune proteins with cancer- related proteins.One extended network,the core network,a summarized form of the extended network, and cell pathway model were constructed. CONCLUSION:Immune-related proteins activated by H pylori infection interact with proto-oncogene proteins.The hub and bottleneck proteins are potential drug targets for gastric inflammation and cancer.展开更多
Proteasome dysfunction has been repeatedly reported in alcoholic liver disease. Ethanol metabolism endproducts affect the structure of the proteasome, and, therefore, change the proteasome interaction with its regulat...Proteasome dysfunction has been repeatedly reported in alcoholic liver disease. Ethanol metabolism endproducts affect the structure of the proteasome, and, therefore, change the proteasome interaction with its regulatory complexes 19S and PA28, as well as its interacting proteins. Chronic ethanol feeding alters the ubiquitin-proteasome activity by altering the interaction between the 19S and the 20S proteasome interaction. The degradation of oxidized and damaged proteins is thus decreased and leads to accumulation of insoluble protein aggregates, such as Mallory-Denk bodies. Ethanol also affects the immunoproteasome formation. PA28a/b interactions with the 20S proteasome are decreased in the proteasome fraction isolated from the liver of rats fed ethanol chronically, thus affecting the cellular antigen presentation and defense against pathogenic agents. Recently, it has been shown that ethanol also affects the proteasome interacting proteins (PIPs). Interaction of the proteasome with Ecm29 and with deubiquitinating enzymes Rpn11, UCH37, and Usp14 has been found to decrease. However, the two UBL-ubiquitin-associated domain (UBA) PIPs p62 and valosin-containing protein are upregulated when the proteasome is inhibited. The increase of these UBL-UBA proteins, as well as the increase in Hsp70 and Hsp25 levels, compensated for the proteasome failure and helped in the unfolding/docking of misfolded proteins. Chronic alcohol feeding to rats causes a significant inhibition of the proteasome pathway and this inhibition results from a decreases of the interaction between the 20S proteasome and the regulatory complexes, PIPs, and the ubiquitin system components.展开更多
AIM： To investigate the biological function of p7 protein and to look for proteins interacting with p7 protein in hepatocytes. METHODS： We constructed p7 protein bait plasmid by cloning the gene of p7 protein into p...AIM： To investigate the biological function of p7 protein and to look for proteins interacting with p7 protein in hepatocytes. METHODS： We constructed p7 protein bait plasmid by cloning the gene of p7 protein into pGBKTT, then transformed it into yeast AH109 （a type）. The transformed yeast was mated with yeast Y187 （α type） containing liver cDNA library plasmid, pACT2 in 2×YPDA medium. Diploid yeast was plated on synthetic dropout nutrient medium （SD/- Trp-Leu-His-Ade） containing x-α-gal for selection and screening. After extracting and sequencing of plasmids from blue colonies, we performed sequence analysis by bioinformatics. RESULTS： Fifty colonies were selected and sequenced. Among them, one colony was Homo sapiens signal sequence receptor, seven colonies were Homo sapiens H19, seven colonies were immunoglobulin superfamily containing leucine-rich repeat, three colonies were spermatid peri-nuclear RNA binding proteins, two colonies were membrane-spanning 4-domains, 24 colonies were cancer-associated antigens, four colonies were nudeoporin 214 ku and two colonies were CLL-associated antigens. CONCLUSION： The successful cloning of gene of protein interacting with p7 protein paves a way for the study of the physiological function of p7 protein and its assodated protein.展开更多
To screen for novel binding proteins interacting with high-risk HPV 18 E6 oncogene, the strain AH 109 was transformed with pGBKT7-HPV 18 E6 plasmid, and subsequent transference was utilized to screen for interacting p...To screen for novel binding proteins interacting with high-risk HPV 18 E6 oncogene, the strain AH 109 was transformed with pGBKT7-HPV 18 E6 plasmid, and subsequent transference was utilized to screen for interacting proteins with HPV 18 E6 in human Hela cDNA library. HPV 18 E6 mRNA was expressed in yeast and there was no self-activation and toxicity in AH109. Seven proteins that interacted with HPV18 E6, including transmembrane protein 87B, phosphonoformate immuno-associated protein 5, vimentin, KM-HN-1 protein, dedicator of cytokinesis 7, vaccinia related kinase 2 and a hypothetical protein, were identified. It was suggested that yeast two-hybrid system is an efficient for screening interacting proteins. The high-risk HPV 18 E6 oncogene may interact with the proteins, which may be associated with signal transduction and transcriptional control, epithelial cell invasion and migration, as well as humoral and cellular immune etc. This investigation provides functional clues for further exploration of potential oncogenesis targets for cancer biotherapy.展开更多
Pockets in proteins have been known to be very important for the life process. There have been several studies in the past to automatically extract the pockets from the structure information of known proteins. However...Pockets in proteins have been known to be very important for the life process. There have been several studies in the past to automatically extract the pockets from the structure information of known proteins. However, it is difficult to find a study comparing the precision of the extracted pockets from known pockets on the protein. In this paper, we propose an algorithm for extracting pockets from structure data of proteins and analyze the quality of the algorithm by comparing the extracted pockets with some known pockets. These results in this paper can be used to set the parameter values of the pocket extraction algorithm for getting better results.展开更多
基金supported by grants from the Special Foundation of President of the Chinese Academy of Sciences(Grant No.,YZJJ2020QN27,YZJJ2021QN33)Anhui Provincial Natural Science Foundation(Grant No.,2108085MC79).
文摘HCLS1-associated protein X-1(HAX1)is a multifunctional mitochondrial protein involved in the regulation of apoptosis,a crucial process of programmed cell death,and mRNA processing.Despite its significance,limited structural data is available for HAX1,hindering a comprehensive understanding of its biological function.Notably,the caseinolytic mitochondrial matrix peptidase chaperone subunit B(CLPB)has been identified as an interacting partner of HAX1,yet the biophysical properties and binding affinity governing their interaction remain poorly defined.In this study,we present a thorough biophysical characterization of full-length human HAX1 and CLPB,accomplished through recombinant expression and purification.By employing size exclusion chromatography,dynamic light scattering,and circular dichroism spectroscopy,we successfully established their biophysical properties,revealing contrasting structural features,with CLPB displaying a-helical content and HAX1 exhibiting a disordered nature.Moreover,we employed solutionstate nuclear magnetic resonance(NMR)spectroscopy to probe their binding affinity.Our findings demonstrate the formation of stable multimeric complexes between HAX1 and CLPB,and we quantified a dissociation constant in the low range of micro-molar for their high affinity interaction.These results lay the foundation for further in-depth investigations into the dynamics and energetics governing the HAX1-CLPB interaction,ultimately contributing to a comprehensive understanding of their functional mechanisms.
基金funded by the National Natural Science Foundation of China(32202513)the Applied Technology Research and Development Foundation of Inner Mongolia Autonomous Region,China(2021PT0001)+3 种基金the Natural Science Foundation of Inner Mongolia Autonomous Region,China(2021BS03002)the Inner Mongolia Autonomous Region Universities“Young Science and Technology Talent Support Project”,China(NJYT24067)the Inner Mongolia University High-Level Talent Research Program,China(10000-21311201/056)the Inner Mongolia Autonomous Region Department of Education First-class Scientific Research Project,China(YLXKZX-ND-030)。
文摘Melon(Cucumis melo)is an economically important horticultural crop cultivated worldwide.NAC(NAM/ATAC/CUC)transcription factors play crucial roles in the transcriptional regulation of various developmental stages in plant growth and fruit development,but their gene functions in melon remain largely unknown.Here,we identified 78 CmNAC family genes with an integrated and conserved no apical meristem(NAM)domain in the melon genome by performing genome-wide identification and bioinformatics analysis.Transcriptome data analysis and qRTPCR results showed that most CmNACs are specifically enriched in either the vegetative or reproductive organs of melon.Through genetic transformation,we found that overexpression of CmNAC34 in melons led to early ripening fruits,suggesting its positive role in promoting fruit maturation.Using yeast two-hybrid and bimolecular fluorescence complementation assays,we verified the direct protein interaction between CmNAC34 and CmNACNOR.The expression patterns of CmNAC34 and CmNAC-NOR were similar in melon tissues,and subcellular localization revealed their nuclear protein characteristics.We transformed CmNAC-NOR in melon and found that its overexpression resulted in early ripening fruits.Then,the yeast one-hybrid and dual luciferase reporter gene assays showed that the CmNAC34 protein can bind to the promoters of two glyoxalase(GLY)genes,which are involved in the abscisic acid signal pathway and associated with fruit regulation.These findings revealed the molecular characteristics,expression profiles,and functional patterns of the NAC family genes and provide new insights into the molecular mechanism by which CmNAC34 regulates climacteric fruit ripening.
文摘The yeast two\|hybrid system is a molecular genetic approach for protein interaction and it is widely used to screen for proteins that interact with a protein of interest in recent years.This process includes,construction and testing of the bait plasmid,screening a plasmid library for interacting fusion protein,elimination of false positives and delection analysis of true positives.This procedure is designed to allow investigators to identify proteins and their encoding cDNAs that have a biologically significant interaction with a protein of interest.More and more studies have demonstrated that the two\|hybrid system is a powerful and sensitive technique for the identification of genes that code for proteins that interact in a biologically significant fashion with a protein of interest in higher plants.This method has been used to identify new interaction protein in many laboratories.The recently reported yeast tri\|brid system,should allow the investigation of more complex protein\|protein interactions.The aim of this review is to outline the recent progress made in protein interactions by using yeast two\|hybrid system.
基金financially supported by grants from the Natural Science Foundation of Shandong Province,China(ZR2018LC005 and ZR2019BC107)the Agricultural Science and Technology Innovation Project of Shandong Academy of Agricultural Sciences,China(CXGC2022C02)。
文摘The B-box(BBX)family of proteins consists of zinc-finger transcription factors with one or two highly conserved B-box motifs at their N-termini.BBX proteins play crucial roles in various aspects of plant growth and development,including seedling photomorphogenesis,shade avoidance,flowering time,and biotic and abiotic stress responses.Previous studies have identified many different BBXs from several plant species,although the BBX family members in maize are largely unknown.Genome-wide identification and comprehensive analysis of maize BBX(ZmBBX)expression and interaction networks would therefore provide valuable information for understanding their functions.In this study,36 maize BBXs in three major clades were identified.The ZmBBXs within a given clade were found to share similar domains,motifs,and genomic structures.Gene duplication analyses revealed that the expansion of BBX proteins in maize has mainly occurred by segmental duplication.The expression levels of ZmBBXs were analyzed in various organs and tissues,and under different abiotic stress conditions.Protein–protein interaction networks of ZmBBXs were established using bioinformatic tools and verified by bimolecular fluorescence complementation(BiFC)assays.Our findings can facilitate a greater understanding of the complexity of the ZmBBX family and provide novel clues for unravelling ZmBBX protein functions.
文摘The mechanism and interaction among Rb/p16, Rb/E2F1 and HDAC1 proteins in gallbladder carcinoma were investigated. By using the immunoprecipitation method, the interactions among Rb, p16, E2F1, HDAC1 proteins in gallbladder carcinoma cell line （Mz-ChA-1） were studied. It was found that there were Rb and E2F1 proteins in the precipitates with anti-HDAC1, and there were HDAC1 and E2F1 proteins in the precipitate with anti-Rb. It was concluded that there are specific interactions among Rb, HDAC1 and E2F1 proteins in gallbladder carcinoma, indicating the existence of the direct Rb/E2F1/HDAC1 signal transduction pathway. There is no direct relationship between p16 proteins with Rb, HDAC1, and E2F1 proteins.
基金funded by the National Natural Science Foundation of China(grant no.32260760)the Science and Technology Program of Guizhou Province(grant no.20201Z002)the Platform Construction Project of Engineering Research Center for Protected Vegetable Crops in Higher Learning Institutions of Guizhou Province(Qianjiaoji[2022]No.040).
文摘Hot pepper(Capsicum annuum var.conoides)is a significant vegetable that is widely cultivated around the world.Currently,global climate change has caused frequent severe weather events,and waterlogging stress harms the pepper industry by affecting the planting period,growth conditions,and disease susceptibility.The gene CaABI3/VP1-1 could improve pepper waterlogging tolerance.In order to explore the upstream regulatory mechanism of CaABI3/VP1-1,a high-quality standardized yeast hybrid library was successfully constructed for yeast one-,two-,and threehybrid screening using pepper‘ZHC2’as the experimental material,with a library recombinant efficiency of up to 100%.The length of inserted fragments varied from 650 to 5000 bp,the library titer was 5.18×10^(6)colony-forming units(CFU)·mL-1,and the library capacity was 1.04×10^(7)CFU of cDNA inserts.The recombinant bait plasmid was used to successfully identify 78 different proteins through the yeast one-hybrid system,including one transcription factor within the ethylene-responsive factor family and the other within the growth-regulating factor family.The interaction happened between LOC124895848 and CaABI3/VP1-1 promoter by point-to-point yeast one-hybrid experiment.The expression level of the 12 selected protein-coding genes was then evaluated by quantitative real-time polymerase chain reaction.Results indicated the protein coding genes showed different responses to waterlogging stress and that the activity of the CaABI3/VP1-1 promoter could be inhibited or activated by up-regulating or down-regulating gene expression,respectively.The identification of these proteins interacting with the promoter provides a new perspective for understanding the gene regulatory network of hot pepper operating under waterlogging stress and provides theoretical support for further analysis of the complex regulatory relationship between transcription factors and promoters.
基金Project supported by the Gansu Province Industrial Support Plan (Grant No.2023CYZC-25)the Natural Science Foundation of Gansu Province (Grant No.23JRRA770)the National Natural Science Foundation of China (Grant No.62162040)。
文摘Essential proteins are inseparable in cell growth and survival. The study of essential proteins is important for understanding cellular functions and biological mechanisms. Therefore, various computable methods have been proposed to identify essential proteins. Unfortunately, most methods based on network topology only consider the interactions between a protein and its neighboring proteins, and not the interactions with its higher-order distance proteins. In this paper, we propose the DSEP algorithm in which we integrated network topology properties and subcellular localization information in protein–protein interaction(PPI) networks based on four-order distances, and then used random walks to identify the essential proteins. We also propose a method to calculate the finite-order distance of the network, which can greatly reduce the time complexity of our algorithm. We conducted a comprehensive comparison of the DSEP algorithm with 11 existing classical algorithms to identify essential proteins with multiple evaluation methods. The results show that DSEP is superior to these 11 methods.
基金supported by the National Natural Science Foundation of China,Nos.91849115 and U1904207(to YX),81974211 and 82171247(to CS)Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences,No.2020-PT310-01(to YX).
文摘The E3 ubiquitin ligase,carboxyl terminus of heat shock protein 70(Hsp70)interacting protein(CHIP),also functions as a co-chaperone and plays a crucial role in the protein quality control system.In this study,we aimed to investigate the neuroprotective effect of overexpressed CHIP on Alzheimer’s disease.We used an adeno-associated virus vector that can cross the blood-brain barrier to mediate CHIP overexpression in APP/PS1 mouse brain.CHIP overexpression significantly ameliorated the performance of APP/PS1 mice in the Morris water maze and nest building tests,reduced amyloid-βplaques,and decreased the expression of both amyloid-βand phosphorylated tau.CHIP also alleviated the concentration of microglia and astrocytes around plaques.In APP/PS1 mice of a younger age,CHIP overexpression promoted an increase in ADAM10 expression and inhibitedβ-site APP cleaving enzyme 1,insulin degrading enzyme,and neprilysin expression.Levels of HSP70 and HSP40,which have functional relevance to CHIP,were also increased.Single nuclei transcriptome sequencing in the hippocampus of CHIP overexpressed mice showed that the lysosomal pathway and oligodendrocyte-related biological processes were up-regulated,which may also reflect a potential mechanism for the neuroprotective effect of CHIP.Our research shows that CHIP effectively reduces the behavior and pathological manifestations of APP/PS1 mice.Indeed,overexpression of CHIP could be a beneficial approach for the treatment of Alzheimer’s disease.
基金supported by the Research Project of Maternal and Child Health Hospital of Hubei Province(No.2023SFYM008)Key Project of Hubei Provincial Natural Science Foundation(No.JCZRLH202500304).
文摘Objective ZW10 interacting kinetochore protein(ZWINT)has been demonstrated to play a pivotal role in the growth,invasion,and migration of cancers.Nevertheless,whether the expression levels of ZWINT are significantly correlated with clinicopathological characteristics and prognostic outcomes of patients with breast cancer remains elusive.This study systematically investigated the clinical significance of ZWINT expression in breast cancer through integrated molecular subtyping and survival analysis.Methods We systematically characterized the spatial expression pattern of ZWINT across various breast cancer subtypes and assessed its prognostic significance using an integrated bioinformatics approach that involved multi-omics analysis.The approach included the Breast Cancer Gene-Expression Miner v5.1(bc-GenExMiner v5.1),TNMplot,MuTarget,PrognoScan database,and Database for Annotation,Visualization,and Integrated Discovery(DAVID).Results Our analysis revealed consistent upregulation of ZWINT mRNA and protein expression across distinct clinicopathological subtypes of breast cancer.ZWINT overexpression demonstrated significant co-occurrence with truncating mutations in cadherin 1(CDH1)and tumor protein p53(TP53),suggesting potential functional crosstalk in tumor progression pathways.The overexpression of ZWINT correlated with adverse clinical outcomes,showing 48%increased mortality risk(overall survival:HR 1.48,95%CI 1.23–1.79),66%higher recurrence probability(relapse-free survival:1.66,95%CI 1.50–1.84),and 63%elevated metastasis risk(distant metastasis-free survival:HR 1.63,95%CI 1.39–1.90).Multivariate Cox regression incorporating TNM staging and molecular subtypes confirmed ZWINT as an independent prognostic determinant(P<0.001,Harrell’s C-index=0.7827),which was validated through bootstrap resampling(1000 iterations).Conclusion ZWINT may serve as a potential biomarker for prognosis and a possible therapeutic target alongside TP53/CDH1 in breast cancer.
基金supported by the National Natural Science Foundation of China(31871622)the Key R&D Program of Shandong Province,China(2022LZG001)。
文摘FCS-like zinc finger(FLZ)gene family members are C2-C2 zinc finger proteins that take part in seed dormancy,resistance to Myzus persicae 1,sucrose signaling and abiotic stresse tolerance.However,their functions,especially the molecular mechanism through which FLZs function,are not well understood.In this study,we characterized 120FLZs in wheat and revealed the function and mechanism of TaFLZ54D increasing salt stress tolerance in transgenic wheat.Expression analysis demonstrated that TaFLZ54D can be induced by NaCl treatment and it had the highest expression level under NaCl treatment among the 120 FLZs.Over-expression of TaFLZ54D increased wheat salt stress tolerance and the transgenic plants had higher levels of superoxide dismutase(SOD)and peroxidase(POD)activities and soluble sugar content,but a lower Na^(+)/K^(+)ratio and malondialdehyde(MDA)content than the wild type(WT)plants.Potassium ion transmembrane transporters and serine/threonine kinase inhibitor proteins showed differential expression between Ta FLZ54D transgenic wheat and the WT.Yeast two hybrid and luciferase complementation assays revealed that TaSGT1 and TaPP2C are the proteins that interact directly with TaFLZ54D.In summary,TaFLZ54D enhances salt stress tolerance through interaction with TaSGT1 and TaPP2C to reduce Na^(+)absorption and mitigate oxidative stress.The interaction between TaFLZ54D and TaSGT1,as well as TaPP2C indicated a link between salt stress tolerance of TaFLZ54D and the ubiquitin-mediated degradation of negative regulatory proteins.
文摘Objective Oral squamous cell carcinoma(OSCC)is an aggressive cancer with a high mortality rate.San-Zhong-Kui-Jian-Tang(SZKJT),a Chinese herbal formula,has long been used as an adjuvant therapy in cancer clinical practice.Although its therapeutic effects and molecular mechanisms in OSCC have been previously elucidated,the potential interactions and mechanisms between the active phytochemicals and their therapeutic targets are still lacking.Methods The present study employed network pharmacology and topology approaches to establish a“herbal ingredients–active phytochemicals–target interaction”network to explore the potential therapeutic targets of SZKJT-active phytochemicals in the treatment of OSCC.The role of the target proteins in oncogenesis was assessed via GO and KEGG enrichment analyses,and their interactions with the active phytochemicals of SZKJT were calculated via molecular docking and dynamic simulations.The pharmacokinetic properties and toxicity of the active phytochemicals were also predicted.Results A total of 171 active phytochemicals of SZKJT fulfilled the bioavailability and drug-likeness screening criteria,with the flavonoids quercetin,kaempferol,and naringenin having the greatest potential.The 4 crucial targets of these active phytochemicals are PTGS2,TNF,BCL2,and CASP3,which encode cyclooxygenase-2,tumor necrosis factor(TNF),BCL-2 apoptosis regulator,and caspase-3,respectively.The interactions between phytochemicals and target proteins were predicted to be thermodynamically feasible and stable via molecular docking and dynamics simulations.Finally,the results revealed that the IL-6/JAK/STAT3 pathway and TNF signaling via NF-κB are the two prominent pathways targeted by SZKJT.Conclusion In summary,this study provides computational data for in-depth exploration of the mechanism by which SZKJT activates phytochemicals to treat OSCC.
基金supported by National Natural Science Foundation of China(Grant Nos.32072653,32372794,31772357)Natural Science Foundation of Hubei Province(Grant No.2019CFA017)+1 种基金Ningbo Scientific and Technological Project(Grant No.2021Z006)the Fundamental Research Funds for the Central Universities(Grant No.2662023YLPY008)。
文摘Pumpkin is of great economic importance not only as food resources but also as the most widely used rootstock to graft cucurbit crops.Pumpkin rootstock improves salt tolerance of cucumber scion through respiratory burst oxidase homolog protein D(CmRbohD)-mediated reactive oxygen species(ROS)burst,which further enhances Na^(+)export and K^(+)uptake.Rboh D activation requires calcium signaling.However,the underlying mechanism remains largely unknown.In this study,we discovered two Rboh D members from pumpkin involved in the ROS burst at the early stage of salt stress.CmRbohD1 and CmRbohD2 were functionally redundant and double mutation significantly impaired salt tolerance in pumpkin.Overexpression of CmRbohD1 and CmRbohD2 mitigated salinity-induced damage and maintained a relatively low Na+content and high K+content.We screened the potential calcineurin B-like interacting protein kinases(Cm CIPKs)which could bind with CmRbohD1 and CmRbohD2.Our results revealed that two Rboh Ds formed complexes specifically with CmCIPK1,thereby bursting ROS production.Overexpression of CmCIPK1 promoted the early ROS burst under salt stress condition and maintained a relatively balanced Na+/K+homeostasis.Altogether,we proposed a CmCIPK1-CmRbohD1/D2 complex for pumpkin salt stress signaling transduction,which regulates the ROS burst and Na+/K+homeostasis.Our findings offer unprecedented insights into the general mechanism of pumpkin salt tolerance.
基金supported by the National Natural Science Foundation of China(31970348 and 31600256)the International Scientifc and Technological Cooperation Projects of Shaanxi Province,China(2022KW-45)+1 种基金the Young Academic Talent Support Program of Northwest Universitythe Xi’an Agriculture Technology Research General Project,China(24NYGG0088)。
文摘Stilbenes,a natural plant phytoalexin,are involved in the plant's response to various biotic and abiotic stresses in its environment.STILBENE SYNTHASE(STS)is the key enzyme regulating resveratrol synthesis in grapevine.However,the regulatory mechanism of STS gene expression remains unclear.In this study,we reported a NAC transcription factor,VqNAC17,in Vitis quinquangularis,which can improve plant resistance to salt stress,drought stress,and Pseudomonas syringae pv.Tomato DC3000(Pst DC3000)in transgenic Arabidopsis thaliana.Additionally,the interaction between the transcription factors VqNAC17 and VqMYB15 was confrmed using yeast two-hybrid and BiFC.In transgenic A.thaliana,VqNAC17 participates in plant immunity through interaction with VqMYB15 to affect the stilbene synthesis.Furthermore,the experimental results of the yeast one-hybrid assay and LUC transient expression assay found that VqNAC17 can also bind to the promoter of VqMYB15.These results indicate that VqNAC17 is a key regulator that can promote the expression of STS by interacting with VqMYB15.
基金funded under the National key research and development plan(2021YFC2101400)Chinese Academy of Engineering Strategic Research and Consulting Project(2023-XZ-79,2022-30-19)National Natural Science Foundation of China(22005019)。
文摘Three-dimensional(3D)bio-printing is an emerging tissue engineering technology,and its printing parameters have been upgraded to enable in-depth application in cell-cultured meat.However,excellent printable and edible bio-inks for cell-cultured meat are in urgent need of development.Therefore,a low-cost bio-ink based on albumin and gelatin was developed.At first,suitable printability of the bio-ink was determined by rheology analysis,excellent mechanical stability,and excellent mechanical stability of the printed scaffold was also proved by water absorption and degradation rate.Next,the biocompatibility of the scaffold and its interaction with cells were clarified through cell proliferation culture,cell status research and omics analysis.Notably,AG7 demonstrated better printability and AGS7 provided better conditions for cell attachment,proliferation and migration,S-shaped exponential growth curve further revealed the significant advantages of AGS7 scaffolds in cell culture.More importantly,the tissue culture process of muscle cells was simulated to organoid culture,which elucidated the interaction information between cells and scaffolds.This work has filled the vacancy in the industry and provides a novel strategy for the development of production of cell cultured meat.
基金supported by the National Natural Science Foundation of China(32072461)the Open Foundation of Shaanxi Key Laboratory of Plant Nematology,China(2021-SKL-01).
文摘The velvet protein family serves as a crucial factor in coordinating development and secondary metabolism in numerous pathogenic fungi.However,no previous research has examined the function of the velvet protein family in Fusarium oxysporum f.sp.niveum(FON),a pathogen causing a highly destructive disease in watermelon.In this study,∆fovel1 and∆folae1 deletion mutants and∆fovel1-C and∆folae1-C corresponding complementation mutants of FON were validated.Additionally,the phenotypic,biochemical,and virulence effects of the deletion mutants were investigated.Compared to the wild-type strains,the∆fovel1 and∆folae1 mutants exhibited altered mycelial phenotype,reduced conidiation,and decreased production of bikaverin and fusaric acid.Furthermore,their virulence on watermelon plant roots significantly decreased.All these alterations in mutants were restored in corresponding complementation strains.Notably,yeast two-hybrid results demonstrated an interaction between FoVel1 and FoLae1.This study reveals that FoVEL1 and FoLAE1 play essential roles in secondary metabolism,conidiation,and virulence in FON.These findings enhance our understanding of the genetic and functional roles of VEL1 and LAE1 in pathogenic fungi.
文摘AIM:To understand the complex reaction of gastric inflammation induced by Helicobacter pylori(H pylori) in a systematic manner using a protein interaction network. METHODS:The expression of genes significantly changed on microarray during H pylori infection was scanned from the web literary database and translated into proteins.A network of protein interactions was constructed by searching the primary interactions of selected proteins.The constructed network was mathematically analyzed and its biological function was examined.In addition,the nodes on the network were checked to determine if they had any further functional importance or relation to other proteins by extending them. RESULTS:The scale-free network showing the relationship between inflammation and carcinogenesis was constructed.Mathematical analysis showed hub and bottleneck proteins,and these proteins were mostly related to immune response.The network contained pathways and proteins related to H pylori infection,such as the JAK-STAT pathway triggered by interleukins.Activation of nuclear factor (NF)-κB,TLR4,and other proteins known to function as core proteins of immune response were also found. These immune-related proteins interacted on the network with pathways and proteins related to the cell cycle,cell maintenance and proliferation,andtranscription regulators such as BRCA1,FOS,REL,and zinc finger proteins.The extension of nodes showed interactions of the immune proteins with cancer- related proteins.One extended network,the core network,a summarized form of the extended network, and cell pathway model were constructed. CONCLUSION:Immune-related proteins activated by H pylori infection interact with proto-oncogene proteins.The hub and bottleneck proteins are potential drug targets for gastric inflammation and cancer.
基金Supported by NIH/NIAAA 8116Alcohol Center Grant on Liver and Pancreas P50-011999, Morphology Core
文摘Proteasome dysfunction has been repeatedly reported in alcoholic liver disease. Ethanol metabolism endproducts affect the structure of the proteasome, and, therefore, change the proteasome interaction with its regulatory complexes 19S and PA28, as well as its interacting proteins. Chronic ethanol feeding alters the ubiquitin-proteasome activity by altering the interaction between the 19S and the 20S proteasome interaction. The degradation of oxidized and damaged proteins is thus decreased and leads to accumulation of insoluble protein aggregates, such as Mallory-Denk bodies. Ethanol also affects the immunoproteasome formation. PA28a/b interactions with the 20S proteasome are decreased in the proteasome fraction isolated from the liver of rats fed ethanol chronically, thus affecting the cellular antigen presentation and defense against pathogenic agents. Recently, it has been shown that ethanol also affects the proteasome interacting proteins (PIPs). Interaction of the proteasome with Ecm29 and with deubiquitinating enzymes Rpn11, UCH37, and Usp14 has been found to decrease. However, the two UBL-ubiquitin-associated domain (UBA) PIPs p62 and valosin-containing protein are upregulated when the proteasome is inhibited. The increase of these UBL-UBA proteins, as well as the increase in Hsp70 and Hsp25 levels, compensated for the proteasome failure and helped in the unfolding/docking of misfolded proteins. Chronic alcohol feeding to rats causes a significant inhibition of the proteasome pathway and this inhibition results from a decreases of the interaction between the 20S proteasome and the regulatory complexes, PIPs, and the ubiquitin system components.
基金Supported by the National Natural Scientific Foundation, No. C03011402, No. C30070690the Research and Technique Foundation of PLA during the 9th-five year plan period, No. 98D063the Launching Foundation for Student Studying Abroad of PLA, No. 98H038and the Youth Research and Technique Foundation of PLA during the 10th-five year plan period, No. 01Q138the Research and Technique Foundation of PLA during the 10th-five year plan period, No. 01MB135
文摘AIM： To investigate the biological function of p7 protein and to look for proteins interacting with p7 protein in hepatocytes. METHODS： We constructed p7 protein bait plasmid by cloning the gene of p7 protein into pGBKTT, then transformed it into yeast AH109 （a type）. The transformed yeast was mated with yeast Y187 （α type） containing liver cDNA library plasmid, pACT2 in 2×YPDA medium. Diploid yeast was plated on synthetic dropout nutrient medium （SD/- Trp-Leu-His-Ade） containing x-α-gal for selection and screening. After extracting and sequencing of plasmids from blue colonies, we performed sequence analysis by bioinformatics. RESULTS： Fifty colonies were selected and sequenced. Among them, one colony was Homo sapiens signal sequence receptor, seven colonies were Homo sapiens H19, seven colonies were immunoglobulin superfamily containing leucine-rich repeat, three colonies were spermatid peri-nuclear RNA binding proteins, two colonies were membrane-spanning 4-domains, 24 colonies were cancer-associated antigens, four colonies were nudeoporin 214 ku and two colonies were CLL-associated antigens. CONCLUSION： The successful cloning of gene of protein interacting with p7 protein paves a way for the study of the physiological function of p7 protein and its assodated protein.
基金grants from "973" Program of China (No. 2002CB513100)National Natural Sci-ences Foundation of China (No. 30500596)
文摘To screen for novel binding proteins interacting with high-risk HPV 18 E6 oncogene, the strain AH 109 was transformed with pGBKT7-HPV 18 E6 plasmid, and subsequent transference was utilized to screen for interacting proteins with HPV 18 E6 in human Hela cDNA library. HPV 18 E6 mRNA was expressed in yeast and there was no self-activation and toxicity in AH109. Seven proteins that interacted with HPV18 E6, including transmembrane protein 87B, phosphonoformate immuno-associated protein 5, vimentin, KM-HN-1 protein, dedicator of cytokinesis 7, vaccinia related kinase 2 and a hypothetical protein, were identified. It was suggested that yeast two-hybrid system is an efficient for screening interacting proteins. The high-risk HPV 18 E6 oncogene may interact with the proteins, which may be associated with signal transduction and transcriptional control, epithelial cell invasion and migration, as well as humoral and cellular immune etc. This investigation provides functional clues for further exploration of potential oncogenesis targets for cancer biotherapy.
基金Project supported by Creative Research Initiative from the Ministry of Science and Technology (MOST), Korea. BHAK Jonghwa is supported by Biogreen21 Fund and MOST Funds, Korea
文摘Pockets in proteins have been known to be very important for the life process. There have been several studies in the past to automatically extract the pockets from the structure information of known proteins. However, it is difficult to find a study comparing the precision of the extracted pockets from known pockets on the protein. In this paper, we propose an algorithm for extracting pockets from structure data of proteins and analyze the quality of the algorithm by comparing the extracted pockets with some known pockets. These results in this paper can be used to set the parameter values of the pocket extraction algorithm for getting better results.
