Screening and identification of genes trans-regulated by hepatitis C virus NC3 protein with microarray assay

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Hepatitis C virus NS3 protein up-regulates expression of thioredoxin reductase 1 gene

AIM: To investigate the transactivating effect of HCV NS3 protein on TXNRD1 gene promoter and the molecular biological mechanisms of HCV NS3 protein in HCV pathogeneicity.

METHODS: Polymerase chain reaction (PCR) technique was employed to amplify the sequence of TXNRD1 promoter from HepG2 genomic DNA, and the product was subcloned into pCAT3-Basic by Kpn I and Xho I, named pCAT3-TXNRD1p. pCAT3-TXNRD1p was transfected into the hepatoblastoma cell line HepG2, then cotransfected with pcDNA3.1(-)-NS3 by FuGENE 6 transfection reagents. The HepG2 cells transfected with pCAT3-Basic was used as negative control. The activity of CAT in HepG2 cells transfected was detected by an ELISA kit after 48 hours, which reflected the transactivating function of HCV NS3 protein to TXNRD1 gene promoter.

RESULTS: The expression vector pcDNA3.1(-)-NS3 and report vector pCAT3-TXNRD1p were constructed and confirmed by restriction enzyme digestion and sequencing. The expression of CAT in HepG2 cells co-transfected with pCAT3-TXNRD1p and pcDNA3.1(-)-NS3 is 9 times as higher as that of pCAT3-Basic, and twice as higher as that of pCAT3-TXNRD1p.

CONCLUSION: HCV NS3 protein can transactivate TXNRD1 promoter, and therefore up-regulate the expression of TXNRD1 gene.

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.

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.

Screening and identification of genes transactivated by human augmenter of liver regeneration by microarray assay

AIM: Augmenter of liver regeneration (ALR) is a protein that plays a role in liver regeneration. In order to clarify the effect of the expression of ALR on profile of the hepatocytic gene expression, we analyzed difference between the HepG2 cells transfected with ALR and controls by using gene chip technology.

METHODS: Total RNA was extracted from HepG2 cells,and RT-PCR was performed to amplify the coding region of ALR. The expression of ALR in the transfected HepG2 cells was confirmed by Western blot. Total mRNA was isolated from the transfected HepG2 cells with pcDNA3.1(-) and pcDNA3-ALR, respectively. cDNA was prepared by reverse transcription. Microarray assay was conducted for screening of up-and down-regulated genes in both HepG2 cells.

RESULTS: The expressive vector of pcDNA3(-)-ALR was constructed and confirmed by restriction enzyme digestion and DNA sequencing. The expression of ALR was confirmed by Western blot. After screening with cDNA microarray, we found 2 genes were up-regulated, and 24 genes including TNFRSF1A-associated via death domain, tissue inhibitor of metalloproteinase 1, epididymal androgen-related protein, down-regulated.

CONCLUSION: ALR is a cell growth factor, which has some influences on gene expression profile of hepatocytes; Microarray technology is a method to analyze gene expression spectra of trans-regulation of a protein and conducive to understand the regulative effect of ALR on hepatocytes and other biological function.

Screening and identification of genes transactivated by NS5A-TP4 protein by cDNA microarray assay

AIM: To study the molecular mechanism of NS5A-TP4 in the up- and down-regulated genes of hepatocyte by cDNA microarray assay.

METHODS: HepG2 cells were transfected by recombined expression plasmid pcDNA3.1(-)-NS5A-TP4. Total RNA was isolated from the transfected HepG2 cells with pcDNA3.1(-) and pcDNA3.1(-)-NS5A-TP4, respectively. cDNA was prepared by reverse transcription. cDNA microarray was conducted for screening of up- and down-regulated genes of both HepG2 cells.

RESULTS: After screening with cDNA microarray, we found that 12 genes were up-regulated, and 6 genes down-regulated. Some of them were involved in cell signal transduction, cell proliferation, and carcinogenesis.

CONCLUSION: cDNA microarray is an important choice for the analysis of target genes of NS5ATP4 transactivation. The obtained sequences bring some new clues for studying the biological functions of NS5ATP4 and infection mechanism of HCV.

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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.

Comparisons of differentially expressed genes transactivated by hepatitis B and C viral proteins using suppression subtractive hybridization and cDNA micro-array techniques

AIM: To clone and identify human genes transactivated by hepatitis B and C viral proteins via construction of a cDNA subtractive library with suppression subtractive hybridization (SSH) technique and cDNA microarray techniques.

METHODS: Suppression subtractive hybridization (SSH) and cDNA microarray techniques were used for screening and cloning of the target genes transactivated by hepatitis B and C viral proteins. The mRNA was isolated from HepG2 cells transfected recombinant vector expressing hepatitis B and C viral proteins and pcDNA3.1(-) empty vector,respectively. SSH and cDNA microarray were employed to analyze the differentially expressed DNA sequence between the two groups. In SSH assay, after restriction enzyme Rsa I digestion, small sizes of cDNAs were obtained. Then tester cDNA was divided into two groups and ligated to the specific adaptor 1 and adaptor 2, respectively. After tester cDNA was hybridized with driver cDNA twice and underwent two times of nested PCR and then was subcloned into T/A plasmid vectors to set up the subtractive library. Amplification of the library was carried out with E. coli strain JM109. The cDNA was sequenced and analyzed in GenBank with Blast search after PCR.

RESULTS: The subtractive library of genes transactivated by hepatitis B and C viral proteins was constructed successfully. The up-regulated and down-regulated genes from cDNA microarray assay was conducted for each of the hepatitis B and C viral proteins. The results were compared.

CONCLUSION: The obtained sequences may be target genes transactivated by hepatitis B and C viral proteins, among which some genes coding proteins involve cell cycle regulation, signal transduction, tumor immunity and development, and apoptosis.

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.

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.