Bioinformatics analysis of human hepatitis C virus core protein-binding protein 6 gene and protein

Proteomic analysis of etiolated juvenile tetraploid Robinia pseudoacacia branches during different cutting periods

The propagation of hard-branch cuttings of tetraploid Robinia pseudoacacia (black locust) is restricted by the low rooting rate; however, etiolated juvenile tetraploid black locust branches result in a significantly higher rooting rate of cuttings compared with non-etiolated juvenile tetraploid branches. To identify proteins that influence the juvenile tetraploid branch rooting process, two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectra (MALDI-TOF/TOF-MS) were used to analyze proteomic differences in the phloem of tetraploid R. pseudoacacia etiolated and non-etiolated juvenile branches during different cutting periods. A total of 58 protein spots differed in expression level, and 16 protein spots were only expressed in etiolated branches or non-etiolated ones. A total of 40 highly expressed protein spots were identified by mass spectrometry, 14 of which were accurately retrieved. They include nucleoglucoprotein metabolic proteins, signaling proteins, lignin synthesis proteins and phyllochlorin. These results help to reveal the mechanism of juvenile tetraploid R. pseudoacacia etiolated branch rooting and provide a valuable reference for the improvement of tetraploid R. pseudoacacia cutting techniques.

Screening and identification of interacting proteins with hepatitis B virus core protein in leukocytes and cloning of new gene C1

AIM: To investigate the biological function of HBcAg in pathogenesis of HBV replication in peripheral blood mononuclear cells (PBMCs).

METHODS: HBcAg region was amplified by polymerase chain reaction (PCR) and HBV HBcAg bait plasmid pGBKT7-HBcAg was constructed by routine molecular biological methods. Then the recombinant plasmid DNA was transformed into yeast AH109. After the HBV core protein was expressed in AH109 yeast strains (Western blot analysis), yeast-two hybrid screening was performed by mating AH109 with Y187 containing leukocyte cDNA library plasmid. Diploid yeast cells were plated on synthetic dropout nutrient medium (SD/-Trp-Leu-His-Ade) (QDO) and synthetic dropout nutrient medium (SD/-Trp-Leu-His-Ade) (TDO). The second screening was performed with the LacZ report gene ( yeast cells were grown in QDO medium containing X-α-gal). The interaction between HBV core protein and the protein obtained from positive colonies was further confirmed by repeating yeast-two hybrid. After plasmid DNA was extracted from blue colonies and sequenced, the results were analyzed by bioinformatic methods.

RESULTS: Eighteen colonies were obtained and sequenced, including hypermethylated in cancer 2 (3 colones), eukaryotic translation elongation factor 2 (2 colones), acetyl-coenzyme A synthetase 3 (1 colone), DNA polymerase gamma (1 colone), putative translation initiation factor (1 colone), chemokine (C-C motif) receptor 5 (1 colone), mitochondrial ribosomal protein L41 (1 colone), kyot binding protein genes (1 colone), RanBPM (1 colone), HBeAg-binding protein 3 (1 colone), programmed cell death 2 (1 colone). Four new genes with unknown function were identified.

CONCLUSION: Successful cloning of genes of HBV core protein interacting proteins in leukocytes may provide some new clues for studying the biological functions of HBV core protein.

Identification and analysis of rat homologous gene to human HBV pre-S1 protein-binding protein

AIM: To identify and analyze rat homologous gene to human hepatitis B virus (HBV) pre-S1-binding protein (PS1BP) coding gene.

METHODS: The human PS1BP was screened and identified from a hepatocyte expressive cDNA library by phage display technique with purified recombinant pre-S1 protein of HBV as the solidified matrix. The nucleotide sequence database GenBank, established by National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institute of Health (NIH), was searched for rat cDNA sequence homologous to human PS1BP cDNA by BLASTn tools online. A homologous cDNA sequence was identified as the rat PS1BP cDNA. The similarity and identity of rat PS1BP cDNA and amino acid (aa) sequences to human and mouse PS1BP genes were compared. The potential functional domains were predicted by online analysis tools.

RESULTS: The human PS1BP cDNA was identified by phage display technique. The rat PS1BP cDNA was identified by bioinformatics methods. The rat PS1BP cDNA consisted of 1 455 nt, and encoded a protein of 484 aa. The identity of rat PS1BP protein to human and mouse PS1BP proteins was 80.79% (391/484) and 92.98% (450/484), respectively. In the rat PS1BP protein sequence, several potential modification domains were identified.

CONCLUSION: Rat PS1BP cDNA and protein primary sequences are identified and analyzed.

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Identification and analysis of murine and rat homologous gene to human NS5ATP4 by bioinformatics method

AIM: To identify and analyze murine and rat NS5ATP4 cDNA sequences homologous to human NS5ATP4 cDNA sequence.

METHODS: The human NS5ATP4 cDNA was identified by combination of molecular biology and bioinformatics methods. The GenBank was searched for NS5ATP4 homologous cDNA sequences from mouse and rat. The identity and similarity were compared between human mouse and rat NS5ATP4 cDNA sequences.

RESULTS: The murine and rat NS5ATP4 cDNAs were consisted of 762 nucleotides (nt) and 756 nt, respectively. They encoded a protein of 253 amino acid residues (aa) and 251 aa, respectively. The similarity of murine and rat NS5ATP4 to human homologue was 90.29% and 84.25%, respectively, and the identity of murine and rat NS5ATP4 to human homologue was 95.65% and 86.96%, respectively.

CONCLUSION: The murine and rat NS5ATP4 cDNAs are identified.

Screening and identification of genes trans-regulated by a novel HBeAg binding protein E-18 with microarray assay

AIM: To investigate the biological functions of a novel hepatitis B virus e antigen (HBeAg) binding protein E-18, and to use cDNA microarray technique to screen genes regulated by E-18.

METHODS: A novel gene E-18 coding for HBeAg was screened and identified by using yeast two-hybrid system 3 and co-immunoprecipitation technique. The E-18 coding DNA fragment was amplified by reverse transcription polymerase chain reaction (RT-PCR) technique from HepG2 cell. The expressive vector of pcDNA3.1-E-18 was constructed by routine molecular biological methods. The HepG2 cells were transfected with pcDNA3.1(-) and pcDNA3.1-E-18, respectively by using lipofectamine. The total RNA was isolated and reverse transcribed. The cDNA of each sample were subjected to microarray screening with 1 152 cDNA probes and analyzed by bioinformatics.

RESULTS: E-18 cDNA sequence was obtained and identified by yeast two-hybrid screening and bioinformatics analysis. The expressive vector was constructed and confirmed by DNA sequencing analysis and restriction enzyme digestion. High quality mRNA and cDNA of transfected HepG2 cells had been prepared and successful microarray screening conducted. From the scanning results, there were 52 differential expression genes, of which 36 genes were down-regulated, and 16 genes were up-regulated.

CONCLUSION: Microarray technique is successfully used to screen the genes trans-regulated by E-18. The expression of E-18 protein affects the expression spectrum of HepG2 cell.

Cloning and identification of NS5ATP2 gene and its spliced variant transactivated by hepatitis C virus non-structural protein 5A

AIM: To clone and identify a new gene NS5ATP2 and its spliced variant transactivated by hepatitis C virus non-structural protein 5A.

METHODS: On the base of subtractive cDNA library of genes transactivated by NS5A protein of hepatitis C virus, the coding sequence of new gene and its spliced variant were obtained by bioinformatics methods. Polymerase chain reaction (PCR) was conducted to amplify NS5ATP2 gene.

RESULTS: The coding sequence of new gene and its spliced variant were cloned and Identification successfully.

CONCLUSION: A novel gene has been recognized as the new target transactivated by HCV NS5A protein. These results bring some new clues for studying the biological functions of the new gene and pathogenesis of the viral proteins.

Effects of HCBP6 protein on transact-ivating function of HCV core protein

AIM: To study the inhibitory effects of HCBP6 on the transactivating effect of HCV core protein.

METHODS: The recombinant vectors expressive HCV core protein and HCBP6 protein were constructed, respectively, by routine molecular techniques. The hepatoblastoma cell line HepG2 were co-transfected. The chloramphenicol transferase (CAT) expressive levels under the SV40 early promoter were determined by an enzyme-linked immuno-sorbent assay (ELISA) kit.

RESULTS: The recombinant vectors of pcDNA3.1(-)-HCBP6 and pcDNA3.1(-)-core were constructed, and demonstrated correctly by restriction enzyme digestion and sequencing analysis. The hepatoblastoma cell line HepG2 was transfected with the vector alone or combined, respectively. The expression level of CAT indicated that the inhibitory rate was 40.4%-62.3%.

CONCLUSION: The expression of HCBP6 has inhibitory effects on the transacting activity of HCV core protein.

Identification and sequence analysis of a Macaca fascicularis homologous gene to human hepatitis B viruse antigen binding protein E-19

AIM: To explore the biological and immunoregulatory functions of hepatitis B e antigen (HBeAg) which is a secreted nonparticulate version of the viral nucleocapsid hepatitis B core antigen (HBcAg), yeast-two hybrid technique was performed to seek proteins in hepatocytes interacting with HBeAg and a novel gene named as E-19 was identified. To clone E-19 homologous gene from different species, a Macaca fascicularis homologous gene E-19 was identified by bioinformatics.

METHODS: HBeAg bait plasmid was constructed and transformed into yeast AH109 (a type). AH109 was mated with yeast cells Y187 (type) containing liver cDNA library plasmid pCAT2 in 2×YPDA medium. Plasmid of true positive blue colonies were extracted and analyzed by DNA sequencing and a new human gene E-19 was identified. A Macaca fascicularis homologous gene E-19 was identified by bioinformatics methods.

RESULTS: A Macaca fascicularis homologous gene E-19 was identified by bioinformatics. The Macaca fascicularis homologous gene E-19 was consisted of 378 nt and encoded a protein of 125 aa.

CONCLUSION: Human gene E-19, a HBeAg interacting proteins in hepatocytes, is successfully cloned by yeast-two hybrid technique and a Macaca fascicularis homologous gene E-19 is identified by bioinformatics.

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Identification and characterization of retinol dehydrogenase 11 as a hepatitis C virus core protein-binding protein by yeast-two hybrid technique

AIM: To screen the hepatocyte protein interacting with HCV core protein.

METHODS: By using HCV core protein as a bait, yeast-two hybrid system 3 was employed for screening and identification of HCV core protein-binding proteins from a hepatocyte cDNA library expressed in yeast cells. The protein-protein interaction was confirmed by back-cross experiment, and the inserts of the expressive vectors were sequenced and analyzed by bioinformatics methods.

RESULTS: Among them we identified retinol dehydrogenase 11(RDH11/androgen- regulated short-chain dehydrogenase/reductase 1 (ARSDR1) as a HCV core protein-interacting protein. This is the first time, to the best of our knowledge, to know the fact that there are interactions of HCV core protein-retinol dehydrogenase 11.

CONCLUSION: The identification of retinol dehydrogenase 11 as the HCV core protein binding partner paves a new way for further understanding of the pathogenesis of HCV infection.

Identification and sequence analysis of mouse homologous gene coding for hepatitis C virus non-structural protein 5A-binding protein 37

AIM: To clone murine homologous gene to human NS5ABP37 gene, and to elucidate its biological functions and the possible effects in the pathogenesis of hepatitis C virus (HCV) infection.

METHODS: Yeast-two hybrid system was employed to screen the human liver cDNA library by using non-structural protein 5A (NS5A) of hepatitis C virus (HCV) as the bait. According to the homologous role between the species, a murine NS5ABP37 homologous to human NS5ABP37 was deduced by bioinformatics methods. The primary sequence of murine NS5ABP37 was searched for conserved domains by online tools of GeneBank.

RESULTS: Human NS5ABP37 was screened and cloned from human liver cDNA library by yeast-two hybrid system 3. The murine NS5ABP37 was deduced by bioinformatics methods. The open reading frame (ORF) of murine NS5ABP37 consisted of 1 488 nt encoding a protein of 495 amino acids. Calculated molecular weight was 54 583.67 dalton and predicted pI was 4.70. From the homologous protein search, murine NS5ABP37 was demonstrated homologous to leukocyte antigen related (LAR) protein precursor. The sequence of murine NS5ABP37 was deposited into GenBank, and the accession number was AY234860.

CONCLUSION: Successful identification and cloning of murine NS5ABP37, which is homologous to LAR protein precursor, paves a way for elucidating the biological function of murine NS5ABP37 and pathogenesis of hepatitis C virus infection.

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Cloning of the gene of preS1 promoter of hepatitis B virus specific DNA-binding protein 1

AIM: To identify the protein which has unknown function binding with the preS1 promoter of hepatitis B virus, and to clone its coding sequence.

METHODS: Yeast one-hybrid system was employed to screen a human liver cDNA library using 3 copies of SP I core sequence as a bait, and one unknown gene was obtained. The coding sequence of the preS1 promoter of hepatitis B virus specific DNA-binding protein 1 (SBP I) was cloned by bioinformatics methods.

RESULTS: The coding sequence of SBP1 was cloned successfully.

CONCLUSION: SBP1 has a complete open reading frame, and biological functions by binding with SP I. The sequence similarity results indicate that the human SBP1 is a new member of transcription factor C/EBP.

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Screening of the genes of HCV core interacting proteins from human leucocyte cDNA library by yeast two-hybrid system

AIM: To investigate the binding protein of hepatitis C virus core protein (HCVcore).

METHODS: The HCVcore gene was amplified by polymerase chain reaction (PCR) and HCVcore bait plasmid was constructed by using yeast-two hybrid system 3, then transformed into yeast AH109. The transformed yeast mated with yeast Y187 containing leucocyte cDNA library plasmid in 2×YPDA medium. Diploid yeast was plated on synthetic dropout nutrient medium (SD/-Trp-Leu-His-Ade) and synthetic dropout nutrient medium (SD/-Trp-Leu-His-Ade) containing x-α-gal for selecting two times and screening. After extracting and sequencing of plasmid from blue colonies, we underwent analysis by bioinformatics.

RESULTS: Six colonies were sequenced, among which,two colonies were golgi complex associated protein 1 (GOCAP1), one colony was Ran binding protein M (RanBPM), one colony was pellino homolog 2 (PELI2), and two colonies were KIAA1949 protein (KIAA1949).

CONCLUSION: Genes of HCV core interacting proteins in leucocyte are successfully cloned and the results bring some new clues for studying the biological functions of HCVcore and associated proteins.

Screening and identification of genes trans-regulated by a novel HBeAg binding protein E-36 with cDNA microarray assay

AIM: To investigate the biological functions of a novel hepatitis B virus e antigen (HBeAg) binding protein E-36, and to screen genes regulated by E-36.

METHODS: The E-36 coding DNA fragment was amplified by reverse transcription polymerase chain reaction (RT-PCR) technique from HepG2 cell. The expressive vector of pcDNA 3.1-E-36 was constructed by routine molecular biological methods. The HepG2 cells were transfected by pcDNA3.1(-) and pcDNA3.1-E-36, respectively by using lipofectamine. The total RNA was isolated and reverse transcribed. The cDNAs were subjected to microarray screening with 1 152 cDNA probes.

RESULTS: The expressive vector was constructed and confirmed by restriction enzyme digestion and DNA sequencing analysis. High quality mRNA and cDNA of transfected HepG2 cells were prepared and successful microarray screening conducted. From the scanning results, 20 genes were found to be up-regulated, including PTH-responsive osteosarcoma B1 protein, slit homolog 2, nuclear factor of kappa light polypeptide gene enhancer in B-cells 1, interleukin 3 receptor, caspase 2, angiotensin I converting enzyme, Low density lipoprotein 1, interkeukin 6, T-cell receptor rearranged beta chain gene V-region, activator of NFB, tumor suppressing subtransferable candidate 1, cyclin-dependent kinase-like 2, sialyltransferase 8, glutamate receptor, metabotropic 7, and 5 novel genes. Expression of the gene of eukaryotic translation elongation factor 2 could be down-regulated by E-36 protein.

CONCLUSION: The expression of E-36 protein affects the expression spectrum of HepG2 cell. The microarray is an important technique for the study of transactivating effects for viral proteins.