Genomic analysis utilizing the yeast two-hybrid system

The Human Isoform of RNA Polymerase II Subunit hRPB11bα Specifically Interacts with Transcription Factor ATF4

Rpb11 subunit of RNA polymerase II of Eukaryotes is related to N-terminal domain of eubacterial α subunit and forms a complex with Rpb3 subunit analogous to prokaryotic α2 homodimer, which is involved in RNA polymerase assembly and promoter recognition. In humans, a POLR2J gene family has been identified that potentially encodes several hRPB11 proteins differing mainly in their short C-terminal regions. The functions of the different human specific isoforms are still mainly unknown. To further characterize the minor human specific isoform of RNA polymerase II subunit hRPB11bα, the only one from hRPB11 (POLR2J) homologues that can replace its yeast counterpart in vivo, we used it as bait in a yeast two-hybrid screening of a human fetal brain cDNA library. By this analysis and subsequent co-purification assay in vitro, we identified transcription factor ATF4 as a prominent partner of the minor RNA polymerase II (RNAP II) subunit hRPB11bα. We demonstrated that the hRPB11bα interacts with leucine b-Zip domain located on the C-terminal part of ATF4. Overexpression of ATF4 activated the reporter more than 10-fold whereas co-transfection of hRPB11bα resulted in a 2.5-fold enhancement of ATF4 activation. Our data indicate that the mode of interaction of human RNAP II main (containing major for of hRPB11 subunit) and minor (containing hRPB11bα isoform of POLR2J subunit) transcription enzymes with ATF4 is certainly different in the two complexes involving hRPB3-ATF4 (not hRPB11a-ATF4) and hRpb11bα-ATF4 platforms in the first and the second case, respectively. The interaction of hRPB11bα and ATF4 appears to be necessary for the activation of RNA polymerase II containing the minor isoform of the hRPB11 subunit (POLR2J) on gene promoters regulated by this transcription factor. ATF4 activates transcription by directly contacting RNA polymerase II in the region of the heterodimer of α-like subunits (Rpb3-Rpb11) without involving a Mediator, which provides fast and highly effective activation of transcription of the desired genes. In RNA polymerase II of Homo sapiens that contains plural isoforms of the subunit hRPB11 (POLR2J), the strength of the hRPB11-ATF4 interaction appeared to be isoform-specific, providing the first functional distinction between the previously discovered human forms of the Rpb11 subunit.

High throughput flow cytometry based yeast two-hybrid array approach for large-scale analysis of protein-protein interactions

The analysis of protein-protein interactions is a key focus of proteomics efforts. The yeast two-hybrid system (Y2H) has been the most commonly used method in genome-wide searches for protein interaction partners. However, the throughput of the current yeast two-hybrid array approach is hampered by the involvement of the time-consuming LacZ assay and/or the incompatibility of liquid handling automation due to the requirement for selection of colonies/diploids on agar plates. To facilitate large-scale Y2H assays, we report a novel array approach by coupling a GFP reporter based Y2H system with high throughput flow cytometry that enables the processing of a 96-well plate in as little as 3 min. In this approach, the yEGFP reporter has been established in both AH109 (MATa) and Y187 (MATα) reporter cells. It not only allows the generation of two copies of GFP reporter genes in diploid cells, but also allows the convenient determination of self-activators generated from both bait and prey constructs by flow cytometry. We demonstrate a Y2H array assay procedure that is carried out completely in liquid media in 96-well plates by mating bait and prey cells in liquid YPD media, selecting the diploids containing positive interaction pairs in selective media and analyzing the GFP reporter directly by flow cytometry. We have evaluated this flow cytometry based array procedure by showing that the interaction of the positive control pair P53/T is able to be reproducibly detected at 72 hr postmating compared with the negative control pairs. We conclude that our flow cytometry based yeast two-hybrid approach is robust, convenient, quantitative, and is amenable to large-scale analysis using liquid-handling automation.

Identification of candidate genes with pro-apoptotic properties by functional screening of randomly fragmented cDNA libraries

The sequences of many genomes are available; therefore, relevant methods are needed for rapid and efficient identification of functional genes. The ability of tumour cells to resist apoptosis induced by anticancer agents may decide the success of failure of tumour elimination. Although the CD95-signalling pathway is functional in tumour cells, the increased resistance of tumour cells to CD95-mediated apoptosis has been widely reported. In order to identify genes that might determine the response of tumour cells to CD95-mediated apoptosis, we modified the conventional technical knock out (TKO) strategy for isolation of genes that function in CD95-mediated apoptosis. Due to the fact that multiple different plasmids are usually introduced into the same cells, the effectiveness of the conventional TKO strategies is low. To overcome this obstacle, we replaced the conventional TKO strategy (based on stably expressed randomly fragmented cDNA libraries) with a multi-cycle selection procedure (based on transiently expressed randomly fragmented cDNA libraries with multi-cycle selection). Using this approach we could rapidly and significantly identify small numbers of antisense mRNA molecules, whose re-introduction into different tumour types confirmed their ability to block the pro-apoptotic function of their cognate genes. Thus, our modified TKO strategy provides a generally applicable procedure for the identification of functional genes with pro-apoptotic properties that may be clinically relevant to tumor therapy.

Cloning of spliced variant HBeBP4A of hepatitis B virus e antigen binding protein 4

AIM: To clone a new gene, binding protein 4 spliced variant HBeBP4A of hepatitis B virus e antigen (HBeAg), and to explore its function and structure by bioinformatical analysis.

METHODS: HBeBP4A was amplified by reverse transcription-polymerase chain reaction (RT-PCR) using HepG2 cDNA as template and inserted into pGEM-T easy vector by TA cloning. Recombinant eukaryotic expression vector (pcDNA^TM3.1/myc-HisA-HBeBP4A) was constructed by subcloning followed by restriction enzyme digestion analysis and sequencing. Bioinformatical methods were used to analyze its possible physical and chemical characteristics, structure, and function.

RESULTS: Spliced form of HBeBP4, named HBeBP4A, was amplified successfully by RT-PCR from HepG2 cDNA. Bioinformatical analysis showed that its new open reading frame (ORF) is 1104 bp in length and translated a protein containing 367 amino acid residues.

CONCLUSION: A new gene, spliced variant HBeBP4A of HBeAg binding protein 4, is recognized, and its recombinant eukaryotic expression vector is constructed.

Cloning and characterization of a novel hepatitis B virus core binding protein C12

AIM: To elucidate the biological function of HBV core antigen (HBcAg) on pathogenesis of hepatitis B, a novel gene C12 coding for protein with unknown function interacting with HBcAg in hepatocytes was identified and characterized.

METHODS: HBcAg bait plasmid pGBKT7-HBcAg was constructed and transformed into yeast AH109, then the transformed yeast was mated with yeast Y187 containing liver complementary DNA (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 screening twice. After extracting and sequencing of plasmid from blue colonies, we isolated a cDNA clone encoding a novel protein designated as C12 that directly interacted with HBcAg. The interaction between HBcAg and C12 was verified again by re-mating. pEGFP-N1-C12 fluorescent protein fusion gene was transfected in 293 and L02 cell, and observed by fluorescent microscope. MTT reduction assay was used to study the action of C12 protein effect on metabolism of mammal cell. Yeast two-hybrid and cDNA microarray were performed to search binding protein and differential expression genes regulated by C12 protein.

RESULTS: C12 gene was screened and identified by yeast two-hybrid system 3. The interaction between HBcAg and the novel protein coded by the new gene C12 was further confirmed by re-mating. After 48 h, fluorescence of fusion protein could be observed steadily in the 293 and L02 cell plasma. Under MTT assay, we found that the expression of C12 did not influence the growth of liver cells. Seventeen differential expression genes in HepG2 cells transfected with C12 protein expression plasmid by cDNA microarray, of which 16 genes were upregulated and 1 gene was downregulated by C12 protein. Twenty-one colonies containing 16 different genes coding for C12 protein binding proteins were isolated by yeast two-hybrid, there were 2 new genes with unknown function.

CONCLUSION: The novel protein C12 is located in cell plasma, and its overexpression has no significant effect on the metabolism of liver cell. It interacts with many proteins in hepatocytes and may be involved in many processes of gene expression.

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Autonomous activation of hepatitis B virus large surface protein

AIM: To construct the yeast expression vector of hepatitis B virus large surface protein (LHBs), and to study its autonomous activation.

METHODS: The Matchmaker GAL4 two-hybrid technique was used. The LHBs, pre-S1, pre-S2 and SHBs genes were amplified by polymerase chain reaction (PCR) with respective primers. The amplified PCR fragments were then subcloned into the EcoR I/BamH I sites (5'ands) of pGBKT7 vector to obtain the expression vectors including pGBKT7(-)-LHBs, pGBKT7(-)-preS1, pGBKT7(-)-preS2 and pGBKT7(-)-SHBs. This vectors were identifed by PCR and digestion of EcoR I/BamH I. After the constructed vectors were transformed into yeast AH109, the yeast cells were plated on synthetic dropout nutrient medium (SD/-Trp and SD/-Trp-His-Ade) containing x-a-gal for testing their autonomous activation.

RESULTS: The yeast expression vectors were constructed. The yeast cells transformed with pGBKT7-LHB and pGBKT7-preS1 vectors could grow well on both of the media. However, cells transformed with pGBKT7-preS2 and pGBKT7-SHBs vectors could only grow on the SD/-Trp medium.

CONCLUSION: The LHBs functions as a transcriptional transactivator, and serves as the functional GAL4 activation domain (AD) to activate transcription of reporter genes (ADE2, HIS3, MEL1 and LacZ). The autonomous activation of LHBs roots in its pre-S1 domain.

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Screening of HCTP4 interacting proteins in leukocytes by yeast-two hybrid technique

AIM: To investigate the biological function of HCTP4, yeast-two hybrid was performed to screen proteins interacting with HCTP4 in leukocytes.

METHODS: The HCTP4 gene was amplified by polymerase chain reaction (PCR) and HCTP4 bait plasmid was constructed by using yeast-two hybrid system 3, then the constructed vector was transformed into yeast AH109. The transformed yeast mated with yeast Y187 containing leukocytes 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--gal for selecting two times and screening. After extracting and sequencing of plasmid from blue colonies, we underwent analysis by bioinformatics.

RESULTS: Forty-four colonies were sequenced, among which twenty-five colonies were immunoglobulin lambda light chain, six human DNA sequences from clone RP11-189K21, four human DNA sequences from clone RP11-507C10, two homo sapiens 12p BAC RPCI11-75L1, one homo sapiens BAC clone RP11-21M10, one homo sapiens ubiquitin ligase mind bomb (MIB), one homo sapiens genomic DNA, chromosome 11 clone: RP11-867O8, one human DNA sequence from clone RP3-509I19, one homo sapiens small nuclear ribonucleoprotein polypeptide G, one homo sapiens UMP-CMP kinase (UMP-CMPK), and a new gene.

CONCLUSION: Genes of HCTP4 interacting proteins in leukocytes are successfully cloned and the results bring some new clues for studying the biological functions of HCTP4 and associated proteins.

Screening and cloning of genes coding for leukocyte proteins interacting with NS5ATP9 by yeast-two hybrid technique

AIM: To investigate the biological functions of NS5ATP9, and to screen proteins in leukocytes interacting NS5ATP9 protein by yeast-two hybrid.

METHODS: The NS5ATP9 gene was amplified by polymerase chain reaction (PCR) and NS5ATP9 bait plasmid was constructed by using yeast-two hybrid system 3, and the yeast AH109 was then transformed. The transformed yeast mated with yeast Y187 containing leukocytes 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--gal for selecting two times and screening. After extracting and sequencing of plasmid DNA from blue colonies, we underwent analysis by bioinformatics.

RESULTS: Forty six colonies were sequenced, among which thirteen colonies were Homo sapiens immunoglobulin light chain, ten ubiquitin, two ferritin heavy chain, eleven Homo sapiens rearranged immunoglobulin lambda light chain, one 14-3-3 family protein, one Meningococcus PorA protein, three RNA polymerase III, one tobacco mitogen activated protein kinase, two cytochrome P450 II, one SLIT2 protein, and one dependent-protein kinase catalylic subunit.

CONCLUSION: Genes of NS5ATP9 interacting proteins in leukocytes are successfully cloned and the results bring some new clues for studying the biological functions of NS5ATP9 and associated proteins.

Screening and cloning of human gene 5 transactivated by nonstructural protein 5A of hepatitis C virus

AIM: Human gene 5 transactivated by nonstructural protein 5A of hepatitis C virus (NS5ATP5) is a kind of protein with unknown function from the study with suppression subtractive hybridization (SSH). To investigate the biological function of NS5ATP5, we performed yeast-two hybrid to seek for proteins in leucocytes interacting with NS5ATP5.

METHODS: NS5ATP5 bait plasmid was constructed by ligating the gene of NS5ATP5 into pGBKT7, then transformed into yeast AH109 (a type), the transformed yeast mated with yeast Y187 (α type) containing leucocyte cDNA library plasmid 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 underwent sequence analysis by bioinformatics.

RESULTS: Ten colonies were sequenced. Among them, 8 colonies were genes with known functions and two colonies were new genes.

CONCLUSION: The preliminary successful cloning of gene of protein interacting with NS5ATP5 paves the way for studying the physiological function of NS5ATP5 and associated protein.

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.

Cloning of a gene coding for novel mutant of asialoglycoprotein receptor 2 binding to hepatitis B virus X protein in hepatocytes

AIM

The pathogenesis of HBV-induced malignant transformation is incompletely understood. The X protein of hepatitis B virus (HBxAg) is a multifunctional protein that can influence a variety of signal transduction pathways within the cell and is essential for establishing natural viral infection, it also has been implicated in the development of liver cancer associated with chronic infection. Further understanding of the interaction between HBxAg and proteins in hepatocytes is of great significance for the prevention of the development of hepatocellular carcinoma (HCC).

METHODS

HBxAg bait plasmid was constructed by ligating the HBxAg gene with a yeast expression vector pGBKT7, then transformed into yeast AH109 (a type). The transformed yeast cells were amplified and mated with yeast cells Y187(α type) containing liver cDNA library plasmid pCAT2 in 2×YPDA medium. Diploid yeast cells were 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 selection twice. Plasmid of true positive blue colonies was extracted and analysed by DNA sequencing and blast in GenBank. After the complete sequence of the novel mutant of asialoglycoprotein receptor 2 (ASGPR2) was amplified from the mRNA of HepG2 cell by reverse transcription polymerase chain reaction (RT-PCR) and cloned into pGADT7 vector, the recombined plasmid was translated by using reticulocyte lysate and analysed by immunoprecipitation technique in vitro together with HBxAg.

RESULTS

Eighteen genes in forty-one positive colonies were obtained, one of them is a novel mutant of ASGPR2, which is 80 % homologous to natural ASGPR2. The complete sequence of the mutant was amplified from the mRNA of HepG2 cell by RT-PCR successfully. The interaction between HBx and ASGPR2 mutant was further confirmed by immunoprecipitation technique.

CONCLUSION

Interaction between HBx and ASGPR2 mutant can be observed in both yeast cell and in vitro.