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Lyu S, Yuan X, Zhang H, Shi W, Hang X, Liu L, Cao Z, Wu Y. Complete genome sequence and analysis of a new lethal arterivirus, Trionyx sinensis hemorrhagic syndrome virus (TSHSV), amplified from an infected Chinese softshell turtle. Arch Virol 2019; 164:2593-2597. [PMID: 31270606 PMCID: PMC7087228 DOI: 10.1007/s00705-019-04324-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 05/22/2019] [Indexed: 11/05/2022]
Abstract
Trionyx sinensis hemorrhagic syndrome virus (TSHSV) is a newly discovered lethal arterivirus that causes serious disease in Trionyx sinensis in China. In this study, the complete genome sequence of TSHSV was determined by RACE cloning, and the functions of the predicted proteins were predicted. The complete genome of TSHSV was found to be 17,875 bp in length, and a 3'-end poly(A) tail was detected. Eight TSHSV hypothetical proteins (TSHSV-HPs) were predicted by gene model identification. TSHSV-HP2, 3 and 4 were associated with replicase activity, since papain-like protease (PLPs), serine-type endopeptidase, P-loop-containing nucleoside triphosphate hydrolase, and EndoU-like endoribonuclease motifs were detected. Phylogenetic analysis showed that TSHSV clusters with an arterivirus from a Chinese broad-headed pond turtle.
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Xu JK, Ye JY, Cao X, Zhang YH, Yuan XM, Zhao CM. [Polysomnographic comparation between dexmedetomidine-induced sleep and natural sleep]. ZHONGHUA ER BI YAN HOU TOU JING WAI KE ZA ZHI = CHINESE JOURNAL OF OTORHINOLARYNGOLOGY HEAD AND NECK SURGERY 2019; 54:405-409. [PMID: 31262103 DOI: 10.3760/cma.j.issn.1673-0860.2019.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To compare the parameters of polysomnography (PSG) in sleep structure and respiratory events between dexmedetomidine-induced sleep and natural sleep. Methods: From April 2016 to September 2018, a total of 44 patients with obstructive sleep apnea (OSA) and 3 patients with simple snoring completed PSG monitor both in natural sleep and dexmedetomidine-induced sleep in Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tsinghua Changgung Hospital. The PSG parameters were statistically analysed with SPSS 22.0 software. Results: The average dose of dexmedetomidine was (104.60±27.93) μg, and there was no significant difference between the induced-sleep efficiency and the natural sleep efficiency (82.14%±16.66% vs. 86.50%±9.18%, t=-1.559, P>0.05). There was no rapid eye movement(REM) stages in all 47 subjects and only 1 case of them had non-rapid eye movement(NREM) stage 3 in induced sleep. The percentage of NREM1 in total sleep time was statistically different between the two groups (42.10%±26.71% vs. 17.47%±11.68%, t=5.997, P<0.001),but there was no significant difference in the percentage of NREM2 in total sleep time between the two groups (56.96%±26.0% vs. 62.95%±9.03%, t=-1.521, P=0.135). About respiratory events, there were significant differences in apnea hypopnea index ((46.29±20.23)/h vs. (39.67±25.41)/h), obstructive apnea index (25.20[10.50,45.40]/h vs. 16.20[3.30,35.20]/h) between induced-sleep and natural sleep (t=2.297, Z=-3.008, all P<0.05), these difference were more significant in mild-to-moderate OSA. There were no statistically significant differences in central apnea index (0.00[0.00,2.80]/h vs. 0.40[0.10,1.20]/h), mixed apnea index (0.00[0.00,6.20]/h vs. 0.00[0.00,3.40]/h, hypopnea index (4.20[0.00,3.30]/h vs. 12.00[5.20,17.40]/h), Z=-0.110,-0.508,-1.544, all P>0.05). There were statistical differences in the lowest oxygen saturation (84.77%±7. 59% vs. 80.21%±11.62%, t=2.558, P=0.014). Conclusions: There is no significant difference in sleep efficiency and NREM2 between dexmedetomidine induced sleep and natural sleep.NREM3 sleep is rare induced, but REM sleep is none of all. And dexmedetomidine induced sleep may aggravate obstructive sleep apnea, but not central apnea.
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Yao J, Jiang X, Liu Q, Yuan X, Feng T, Li K, Zhao L. An available strategy based on accurate mass by ultra high performance liquid chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry technology to characterization of metabolic profile of palbociclib in rat urine, feces and bile. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1124:37-46. [PMID: 31176268 DOI: 10.1016/j.jchromb.2019.05.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 05/09/2019] [Accepted: 05/28/2019] [Indexed: 11/25/2022]
Abstract
Palbociclib (named PD 0332991) is a novel highly selective cyclin-dependent kinase 4 and 6 (CDK 4/6) inhibitor, which has been approved by the Food and Drug Administration (FDA) for the treatment of hormone-receptor-positive advanced breast cancer. This present study developed a comprehensive strategy to investigate the metabolic profile of palbociclib in rat urine, feces and bile samples based on an ultra high performance liquid chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry (UHPLC-FT-ICR MS). A total of 29 metabolites, including 18 phase I metabolites and 11 phase II metabolites, were detected and identified. The metabolic pathways included hydroxylation, oxidation, dehydrogenation, N-dealkylation, carbonylation, oxidative deamination, acetylation, glucuronidation, sulphate conjugation as well as the crossover of multiple metabolic pathways in vivo, and 16 of these metabolites were proposed for the first time. This study showed an insight into the metabolism of palbociclib in vivo, which may provide relevant chemical information for subsequent studies in the future.
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Wen Y, Yuan X, Qin F, Zhao L, Xiong Z. Development and validation of a hydrophilic interaction ultra-high-performance liquid chromatography-tandem mass spectrometry method for rapid simultaneous determination of 19 free amino acids in rat plasma and urine. Biomed Chromatogr 2018; 33:e4387. [PMID: 30238479 DOI: 10.1002/bmc.4387] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 09/04/2018] [Accepted: 09/13/2018] [Indexed: 12/21/2022]
Abstract
Determination of amino acids in biofluids is a challenging task because of difficulties deriving from their high polarity and matrix interference. A simple, reliable and high-throughput hydrophilic interaction UHPLC-MS/MS method was developed and validated for the rapid simultaneous determination of 19 free amino acids in rat plasma and urine samples in this paper. Hydrophilic method with a Waters Acquity UPLC BEH Amide column (100 × 2.1 mm,1.7 μm) was used with a gradient mobile phase system of acetonitrile and water both containing 0.2% formic acid. The analysis was performed on a positive electrospray ionization mass spectrometer via multiple reaction monitoring. Samples of 10 μL plasma and 50 μL urine were spiked with three deuterated internal standards, pretreated with 250 μL acetonitrile for one-step protein precipitation and a final dilution of urine samples. Good linearities (r > 0.99) were obtained for all of the analytes with the lower limit of quantification from 0.1 to 1.2 μg/mL. The relative standard deviation of the intra-day and inter-day precisions were within 15.0% and the accuracy ranged from -12.8 to 12.7%. The hydrophilic interaction UHPLC-MS/MS method was rapid, accurate and high-throughput and exhibited better chromatography behaviors than the regular RPLC methods. It was further successfully applied to detect 19 free amino acids in biological matrix.
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Zhang K, Yuan X, Zang J, Wang M, Zhao F, Li P, Cao H, Han J, Xing J, Dong J. The Kynurenine 3-Monooxygenase Encoding Gene, BcKMO, Is Involved in the Growth, Development, and Pathogenicity of Botrytis cinerea. Front Microbiol 2018; 9:1039. [PMID: 29867912 PMCID: PMC5968091 DOI: 10.3389/fmicb.2018.01039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/02/2018] [Indexed: 11/13/2022] Open
Abstract
A pathogenic mutant, BCG183, was obtained by screening the T-DNA insertion library of Botrytis cinerea. A novel pathogenicity-related gene BcKMO, which encodes kynurenine 3-monooxygenase (KMO), was isolated and identified via thermal asymmetric interlaced PCR, bioinformatics analyses, and KMO activity measurement. The mutant BCG183 grew slowly, did not produce conidia and sclerotia, had slender hyphae, and presented enhanced pathogenicity. The phenotype and pathogenicity of the BcKMO-complementing mutant (BCG183/BcKMO) were similar to those of the wild-type (WT) strain. The activities of polymethylgalacturonase, polygalacturonase, and toxins were significantly higher, whereas acid production was significantly decreased in the mutant BCG183, when compared with those in the WT and BCG183/BcKMO. Moreover, the sensitivity of mutant BCG183 to NaCl and KCl was remarkably increased, whereas that to fluconazole, Congo Red, menadione, H2O2, and SQ22536 and U0126 [cAMP-dependent protein kinase (cAMP) and mitogen-activated protein kinase (MAPK) signaling pathways inhibitors, respectively] were significantly decreased compared with the other strains. Furthermore, the key genes involved in the cAMP and MAPK signaling pathways, Pka1, Pka2, PkaR, Bcg2, Bcg3, bmp1, and bmp3, were significantly upregulated or downregulated in the mutant BCG183. BcKMO expression levels were also upregulated or downregulated in the RNAi mutants of the key genes involved in the cAMP and MAPK signaling pathways. These findings indicated that BcKMO positively regulates growth and development, but negatively regulates pathogenicity of B. cinerea. Furthermore, BcKMO was found to be involved in controlling cell wall degrading enzymes activity, toxins activity, acid production, and cell wall integrity, and participate in cAMP and MAPK signaling pathways of B. cinerea.
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Tong C, Chen N, Liao X, Yuan X, Sun M, Li X, FANG W. Continuous Passaging of a Recombinant C-Strain Virus in PK-15 Cells Selects Culture-Adapted Variants that Showed Enhanced Replication but Failed to Induce Fever in Rabbits. J Microbiol Biotechnol 2017; 27:1701-1710. [DOI: 10.4014/jmb.1704.04065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Pan X, Cao Z, Yuan J, Shi Z, Yuan X, Lin L, Xu Y, Yao J, Hao G, Shen J. Isolation and Characterization of a Novel Dicistrovirus Associated with Moralities of the Great Freshwater Prawn, Macrobrachium rosenbergii. Int J Mol Sci 2016; 17:ijms17020204. [PMID: 26848659 PMCID: PMC4783938 DOI: 10.3390/ijms17020204] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/20/2016] [Accepted: 01/26/2016] [Indexed: 11/17/2022] Open
Abstract
The giant freshwater prawn, Macrobrachium rosenbergii, is an economically important crustacean and is farmed in many countries. Since 2009, a larval mortality syndrome of M. rosenbergii has broken out and spread widely in the main breeding area, including Zhejiang, Jiangsu, Guangxi, and Guangdong Provinces in mainland China. A novel virus, named Macrobrachium rosenbergii Taihu virus (MrTV), was isolated from the moribund larvae and was determined to be the causative agent of the M. rosenbergii larval mortality syndrome by experimental infection. Further genomic sequencing suggested that the MrTV genome is monopartite, 10,303 nt in length, and dicistronic with two non-overlapping open reading frames (ORFs) separated by an intergenic region (IGR) and flanked by untranslated regions (UTRs). Phylogenetic analysis using the full-length genomic sequence and the putative amino acid sequences of the capsid protein revealed that MrTV was more closely related to the taura syndrome virus (TSV) than to any other viruses. According to these molecular features, we proposed that MrTV is a new species in the genus Aparavirus, family Dicistroviridae. These results may shed light on controlling larval mortality syndrome in M. rosenbergii.
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Yi Z, Hao G, Yuan X, Pan X, Xu Y, Yao J, Lin L, Yin W, Shen J. [Inactivated vaccine for hemorrhage of Grass carp up-regulates the expressions of major immune-related genes in spleen of Grass carp]. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 2015; 31:177-181. [PMID: 25652857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
OBJECTIVE To investigate the impact of the injection of inactivated vaccine for hemorrhage of Grass carp on the expressions of main immune-related genes in spleen including immunoglobulin M (IgM), major histocompatibility complexI(MHC I), interferon I(IFN1), complement 3 (C3), interleukin-1β (IL-1β) and intelectin genes. METHODS Ctenopharyngoden idellus kidney (CIK) cells were inoculated with Grass carp reovirus (GCRV). Then inactivated vaccine was prepared by inactivating virus suspension with formaldehyde. Vaccine was 50- and 100-times diluted with normal saline. The experiments included four groups: undiluted group, 50-times diluted group, 100-times diluted group and normal saline control group. Then healthy Grass carps with the average body mass (20 ± 5) g were intraperitoneally injected with vaccine or normal saline separately for each group. Spleens were collected at different time points after injection (0, 6, 12, 24, 72 hours) and total RNA extraction was performed immediately. Real-time quantitative PCR (qRT-PCR) was used to detect mRNA expressions of the six immune-related genes. RESULTS Compared with normal saline control group, inactivated vaccine injection increased mRNA expressions of the six immune-related genes in the spleen of Grass carp, indicating that the vaccine stimulated the Grass carp to generate non-specific and specific immune responses. In the immunized groups, relative expressions of the genes intelectin, MHCI, IL-1β, C3 were all up-regulated at first and then declined as time went on. Relative expression of IFNIgene reached the peak at 6 hours post-injection and then decreased gradually to the normal level. Differently, relative expression of IgM gene increased continuously within 0-72 hours post-injection. CONCLUSION The expressions of the six major immune-related genes were all up-regulated in the spleen of Grass carp injected with different doses of inactivated vaccine for hemorrhage of Grass carp.
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Zhao G, Wang J, Peng X, Li Y, Yuan X, Ma Y. Facile Solvothermal Synthesis of Mesostructured Fe3O4/Chitosan Nanoparticles as Delivery Vehicles for pH-Responsive Drug Delivery and Magnetic Resonance Imaging Contrast Agents. Chem Asian J 2013; 9:546-53. [DOI: 10.1002/asia.201301072] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 10/06/2013] [Indexed: 02/05/2023]
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Wu JX, Xu MY, Miao XR, Lu ZJ, Yuan XM, Li XQ, Yu WF. Functional up-regulation of P2X3 receptors in dorsal root ganglion in a rat model of bone cancer pain. Eur J Pain 2012; 16:1378-88. [PMID: 22528605 DOI: 10.1002/j.1532-2149.2012.00149.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2012] [Indexed: 12/30/2022]
Abstract
BACKGROUND Cancer-induced bone pain remains a clinical challenge due to the poor understanding of the mechanisms. Recent study revealed extracellular adenosine triphosphate (ATP) and P2X receptors may be implicated in nociceptive signalling under cancer pain state. Therefore, here we investigated the potential role of P2X(3) receptor in a rat model of bone cancer pain. METHODS Walker 256 tumour cells were inoculated into the left tibia of Wistar rats. The model was verified by X-ray imaging, pathology and behaviour examinations. The expression of P2X(3) receptors in dorsal root ganglia (DRG) was examined. Functional significance of altered P2X(3) receptors was investigated by measuring influx upon α,β-meATP stimulation in acutely dissociated DRG neurons. Moreover, A-317491, an antagonist of P2X(3) receptors, was administrated intrathecally or locally to evaluate its analgesia effect in the cancer pain animals. RESULTS The P2X(3) receptor was up-regulated for about 50% in DRG neurons in rats with bone cancer at both protein and mRNA levels and correlated with the pain behaviour in bone cancer rats. A 51.9% increase of α,β-me ATP (10 μM, for 4 s) evoked transient response currents and a higher percentage of neurons responsive to the application of α,β-me ATP was detected in bone cancer rats. Intrathecal or local injection of A-317491 significantly attenuated pain behaviour induced by bone cancer. CONCLUSIONS These results suggest that the P2X(3) receptor is functionally up-regulated in DRG in cancer rats. P2X(3) receptor is a promising target for therapeutic intervention in cancer patients for pain management.
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Chen N, Tong C, Li D, Wan J, Yuan X, Li X, Peng J, Fang W. Antigenic analysis of classical swine fever virus E2 glycoprotein using pig antibodies identifies residues contributing to antigenic variation of the vaccine C-strain and group 2 strains circulating in China. Virol J 2010; 7:378. [PMID: 21194462 PMCID: PMC3025870 DOI: 10.1186/1743-422x-7-378] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Accepted: 12/31/2010] [Indexed: 11/10/2022] Open
Abstract
Background Glycoprotein E2, the immunodominant protein of classical swine fever virus (CSFV), can induce neutralizing antibodies and confer protective immunity in pigs. Our previous phylogenetic analysis showed that subgroup 2.1 viruses branched away from subgroup 1.1, the vaccine C-strain lineage, and became dominant in China. The E2 glycoproteins of CSFV C-strain and recent subgroup 2.1 field isolates are genetically different. However, it has not been clearly demonstrated how this diversity affects antigenicity of the protein. Results Antigenic variation of glycoprotein E2 was observed not only between CSFV vaccine C-strain and subgroup 2.1 strains, but also among strains of the same subgroup 2.1 as determined by ELISA-based binding assay using pig antisera to the C-strain and a representative subgroup 2.1 strain QZ-07 currently circulating in China. Antigenic incompatibility of E2 proteins markedly reduced neutralization efficiency against heterologous strains. Single amino acid substitutions of D705N, L709P, G713E, N723S, and S779A on C-strain recombinant E2 (rE2) proteins significantly increased heterologous binding to anti-QZ-07 serum, suggesting that these residues may be responsible for the antigenic variation between the C-strain and subgroup 2.1 strains. Notably, a G713E substitution caused the most dramatic enhancement of binding of the variant C-strain rE2 protein to anti-QZ-07 serum. Multiple sequence alignment revealed that the glutamic acid residue at this position is conserved within group 2 strains, while the glycine residue is invariant among the vaccine strains, highlighting the role of the residue at this position as a major determinant of antigenic variation of E2. A variant Simpson's index analysis showed that both codons and amino acids of the residues contributing to antigenic variation have undergone similar diversification. Conclusions These results demonstrate that CSFV vaccine C-strain and group 2 strains circulating in China differ in the antigenicity of their E2 glycoproteins. Systematic site-directed mutagenesis of the antigenic units has revealed residues that limit cross-reactivity. Our findings may be useful for the development of serological differential assays and improvement of immunogenicity of novel classical swine fever vaccines.
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Chen N, Li D, Yuan X, Li X, Hu H, Zhu B, Wan X, Fang W. Genetic characterization of E2 gene of classical swine fever virus by restriction fragment length polymorphism and phylogenetic analysis. Virus Genes 2010; 40:389-96. [PMID: 20217206 DOI: 10.1007/s11262-010-0465-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 02/23/2010] [Indexed: 11/26/2022]
Abstract
An RT-nested PCR (RT-nPCR)-based restriction fragment length polymorphism (RFLP) analyses of the E2 gene were developed for genetic subtyping and differentiation of vaccinated and infected classical swine fever virus (CSFV) strains. RT-nPCR identified 96 CSFV-positive samples from 321 clinical specimens from southeastern China during 2003-2008. The PCR products of positive samples were further differentiated using MspI digestion, 23 were identified as the C-strain, 62 as field strains, and 11 as mixture of the vaccine strain and field ones. RFLP with BglI, DdeI, DraI, and PstI were then used for subtyping of the field CSFV isolates. Thirty-eight field isolates phylogenetically classified as subgroup 2.1 based on E2 were divided into 11 subtypes by this RFLP scheme. Both RFLP profiling and sequence-based phylogenetic analysis revealed genetic diversity of CSFV in the field. Three novel substitutions at amino acid positions 17, 93, and 286 were identified in the predominant subtype VI strains isolated in 2008 as compared to other strains including historical subtype VI strains. These results suggest that CSFV in China experienced gradual variations and evolutionary accumulation progress. Thus, the RFLP methods targeting on the CSFV E2 gene are suitable for epidemiological survey in endemic area where the C-strain is applied for vaccination. Combination of the RFLP schemes with sequence-based phylogenetic analysis could provide more detailed information on transmission of CSFV in the region or even its evolution.
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Zhou L, Li J, George R, Ruchaud S, Zhou HG, Ladbury JE, Earnshaw WC, Yuan X. Effects of full-length borealin on the composition and protein-protein interaction activity of a binary chromosomal passenger complex. Biochemistry 2009; 48:1156-61. [PMID: 19146389 PMCID: PMC2746994 DOI: 10.1021/bi801298j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The chromosomal passenger complex (CPC) comprises at least four protein components and functions at various cellular localizations during different mitotic stages to ensure correct chromosome segregation and completion of cytokinesis. Borealin, the most recently identified member of the CPC, is an intrinsically unstructured protein of low solubility and stability. Recent reports have demonstrated the formation of binary or ternary CPC subcomplexes incorporating short Borealin fragments in vitro. Using isothermal titration calorimetry, we show that full-length Borealin, instead of a Borealin fragment possessing the complete Survivin and INCENP recognition sequence, is required for the composition of a Borealin-Survivin complex competent to interact with INCENP. In addition, we show evidence that full-length Borealin, which forms high-order oligomers in its isolated form, is a monomer in the Borealin-Survivin CPC subcomplex.
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Yue Z, Carvalho A, Xu Z, Yuan X, Cardinale S, Ribeiro S, Lai F, Ogawa H, Gudmundsdottir E, Gassmann R, Morrison CG, Ruchaud S, Earnshaw WC. Deconstructing Survivin: comprehensive genetic analysis of Survivin function by conditional knockout in a vertebrate cell line. J Cell Biol 2008; 183:279-96. [PMID: 18936249 PMCID: PMC2568024 DOI: 10.1083/jcb.200806118] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Accepted: 09/22/2008] [Indexed: 01/30/2023] Open
Abstract
Survivin is a key cellular protein thought to function in apoptotic regulation, mitotic progression, or possibly both. In this study, we describe the isolation of two conditional knockouts of the survivin gene in chicken DT40 cells. DT40 cells lacking Survivin die in interphase after failing to complete cytokinesis. However, these cells show normal sensitivity to the chemotherapeutic agent etoposide. Expression of Survivin mutants against a null background to reassess the role of several key residues reveals that DT40 cells can grow normally if their sole Survivin is missing a widely studied cyclin-dependent kinase phosphorylation site or sites reportedly essential for binding to Smac or aurora B. Mutations in the nuclear export sequence or dimerization interface render cells temperature sensitive for growth. As an important caveat for other studies in which protein function is studied by transient transfection, three of the Survivin mutants fail to localize in the presence of the wild-type protein but do localize and indeed support life in its absence.
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Beuron F, Dreveny I, Yuan X, Pye VE, Mckeown C, Briggs LC, Cliff MJ, Kaneko Y, Wallis R, Isaacson RL, Ladbury JE, Matthews SJ, Kondo H, Zhang X, Freemont PS. Conformational changes in the AAA ATPase p97-p47 adaptor complex. EMBO J 2006; 25:1967-76. [PMID: 16601695 PMCID: PMC1456939 DOI: 10.1038/sj.emboj.7601055] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Accepted: 02/27/2006] [Indexed: 11/08/2022] Open
Abstract
The AAA+ATPase p97/VCP, helped by adaptor proteins, exerts its essential role in cellular events such as endoplasmic reticulum-associated protein degradation or the reassembly of Golgi, ER and the nuclear envelope after mitosis. Here, we report the three-dimensional cryo-electron microscopy structures at approximately 20 Angstroms resolution in two nucleotide states of the endogenous hexameric p97 in complex with a recombinant p47 trimer, one of the major p97 adaptor proteins involved in membrane fusion. Depending on the nucleotide state, we observe the p47 trimer to be in two distinct arrangements on top of the p97 hexamer. By combining the EM data with NMR and other biophysical measurements, we propose a model of ATP-dependent p97(N) domain motions that lead to a rearrangement of p47 domains, which could result in the disassembly of target protein complexes.
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Yuan X, Simpson P, Mckeown C, Kondo H, Uchiyama K, Wallis R, Dreveny I, Keetch C, Zhang X, Robinson C, Freemont P, Matthews S. Structure, dynamics and interactions of p47, a major adaptor of the AAA ATPase, p97. EMBO J 2004; 23:1463-73. [PMID: 15029246 PMCID: PMC391063 DOI: 10.1038/sj.emboj.7600152] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2003] [Accepted: 02/11/2004] [Indexed: 11/09/2022] Open
Abstract
p47 is a major adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is in regulation of membrane fusion events. Mono-ubiquitin recognition by p47 has also been shown to be crucial in the p97-p47-mediated Golgi membrane fusion events. Here, we describe the high-resolution solution structures of the N-terminal UBA domain and the central domain (SEP) from p47. The p47 UBA domain has the characteristic three-helix bundle fold and forms a highly stable complex with ubiquitin. We report the interaction surfaces of the two proteins and present a structure for the p47 UBA-ubiquitin complex. The p47 SEP domain adopts a novel fold with a betabetabetaalphaalphabeta secondary structure arrangement, where beta4 pairs in a parallel fashion to beta1. Based on biophysical studies, we demonstrate a clear propensity for the self-association of p47. Furthermore, p97 N binding abolishes p47 self-association, revealing the potential interaction surfaces for recognition of other domains within p97 or the substrate.
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Yuan X, Simpson P, Kondo H, McKeown C, Dreveny I, Zhang X, Freemont PS, Matthews S. Complete backbone resonance assignments of p47: the 41kDa adaptor protein of the AAA ATPase p97. JOURNAL OF BIOMOLECULAR NMR 2004; 28:309-310. [PMID: 14752269 DOI: 10.1023/b:jnmr.0000013689.02494.07] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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Lack J, O'Leary JM, Knott V, Yuan X, Rifkin DB, Handford PA, Downing AK. Solution Structure of the Third TB Domain from LTBP1 Provides Insight into Assembly of the Large Latent Complex that Sequesters Latent TGF-β. J Mol Biol 2003; 334:281-91. [PMID: 14607119 DOI: 10.1016/j.jmb.2003.09.053] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Almost all TGF-beta is secreted as part of a large latent complex. This complex is formed from three molecules, a latent transforming growth factor-beta binding protein (LTBP), which plays roles in targeting and activation, a latency associated peptide (LAP), which regulates latency, and the TGF-beta cytokine. LAP is the TGF-beta pro-peptide that is cleaved intracellularly prior to secretion, and TGF-beta binds non-covalently to LAP. Formation of the large latent complex is important for the efficient secretion of TGF-beta. Previous studies have revealed that the LTBP-LAP interaction is mediated by intracellular exchange of a single disulphide bond within the third, and only the third, TB domain (TB3) with LAP. We have previously reported the structure of a homologous TB domain from fibrillin-1. However, TB3 contains a two amino acid insertion, not found in fibrillin-1 TB domains, which is not amenable to molecular modelling. In order to clarify the basis of TB domain function, we have determined the solution NMR structure of TB3(LTBP1). Comparison with the fibrillin-1 TB domain reveals that the two-residue insertion is associated with a significant increase in solvent accessibility of one of the disulphide bonds (linking the second and sixth cysteine residues). Site-directed mutagenesis and NMR studies indicate that this is the only disulphide bond that can be removed without perturbing the TB domain fold. Furthermore, a ring of negatively charged residues has been identified that surrounds this disulphide bond. Homology modelling suggests that the surface properties of TB3 domains from different LTBP isoforms correlate with binding activities. This research provides testable hypotheses regarding the molecular basis of complex formation between LTBPs and LAPs.
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Fleming K, Ghuman J, Yuan X, Simpson P, Szendröi A, Matthews S, Curry S. Solution structure and RNA interactions of the RNA recognition motif from eukaryotic translation initiation factor 4B. Biochemistry 2003; 42:8966-75. [PMID: 12885229 DOI: 10.1021/bi034506g] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Eukaryotic initiation factor 4B (eIF4B) is a multidomain protein with a range of activities that serves primarily to promote association of messenger RNA to the 40S ribosomal subunit during translation initiation. We report here the solution structure of the eIF4B RNA recognition motif (RRM) domain. It adopts a classical RRM fold, with a beta alpha beta beta alpha beta topology. The most striking difference with other RRM structures is in the disposition of loop 3, which connects the beta 2 and beta 3 strands and is implicated in RNA recognition. This loop folds down against the body of the RRM and exhibits restricted motion on a milli- to microsecond time scale. Although it contributes to a large basic patch on the RNA binding surface, it does not protrude out from the domain as observed in other RRM structures, possibly implying a different mode of RNA binding. On its own, the core RRM domain provides only a relative weak interaction with RNA targets and appears to require extensions at the N- and C-terminus for high-affinity binding.
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Yuan X, Werner JM, Lack J, Knott V, Handford PA, Campbell ID, Downing AK. Effects of the N2144S mutation on backbone dynamics of a TB-cbEGF domain pair from human fibrillin-1. J Mol Biol 2002; 316:113-25. [PMID: 11829507 DOI: 10.1006/jmbi.2001.5329] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The calcium-binding epidermal growth factor-like (cbEGF) module and the transforming growth factor beta-binding protein-like (TB) module are the two major structural motifs found in fibrillin-1, the extracellular matrix (ECM) protein defective in the Marfan syndrome (MFS). An MFS-causing mutation, N2144S, which removes a calcium ligand in cbEGF32, does not detectably affect fibrillin-1 biosynthesis, rate of secretion, processing, or deposition of reducible fibrillin-1 into the ECM. Since the residue at position 2144 is normally engaged in calcium ligation, it is unable to mediate intermolecular interactions. We have shown previously that this mutation does not affect the folding properties of the TB or cbEGF domains in vitro, but does decrease calcium-binding in cbEGF and TB-cbEGF domain constructs. Here, we use NMR spectroscopy to probe the effects of the N2144S mutation on backbone dynamic properties of TB6-cbEGF32. Analysis of the backbone (15)N relaxation data of wild-type TB6-cbEGF32 has revealed a flexible inter-domain linkage. Parallel dynamics analysis of the N2144S mutant has shown increased flexibility in the region joining the two domains as well as in the calcium-binding site at the N terminus of cbEGF32. This research demonstrates that a small change in peptide backbone flexibility, which does not enhance proteolytic susceptibility of the domain pair, is associated with an MFS phenotype. Flexibility of the TB-cbEGF linkage is likely to contribute to the biomechanical properties of fibrillin-rich connective tissue microfibrils, and may play a role in the microfibril assembly process.
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Yuan X, Davydova N, Conte MR, Curry S, Matthews S. Chemical shift mapping of RNA interactions with the polypyrimidine tract binding protein. Nucleic Acids Res 2002; 30:456-62. [PMID: 11788707 PMCID: PMC99833 DOI: 10.1093/nar/30.2.456] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2001] [Revised: 11/16/2001] [Accepted: 11/16/2001] [Indexed: 02/05/2023] Open
Abstract
The polypyrimidine tract binding protein (PTB), a homodimer that contains four RRM-type RNA binding domains per monomer, plays important roles in both the regulation of alternative splicing and the stimulation of translation initiation as directed by the internal ribosome entry sites of certain picornaviruses. We have used chemical shift mapping experiments to probe the interactions between PTB-34, a recombinant fragment that contains the third and fourth RRM domains of the protein, and a number of short pyrimidine-rich RNA oligonucleotides. The results confirm that the RNAs interact primarily with the beta-sheet surface of PTB-34, but also reveal roles for the two long flexible linkers within the protein fragment, a result that is supported by mutagenesis experiments. The mapping indicates distinct binding preferences for RRM3 and RRM4 with the former making a particularly specific interaction with the sequence UCUUC.
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Abstract
Transdifferentiation is a process in which a stable cell's phenotype changes to that of a distinctly different cell type. It occurs during certain physiological processes and leads to transition of tumor cell phenotypes. The latter process includes neoplastic epithelial-epithelial transition, neoplastic epithelial-mesenchymal transition, neoplastic mesenchymal-epithelial transition and transition between non-neural and neural neoplastic cell. This phonomenon is exemplified in some origin-debated tumors, such as carcinosarcoma, pleomorphic adenoma, synovial sarcoma, Ewing's/pPNET, and malignant fibrohistiocytoma. We propose that differentiation disturbance of cancer cells should include not only undifferentiation and dedifferentiation, but also transdifferentiation as well. Tumor cell transdifferentiation may be influenced or determined by cellular genetic instabilities, proliferation and apoptosis, as well as by extracellular matrix and growth factors.
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Zhang Z, Yuan XM, Li LH, Xie FP. Transdifferentiation in neoplastic development and its pathological implication. Histol Histopathol 2001; 16:1249-62. [PMID: 11642744 DOI: 10.14670/hh-16.1249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transdifferentiation is a process in which a cell committed to a particular specialization changes to another quite distinct type. It occurs during embryological development and some pathological processes, and causes the tumor cells to express a phenotype different from that of their normal progenitors. Neoplastic transdifferentiation involves pathogenesis of cancer subtype, transition between neoplastic epithelia and neuroendocrine cell, transition between neoplastic epithelia and mesenchyme, as well as transition between non-neuroectodermal and neuroectodermal cells. We propose that differentiation disturbance of cancer cells should include not only lower-, un-, or de-differentiation, but also transdifferentiation. Tumor cell transdifferentiation results from genetic instabilities. In some type of neoplastic transition, the initiation may be induced by extracellular matrix and growth factors.
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Li W, Dalen H, Eaton JW, Yuan XM. Apoptotic death of inflammatory cells in human atheroma. Arterioscler Thromb Vasc Biol 2001; 21:1124-30. [PMID: 11451740 DOI: 10.1161/hq0701.092145] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Although the accumulation of cholesterol and other lipidic material is unquestionably important in atherogenesis, the reasons why this material progressively accumulates, rather than being effectively cleared by phagocytic cells such as macrophages, are not completely understood. We hypothesize that atheromatous lesions may represent "death zones" that contain toxic materials such as oxysterols and in which monocytes/macrophages become dysfunctional and apoptotic. Indeed, cathepsins B and L, normally confined to the lysosomal compartment, are present in the cytoplasm and nuclei of apoptotic (caspase-3-positive) macrophages within human atheroma. The possible involvement of oxysterols is suggested by experiments in which cultured U937 and THP-1 cells exposed to 7-oxysterols similarly undergo marked lysosomal destabilization, caspase-3 activation, and apoptosis. Like macrophages within atheroma, intralysosomal cathepsins B and L are normally present in the cytoplasm and nuclei of these oxysterol-exposed cells. Lysosomal destabilization, cathepsin release, and apoptosis may be causally related, because inhibitors of cathepsins B and L suppress oxysterol-induced apoptosis. Thus, toxic materials such as 7-oxysterols in atheroma may impair the clearance of cholesterol and other lipidic material by fostering the apoptotic death of phagocytic cells, thereby contributing to further development of atherosclerotic lesions.
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Yuan XM, Li W, Brunk UT, Dalen H, Chang YH, Sevanian A. Lysosomal destabilization during macrophage damage induced by cholesterol oxidation products. Free Radic Biol Med 2000; 28:208-18. [PMID: 11281288 DOI: 10.1016/s0891-5849(99)00220-8] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have previously shown that oxidized low-density lipoprotein (LDL) induces damage to the macrophage lysosomal membranes, with ensuing leakage of lysosomal contents and macrophage cell death. Cholesterol oxidation products (ChOx) have been reported to be the major cytotoxic components of oxidized LDL/LDL- and also to stimulate cholesterol accumulation in vascular cells. In the present study, we characterized the initial events during macrophage damage induced by cholesterol oxidation products (ChOx). Within 24 h of exposure, ChOx caused lysosomal destabilization, release to the cytosol of the lysosomal marker-enzyme cathepsin D, apoptosis, and postapoptotic necrosis. Enhanced autophagocytosis and chromatin margination was found 12 h after the exposure to ChOx, whereas apoptosis and postapoptotic necrosis was pronounced 24 and 48 h after the exposure. Some lysosomal vacuoles were then filled with degraded cellular organelles, indicating phagocytosis of apoptotic bodies by surviving cells. Because caspase-3 activation was detected in the ChOx-exposed cells, lysosomal destabilization may associate with the leakage of lysosomal enzymes, and activation of the caspase cascade. MnSOD mRNA levels were markedly increased after 24 h of exposure to ChOx, suggesting associated induction of mitochondrial protection repair or turnover. We conclude that ChOx-induced damage to lysosomes and mitochondria are sequelae to the cascade of oxysterol cytotoxic events. The early disruption of lysosomes induced by ChOx, with resultant autophagocytosis may be a critical event in apoptosis and/or necrosis of macrophages/foam cells during the development of atherosclerotic lesions.
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