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Journal of Virology, January 2003, p. 600-623, Vol. 77, No. 1
0022-538X/03/$08.00+0     DOI: 10.1128/JVI.77.1.600-623.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Role of CCAAT/Enhancer-Binding Protein Alpha (C/EBP{alpha}) in Activation of the Kaposi's Sarcoma-Associated Herpesvirus (KSHV) Lytic-Cycle Replication-Associated Protein (RAP) Promoter in Cooperation with the KSHV Replication and Transcription Activator (RTA) and RAP

Shizhen Emily Wang,1 Frederick Y. Wu,1,2 Masahiro Fujimuro,1 Jianchao Zong,1 S. Diane Hayward,1,2 and Gary S. Hayward1,2*

Molecular Virology Laboratories, Department of Pharmacology and Molecular Sciences,2 Viral Oncology Program, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, The Johns Hopkins University, Baltimore, Maryland 21231-10001

Received 28 June 2002/ Accepted 20 September 2002


   ABSTRACT
Top
 Abstract
Introduction
 Materials and Methods
 Results
 Discussion
 References
 
The Kaposi's sarcoma-associated herpesvirus (KSHV)-encoded replication-associated protein (RAP, or K8) has been shown to induce both CCAAT/enhancer binding protein alpha (C/EBP{alpha}) and p21CIP-1 expression, resulting in G0/G1 cell cycle arrest during the lytic cycle. RAP and C/EBP{alpha} are also known to interact strongly both in vitro and in lytically infected cells. We recognized two potential consensus C/EBP binding sites in the RAP promoter and performed electrophoretic mobility shift assay (EMSA) analysis with in vitro-translated C/EBP{alpha}; this analysis showed that one of these sites has a very high affinity for C/EBP{alpha}. Luciferase (LUC) assays performed with a target RAP promoter-LUC reporter gene confirmed that C/EBP{alpha} can transcriptionally activate the RAP promoter up to 50-fold. Although RAP had no effect on its own promoter by itself, the addition of RAP and C/EBP{alpha} together resulted in a threefold increase in activity over that obtained with C/EBP{alpha} alone. Importantly, the introduction of exogenous Flag-tagged C/EBP{alpha} triggered RAP expression in BCBL-1 cells latently infected with KSHV, as detected by both reverse transcription-PCR and double-label immunofluorescence assay analyses, suggesting the presence of a self-reinforcing loop with C/EBP{alpha} and RAP activating each other. The RAP promoter can also be activated 50- to 120-fold by the KSHV lytic-cycle-triggering protein known as replication and transcription activator (RTA). C/EBP{alpha} and RTA together cooperated to elevate RAP promoter activity four- to sixfold more than either alone. Furthermore, the addition of RAP, C/EBP{alpha}, and RTA in LUC reporter cotransfection assays resulted in 7- to 15-fold more activation than that seen with either C/EBP{alpha} or RTA alone. Site-specific mutational analysis of the RAP promoter showed that the strong C/EBP binding site is crucial for C/EBP{alpha}-mediated transactivation of the RAP promoter. However, the C/EBP binding site also overlaps the previously reported 16-bp RTA-responsive element (RRE), and the same mutation also both reduced RTA-mediated transactivation and abolished the cooperativity between C/EBP{alpha} and RTA. Furthermore, in vitro-translated RTA, although capable of binding directly to the polyadenylated nuclear RNA (PAN) RRE motif, failed to bind to the RAP RRE and interfered with RRE-bound C/EBP{alpha} in EMSA experiments. Partial RTA responsiveness but no cooperativity could be transferred to a heterologous promoter containing added consensus C/EBP binding sites. A chromatin immunoprecipitation assay showed that all three proteins associated specifically with RAP promoter DNA in vivo and that, when C/EBP{alpha} was removed from a tetradecanoyl phorbol acetate-treated JSC-1 primary effusion lymphoma cell lysate, the levels of association of RTA and RAP with the RAP promoter were reduced 3- and 13-fold, respectively. Finally, RTA also proved to physically interact with both C/EBP{alpha} and RAP, as assayed both in vitro and by immunoprecipitation. Binding to C/EBP{alpha} occurred within the N-terminal DNA binding domain of RTA, and deletion of a 17-amino-acid basic motif of RTA abolished both the C/EBP{alpha} and DNA binding activities as well as all RTA transactivation and the cooperativity with C/EBP{alpha}. Therefore, we suggest that RTA transactivation of the RAP RRE is mediated by an interaction with DNA-bound C/EBP{alpha} but that full activity requires more than just the core C/EBP binding site.


   INTRODUCTION
Top
 Abstract
 Introduction
Materials and Methods
 Results
 Discussion
 References
 
Kaposi's sarcoma (KS)-associated herpesvirus (KSHV) is a gamma-2-class herpesvirus that is related to Epstein-Barr virus (EBV) but contains several novel loci (5, 6, 29, 34). KSHV DNA and latency-associated nuclear antigen 1 (LANA1) are present in virtually all tumor samples of classical endemic and AIDS-associated forms of KS (6) as well as in peripheral blood mononuclear cells of up to 50% of homosexual AIDS patients with KS (48); seropositivity is rare in healthy blood donors. KSHV is also present in a limited subset of AIDS-associated lymphoproliferative disorders referred to as primary effusion lymphomas (PELs) and multicentric Castleman's disease (3, 4, 37). PEL cell lines are B-cell lymphoma cells that are latently infected with KSHV, that carry multicopy KSHV episomes, and that can be induced into the lytic cycle by treatment with tetradecanoyl phorbol acetate (TPA) or sodium butyrate (4, 33). KSHV can also infect human primary dermal microvascular endothelial cells and converts them to LANA1-positive spindle-shaped cells that are morphologically similar to the characteristic spindle-shaped cells of nodular KS lesions (3, 11).

Like EBV, KSHV undergoes two distinct phases of infection, namely, latency and a reactivated productive lytic cycle, and the expression patterns for latent genes and lytic genes are mutually exclusive. During KSHV latency, only a small number of oncogenic and antiapoptotic viral genes encoded by KSHV, such as those for LANA1, v-FLIP, v-CycD, and K15/LAMP, are expressed; the rest of the genome is silent (5, 29, 34). Although the KSHV lytic cycle is not directly associated with neoplastic transformation, it is required for the release of infectious particles and the spread of KSHV infections. During reactivation in vivo, higher loads of virus are detected in the systemic circulation as a result of efficient viral lytic gene expression and viral DNA replication.

The KSHV-encoded replication-associated protein (RAP, or K8) is a 237-amino-acid early nuclear protein that is expressed in the lytic cycle and that is evolutionarily distantly related to the EBV lytic-cycle Z transactivator (ZTA) protein. Unlike ZTA, RAP is unable to trigger the viral lytic cycle on its own (26, 32) and is not known to bind to DNA or to function as a direct transcriptional activator (24, 50). Like ZTA, RAP contains a leucine zipper oligomerization domain and may interact with p53 and CBP (18, 31), but it is not known whether RAP can modulate expression from its own promoter. However, RAP evidently plays an important role in KSHV DNA replication because it is efficiently recruited into viral DNA replication compartments both when assembled in vitro in DNA-transfected Vero cells and when formed in vivo during the lytic cycle in KSHV-infected PEL or endothelial cells, as detected by immunofluorescence assay (IFA) studies (50).

During the early stages of the KSHV lytic cycle, RAP is induced approximately 12 h after the initiation of KSHV lytic-cycle replication, and its expression is maintained throughout the lytic cycle (24, 52). When first synthesized, RAP also is targeted to small subnuclear punctate bodies known as PML oncogenic domains (PODs); however, unlike the situation with several other herpesvirus POD-targeting proteins, this targeting does not result in the loss of PML protein from the PODs (50). Recent studies have reported that the immediate-early KSHV replication and transcription activator (RTA, or ORF50), a nuclear protein, is an upstream transcriptional activator of the RAP promoter (16, 25-27, 45). KSHV RTA, a homologue of EBV RTA, is induced within 4 h after lytic-cycle initiation (38) and is capable of inducing the full lytic cycle of KSHV when introduced into latently infected cells (16, 26, 27). After mapping of the RAP promoter through exhaustive linker-scanning mutagenesis, RTA was reported to mediate transcriptional activation of the RAP promoter through an RTA-responsive element (RRE) containing a 16-bp consensus sequence (5'-74769-GTGAAACAATAATGAT-74785-3'); deletion of this 16-bp sequence resulted in a significant loss of RTA responsiveness in all cell types tested (25, 45). Lukac et al. (25) later reported that KSHV RTA is able to bind to this DNA sequence on the RAP promoter directly to activate RAP expression. However, the possibility that cellular transcription factors may also be involved has not yet been evaluated.

It was recently found that KSHV RAP mediates G1 cell cycle arrest through induction of the cellular proteins CCAAT/enhancer binding protein alpha (C/EBP{alpha}) and p21 (49, 50a). C/EBPs (C/EBP{alpha}, C/EBPß, and CHOP-10) belong to the bZIP family of nuclear transcription factors, including also c-JUN, c-FOS, CREB, and ZTA (19), and C/EBP{alpha} plays important roles as the determining factor for adipocyte, granulocyte, and neutrophil differentiation (13, 20, 47, 51). The C/EBP{alpha} gene encodes two predominant isoforms, namely, a 42-kDa full-length form that has antimitotic activity and a 30-kDa truncated form that is made from an alternative translation initiation site and that lacks antimitotic activity (2, 23, 30). C/EBP{alpha} can positively autoregulate its own gene promoter (10, 39, 40) and controls differentiation and G1 cell cycle arrest through three reported mechanisms: (i) up-regulation of the expression of the cdk2, cdk4, and cdk6 inhibitor p21CIP (41, 42); (ii) inhibition of E2F transcription (35); and (iii) direct inhibition of cdk2 and cdk4 (17, 44).

Evidence is accumulating that herpesvirus DNA replication takes place only in G1-arrested host cells, possibly to prevent competition with host cell DNA synthesis for limited free nucleotides and to provide nuclear spaces for progeny viral DNA accumulation (15). In KSHV-infected cells, C/EBP{alpha} expression is induced either during lytic-cycle induction by TPA or by direct introduction of exogenous KSHV RAP, leading to host cell cycle arrest at G1 (49). Importantly, it has also been found that RAP binds strongly to C/EBP{alpha} both in vitro in glutathione S-transferase (GST) affinity assay and electrophoretic mobility shift assay (EMSA) experiments and in lytically infected cells, as detected by immunoprecipitation and colocalization experiments. Furthermore, RAP enhances C/EBP{alpha} expression through transcriptional synergy with C/EBP{alpha} and possibly also through C/EBP{alpha} stabilization (F. Y. Wu, Q. Tang, S. E. Wang, M. Fujimuro, C.-J. Chiou, S. D. Hayward, M. D. Lane, and G. Hayward, unpublished data).

In the present study, we found a strong C/EBP binding site in the RAP promoter which overlaps the known RRE. Therefore, we evaluated how C/EBP{alpha} affects the activation of the KSHV RAP promoter both alone and in combination with RTA and RAP. Indeed, C/EBP{alpha} was able to strongly activate the RAP promoter in transient reporter gene assays and also activated RAP expression after introduction into PEL cells. Furthermore, cotransfected KSHV RTA and C/EBP{alpha} cooperatively enhanced the transcriptional activation of a target KSHV RAP promoter-LUC reporter. We also found that C/EBP{alpha} and RAP both physically interacted with KSHV-encoded RTA. We suggest that RTA activation of the RAP promoter is partially mediated by C/EBP{alpha} and that either C/EBP{alpha} or RTA can trigger RAP expression, with RTA, C/EBP{alpha}, and RAP later acting in synergy to produce rapid high-level expression of RAP at the early stages of the lytic cycle.


   MATERIALS AND METHODS
Top
 Abstract
 Introduction
 Materials and Methods
Results
 Discussion
 References
 
Cells and plasmids. KSHV-positive human PEL cell lines BCBL-1 and JSC-1 as well as KSHV-negative cell line DG75 were grown in RPMI 1640 medium (Invitrogen, Carlsbad, Calif.) containing 10% fetal bovine serum in a humidified 5% CO2 incubator at 37°C. For KSHV lytic-cycle induction, TPA was added to the medium at a final concentration of 20 ng/ml. Vero cells and HeLa cells were grown in Dulbecco's modified Eagle's medium (Invitrogen) containing 10% fetal bovine serum.

Plasmid pSEW-C01 is a full-length C/EBP{alpha}(1-358) mammalian expression plasmid in the pcDNA3.1 vector (Invitrogen) background driven by the human cytomegalovirus enhancer-promoter region, and plasmid pSEW-C02, based on the pCMV-Tag2 vector (Stratagene, La Jolla, Calif.), expresses full-length Flag-tagged C/EBP{alpha}(1-358). Plasmid pSEW-C05 encodes the full-length GST-C/EBP{alpha}(1-358) fusion. Plasmid pYNC172a (7) is a black beetle virus leader region (BBV)-enhanced T7 in vitro translation vector encoding full-length C/EBP{alpha}(1-358). Expression plasmid pJX15, encoding full-length KSHV RTA(1-691), was used to construct the following RTA deletion derivatives: pSEW-R02 encoding RTA(1-548); pSEW-R03 encoding RTA(1-377); pSEW-R04 encoding RTA(1-273); pSEW-R05 encoding RTA(273-691); pSEW-R06 encoding RTA(151-548); pSEW-R07 encoding RTA(210-548); pSEW-R08 encoding RTA(244-548); pSEW-R09 encoding RTA(1-377{Delta}11-67), with an in-frame internal deletion from positions 11 to 67; pSEW-R10 encoding RTA(1-377{Delta}11-112), with an in-frame internal deletion from positions 11 to 112; pSEW-R11 encoding RTA(1-691{Delta}11-272), with an in-frame internal deletion from positions 11 to 272; and pSEW-R23 encoding RTA(1-691{Delta}151-167), with an in-frame internal deletion from positions 151 to 167.

From the parent plasmid pSEW-R06 encoding RTA(151-548), additional amino acid mutations were introduced by PCR-based site-directed mutagenesis to generate pSEW-R12 encoding RTA(151-548K) (Lys at positions 152 and 154 is replaced by Glu), pSEW-R13 encoding RTA(151-548R1) (Arg at positions 160 and 161 is replaced by Glu and Gly, respectively), pSEW-R14 encoding RTA(151-548R2) (Arg at positions 166 and 167 is replaced by Gly and Glu, respectively), pSEW-R15 encoding RTA(151-548KR1) (combining substitutions K152E, K154E, R160E, and R161G), pSEW-R16 encoding RTA(151-548KR2) (combining substitutions R160E, R161G, R166G, and R167E), pSEW-R17 encoding RTA(151-548RR) (combining substitutions K152E, K154E, R166G, and R167E), and pSEW-R18 encoding RTA(151-548KRR) (combining all six substitutions). Plasmids encoding Flag-tagged, c-Myc-tagged, and GST fusion versions of full-length RTA(1-691) were designated pJX16 (pSEW-R19), pSEW-c-Myc-RFL (pSEW-R20), and pFYW39 (pSEW-R21), respectively. The GST-RTA(1-377) DNA binding domain (DBD) fusion (derived from pFYW39) was designated pFYW40 (pSEW-R22). Plasmid pFYW01 encodes intact c-Myc-tagged RAP(1-236) (50), and pCJC514 encodes BBV RAP, used for enhanced in vitro translation of intact RAP(1-236) (Wu et al., unpublished).

Plasmid pFYW41 (pSEW-P01) (pGL3-Basic background) contains the RAP(-190/+10)-LUC reporter gene driven by the RAP promoter region (positions -190 and +10) between coordinates 74655 and 74854 of the KSHV (BC1) genome (GenBank accession no. U75698). Plasmid pSEW-P10 contains the PAN-LUC reporter gene driven by a 220-bp polyadenylated nuclear RNA (PAN) promoter region. Additional deletion derivatives of the target RAP-LUC reporter gene were generated by PCR-based site-directed mutagenesis with pFYW41 as the template to create RAP-(PM1)-LUC, with TGT at positions -87 to -85 replaced by ATC to create an EcoRV site (pSEW-P02); RAP-(PM2)-LUC, with ACA at positions -71 to -69 replaced by TTC to create an EcoRI site (pSEW-P03); and RAP-(PM1 + 2)-LUC, with both mutations (pSEW-P04). Two additional heterologous LUC reporter genes in the A10 minimal simian virus 40 T-antigen promoter (-150/+50) background were generated: (RAP-C/EBP-II)3-A10-LUC (in plasmid pSEW-P05), which contains three tandem copies of a 20-bp oligonucleotide encompassing the core C/EBP-II motif (AAACAAT) found in the KSHV RAP promoter, and (C/EBP-wt)3-A10-LUC (in plasmid pSEW-P06), which contains three tandem copies of a 20-bp oligonucleotide encompassing the wild-type palindromic consensus C/EBP binding site (ATTGCGCAAT) (43).

DNA transfection and LUC assay. BCBL-1 and DG75 cells were transfected by the electroporation method described previously (46). First, 107 cells were mixed with 5 to 10 µg of plasmid DNA in 0.5 ml of RPMI 1640 medium and electroporated at 300 V and 950 µF by using a GenePulser (Bio-Rad, Hercules, Calif.). Transfections of Vero and HeLa cells were performed with Lipofectamine (Invitrogen) according to the manufacturer's protocol. Cells were seeded at 5 x 105 per well in six-well plates 1 day prior to transfection. Cells were transfected with a total amount of 1.5 to 2.5 µg of DNA and harvested at 48 h posttransfection. LUC activity was measured for 10 s with a Lumat LB9501 luminometer (Berthold Systems, Inc.) by using a LUC assay system (Promega, Madison, Wis.).

Extraction of mRNA and RT-PCR. BCBL-1 cells were transfected by electroporation, and mRNA was extracted at 40 h posttransfection by using a GenElute Direct mRNA miniprep kit (Sigma, St. Louis, Mo.) according to the product instructions. Cells were harvested and resuspended by vortexing in 0.5 ml of a lysis solution containing proteinase K (0.2 mg/ml), followed by incubation at 65°C for 10 min. Then, 32 µl of 5 M NaCl and 25 µl of oligo(dT) beads were added to the solution and allowed to stand at room temperature for 10 min. The oligo(dT)-mRNA complexes were pelleted by centrifugation for 5 min at 10,000 x g, washed once in 350 µl of wash solution, and washed twice in 350 µl of low-salt wash solution. The poly(A) mRNA was eluted at 65°C in 100 µl of elution solution. For reverse transcription (RT), the following reagents were mixed and incubated at 42°C for 1 h: 20 U of avian myeloblastosis virus reverse transcriptase (Promega), 10 µl of avian myeloblastosis virus 5x RT buffer (Promega), 1 µl of rRNasin RNA inhibitor (Promega), 4 µl of 5 mM deoxynucleoside triphosphates (dNTPs), 0.5 µg of random primers (Promega), 30 µl of mRNA, and H2O to a final volume of 50 µl. The synthesized cDNA samples were used as templates for PCRs with primers LGH3771 (5'-CGCGGATCCAATTTGAAGAGGAACGCTTA-3') and LGH3774 (5'-CGCGGATCCTCAACATGGTGGGAGTGG-3') in a mixture containing 2 µl of cDNA template, 0.25 µg of each primer, 3 µl of 25 mM MgCl2, 4 µl of 2.5 mM dNTPs, 3.5 µl of dimethyl sulfoxide, 2.5 U of Taq DNA polymerase (Promega), 5 µl of thermophilic DNA polymerase 10x buffer (Promega), and H2O to a final volume of 50 µl. The conditions for PCR were 1 cycle at 94°C for 5 min; 30 cycles at 94°C for 1 min, 55°C for 1 min, and 72°C for 1 min; and 1 cycle at 72°C for 10 min. The PCR products were analyzed on a 2% agarose gel.

EMSA. Proteins used in the EMSA were in vitro translated by using a TNT quick coupled transcription-translation system (Promega) according to the manufacturer's procedures. Mixtures containing 2 µg of plasmid DNA, 1 µl of RNase inhibitor, 2 µl of 1 mM "cold" methionine, and 40 µl of TNT Quick Master Mix were incubated at 30°C for 90 min and stored at -80°C. Correct protein expression was verified by adding 2 µl of [35S]methionine (Amersham Pharmacia, Piscataway, N.J.) instead of nonradioactive methionine to the reaction mixtures, and the products were analyzed by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE) and autoradiography. For the EMSA, 2 to 4 µl of in vitro-translated proteins was used for each reaction in a binding system containing 10 mM HEPES (pH 7.5), 50 mM KCl, 1 mM EDTA, 1 mM dithiothreitol, 1 mM phenylmethylsulfonyl fluoride (PMSF), 1% Triton X-100, 5% glycerol, and 2 µg of poly(dI-dC). After annealing, double-stranded oligonucleotides were radiolabeled with [{alpha}-32P]dCTP by incubation with Klenow DNA polymerase in the presence of dNTP (minus dCTP). Approximately 50,000 cpm of the 32P-labeled probe was added to each sample and incubated for 30 min at room temperature. For competition assays, unlabeled oligonucleotides were added to the sample to compete for binding against the 32P-labeled probe at a molar ratio of 100:1. For supershift experiments, 0.5 µl of C/EBP{alpha} or RTA antiserum was added to the mixture after 30 min and incubated for 30 min before gel loading. Samples were separated on a 4.5% polyacrylamide gel in a buffer containing 10 mM HEPES (pH 7.5), 1 mM EDTA, and 0.5 mM EGTA at 150 V and 4°C as described previously (8). The gel was subsequently dried and subjected to autoradiography with Kodak film.

All oligonucleotides used were purchased from Invitrogen and are listed below (mutated nucleotides are shown in bold type). LGH3973 (5'-GATCGGTTGATTGTGACTATTTGTGAAACAATAATGA-3') and LGH3974 (5'-GATCTCATTATTGTTTCACAAATAGTCACAATCAACC-3') were annealed to form probe RAP-PWT; LGH4262 (5'-GATCGGTTGATATCGACTATTTGTGAAACAATAATGA-3') and LGH4263 (5'-GATCTCATTATTGTTTCACAAATAGTCGATATCAACC-3') were annealed to form probe RAP-PM1; LGH4264 (5'-GATCGGTTGATTGTGACTATTTGTGAATTCATAATGA-3') and LGH4265 (5'-GATCTCATTATGAATTCACAAATAGTCACAATCAACC-3') were annealed to form probe RAP-PM2; LGH4266 (5'-GATCGGTTGATATCGACTATTTGTGAATTCATAATGA-3') and LGH4267 (5'-GATCTCATTATGAATTCACAAATAGTCGATATCAACC-3') were annealed to form probe RAP-PM1 + 2; LGH4268 (5'-GATCGATTGTGACTATTTGTGAAACAATAATGATTAAAGGGGGTGGTATTTCC-3') and LGH4269 (5'-GATCGGAAATACCACCCCCTTTAATCATTATTGTTTCACAAATAGTCACAATC-3') were annealed to form the probe RAP-RRE; LGH4272 (5'-GATCCTTCCAAAAATGGGTGGCTAACCTGTCCAAAATATGGGAAC-3') and LGH4273 (5'-GATCGTTCCCATATTTTGGACAGGTTAGCCACCCATTTTTGGAAG-3') were annealed to form probe PAN-RRE; and LGH4274 (5'-GATCCTTCCAAAAATGGGTGTCTACCCGTGCCAAAATATGGGAAC-3') and LGH4275 (5'-GATCGTTCCCATATTTTGGCACGGGTAGACACCCATTTTTGGAAG-3') were annealed to form probe PAN-PM1.

Indirect IFA. The IFA was performed at 40 h after transfection of BCBL-1 cells. Procedures for IFA and fluorescence microscopy were described previously (50). Secondary donkey- or goat-derived fluorescein isothiocyanate- or rhodamine-conjugated anti-rabbit or anti-mouse immunoglobulin G (Jackson Pharmaceuticals, West Grove, Pa.) was used to detect the primary antibodies, which included rabbit antipeptide antiserum against KSHV RAP (50) and mouse anti-Flag monoclonal antibody (MAb) (Sigma). Mounting solution with 4',6'-diamidino-2-phenylindole (DAPI) (Vector Shield) was used to visualize cellular DNA.

Recombinant protein expression and in vitro GST affinity binding assay. GST fusion protein expression was induced in Escherichia coli (strain BL21) with 1 mM isopropyl-ß-D-thiogalactopyranoside (IPTG) for 4 h at 30°C. Bacterial pellets were resuspended in ice-cold phosphate-buffered saline (PBS) (150 mM NaCl, 16 mM Na2HPO4, 4 mM NaH2PO4 [pH 7.3]) and sonicated for 30 s. After centrifugation, clarified lysates were either analyzed by SDS-PAGE or immobilized on glutathione-Sepharose 4B beads (Amersham Pharmacia). Purified GST proteins can be stored at -80°C in 20% glycerol-PBS. Input [35S]methionine-labeled proteins were synthesized in vitro by using the TNT quick coupled transcription-translation system as described above. Recombinant GST fusion proteins immobilized on beads were pretreated with 0.2 U of DNase I and 0.2 µg of RNase A per µl for 30 min at 20°C in pretreating buffer (50 mM Tris-HCl [pH 8.0], 5 mM MgCl2, 2.5 mM CaCl2, 100 mM NaCl, 5% glycerol, 1 mM dithiothreitol). The beads were washed twice with binding buffer (20 mM Tris-Cl [pH 7.5], 100 mM NaCl, 1 mM EDTA, 0.5% NP-40, 1 mM dithiothreitol) and blocked in the same buffer containing 10 mg of bovine serum albumin (BSA)/ml for 30 min at 4°C. After blocking, the bead-immobilized GST fusion proteins were resuspended in binding buffer containing 1 mg of BSA/ml, and labeled proteins were added and incubated for 1 h at 4°C. The beads were washed five times in binding buffer at 10-min intervals. The beads were resuspended in 15 µl of 2x SDS gel loading buffer and boiled for 5 min before loading on SDS-polyacrylamide gels. After electrophoresis, the gels were fixed in 50% methanol-40% H2O-10% acetic acid for 30 min and dried for X-ray autoradiography.

For in vitro coimmunoprecipitation, 5 to 10 µl of [35S]methionine-labeled in vitro-translated proteins was incubated with 2 µg of mouse anti-c-Myc antibody (Sigma) in 100 µl of immunoprecipitation buffer (50 mM Tris-Cl [pH 7.9], 50 mM NaCl, 0.1 mM EDTA, 1% glycerol, 0.2% NP-40, 1 mM dithiothreitol, 0.5 mM PMSF) for 1 h at 4°C. Then, 50 µl of a 50% slurry of protein A-protein G (50:50) and Sepharose beads (Amersham Pharmacia) was added to the mixture and incubated for 1 h at 4°C. The beads were washed three times with cold immunoprecipitation buffer at 15-min intervals, resuspended and boiled in 2x SDS gel loading buffer, and analyzed by SDS-PAGE followed by autoradiography.

In vivo coimmunoprecipitation and Western immunoblot assay. Nuclear extracts of BCBL-1 cells were prepared for coimmunoprecipitation as described previously (50a). Approximately108 cells were harvested 30 h after TPA induction, washed once with PBS, and gently resuspended in 10 ml of cold hypotonic buffer A (10 mM HEPES [pH 7.9], 10 mM KCl, 0.1 mM EDTA, 0.1 mM EGTA, 1 mM dithiothreitol, 0.5 mM PMSF). The mixture was allowed to swell on ice for 30 min, and NP-40 was added to a final concentration of 0.62%. The mixture was vortexed vigorously for 10 s, and the nuclear pellets were collected after centrifugation for 3 min at 3,500 rpm and 4°C. The nuclear pellets were resuspended in 3 ml of cold immunoprecipitation buffer and sonicated for 2 s at the minimal setting. The samples were centrifuged at 13,000 rpm for 1 min at 4°C, and the supernatants were collected as nuclear extracts.

For coimmunoprecipitation, 400 µl of prepared nuclear extracts was pretreated with 0.2 U of DNase I and 0.2 µg of RNase A per µl and precleared with 5 µl of goat or rabbit preimmune serum and 100 µl of a 50% slurry of protein A-protein G (20:80) and Sepharose beads for 1 h. After preclearing, 3 µg of anti-C/EBP{alpha} goat polyclonal antibody (PAb), anti-RAP or anti-RTA rabbit PAb, or goat or rabbit preimmune serum was added to the precleared nuclear extracts and incubated for 2 h at 4°C. Then, 100 µl of a 50% slurry of protein A-protein G (20:80) and Sepharose beads blocked with 5% BSA in PBS was added to the nuclear extracts and incubated for 1 h at 4°C. The beads were washed three times with cold immunoprecipitation buffer at 15-min intervals, resuspended in 2x SDS gel loading buffer, and boiled for 5 min before loading on SDS-polyacrylamide gels. Western blot analysis was performed as described previously (50). Any recovered RTA was then detected by immunoblotting with rabbit antiserum raised against a synthetic peptide representing the KSHV RTA segment between amino acids 527 and 539 (NH2-527-KKRKALTVPEADT-539-COOH).

ChIP assay. The procedures for the chromatin immunoprecipitation (ChIP) assay were modified from the original protocol (1). After treatment of 20 ml of KSHV-positive JSC-1 cells (5 x 106 cells) with TPA (20 ng/ml) for 40 h, 2 ml of formaldehyde solution (11% formaldehyde, 0.1 M NaCl, 1 mM EDTA, 50 mM HEPES [pH 8.0]) was added to the culture and incubated at 37°C for 30 min. The cross-linking reaction was stopped by the addition of 4 ml of 1 M glycine (final concentration, 0.125 M) to the cell culture mixture. After centrifugation, the cell pellets were washed once with 5 ml of cold wash buffer [5 mM piperazine-N,N'-bis(2-ethanesulfonic acid) (PIPES) (pH 8.0), 85 mM KCl, 0.5% NP-40, 1 mM PMSF, 1 µg of aprotinin/ml, 1 µg of pepstatin/ml]. The cell pellets were resuspended in 500 µl of sonication buffer (1% SDS, 10 mM EDTA, 50 mM Tris-Cl [pH 8.0], 1 mM PMSF) at 20°C in a 1.5-ml microtube and sonicated for 30 s at the minimal setting to shear genomic DNA to ~400-bp fragments. The sonicated mixture (500 µl) was diluted with 5 ml of a cold buffer containing 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-Cl (pH 8.0), 167 mM NaCl, and 1 mM PMSF and was precleared with 120 µl of 50% protein A-protein G-Sepharose beads for 8 h at 4°C. After centrifugation to pellet the Sepharose beads, the supernatants were divided into 500-µl aliquots and stored at -70°C for later use.

For each immunoprecipitation assay, 1 µl of KSHV RTA antiserum, 1 µl of KSHV RAP antiserum, 1 µg of anti-C/EBP{alpha} PAb (Santa Cruz), 1 µg of anti-EBV ZTA MAb (Argene, N. Masepequa, N.Y.), or 1 µl of PBS (negative control) was added to each 500-µl supernatant aliquot and incubated at 4°C for 2 h with constant mixing. Then, 30 µl of 50% protein A-protein G-Sepharose beads was added to each mixture and incubated at 4°C for 4 h with constant mixing. For protein preclearing experiments, the same mixture was incubated with antibody and protein A-protein G-Sepharose beads at 4°C overnight, and supernatants were collected for a second round of immunoprecipitation. After centrifugation and the removal of supernatants, the Sepharose beads were washed once with 1 ml of dilution buffer at 20°C for 3 min. The beads were washed twice with 1 ml of dilution buffer at 4°C for 20 min each, washed three times with 1 ml of dilution buffer at 20°C for 3 min each, and resuspended in 100 µl of Tris-EDTA (pH 8.0) (TE). RNase A (50 µg/ml) was added, followed by incubation at 37°C for 30 min; then, 5 µl of 10% SDS and 50 µl of proteinase K (500 µg/ml) were added, followed by incubation for 4 h at 37°C with occasional mixing. The same mixture was incubated at 65°C overnight to reverse the cross-linked DNA-protein complex. After centrifugation, supernatants were transferred to new microtubes, diluted with 100 µl of fresh TE, and extracted with equal volumes of phenol and then chloroform. DNA was precipitated with ethanol, and the rinsed and vacuum-dried pellets were resuspended in 100 µl of TE.

For PCR detection, 2 µl of each DNA-TE solution was used as a template. For detection of the immunoprecipitated KSHV RAP promoter region, two primers, LGH4361 (5'-GATCCGCGGATCCAGTTTGGTGCAAAGTGGAGT-3') and LGH4362 (5'-GATCCGCGGATCCTGGCAGGGTTACACGTTTAC-3'), specific for a 164-bp region in the KSHV RAP promoter that encompasses the C/EBP binding sites and the RRE, were used for PCR amplification. For detection of the KSHV RTA coding region, two primers, LGH4930 (5'-TTCGCCTGTTAGACGAAGC-3') and LGH4929 (5'-GATTCGCAAGCTTCAGTCTCGGAAGTAATTACG-3'), specific for the RTA coding region from amino acids 591 to 691, were used as a negative control to detect a nonpromoter region. The PCR products were analyzed on a 2.5% agarose gel. Quantification of the PCR products was conducted with a MultiImage light cabinet (Alpha-Innotech Corp.) and the accompanying FluorChem (version 1.02) software.


   RESULTS
Top
 Abstract
 Introduction
 Materials and Methods
 Results
Discussion
 References
 
C/EBP{alpha} and KSHV RTA cooperatively activate the RAP promoter. To examine factors that induce RAP expression during the KSHV lytic cycle, a target LUC reporter gene driven by the KSHV RAP promoter region (between positions -190 and +10) was cotransfected into a variety of cell lines along with different combinations of effector mammalian cDNA expression plasmids. Initially, a KSHV RTA expression plasmid was used as a positive control. The addition of just 0.25 µg resulted in 12-fold activation of the RAP promoter-driven reporter gene in Vero cells and 39-fold activation in HeLa cells. This effect was dose responsive, with activation of the RAP promoter reaching 42-fold in Vero cells and 105-fold in HeLa cells when 1 µg of the RTA expression plasmid was used (Fig. 1A and B). Similarly, electroporation of RTA into DG75 lymphocytes resulted in 40-fold activation at the lowest dose (2.5 µg) and 120-fold activation at the highest dose (10 µg) (Fig. 1C).



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  		FIG. 1. C/EBP{alpha} enhances the transcriptional activation of the KSHV RAP promoter by RTA. Histograms plot the results of dose-response LUC assays in which the target RAP(-190/+10)-LUC reporter gene was transiently expressed either alone or in the presence of mammalian expression plasmids encoding full-length C/EBP{alpha} (open bars), RTA (solid bars), or both (gray bars). (A) Cotransfection in Vero cells with Lipofectamine. (B) Cotransfection in HeLa cells with Lipofectamine. (C) Electroporation into KSHV-negative DG75 B lymphocytes.

 
We then examined whether C/EBP{alpha} has any role in activating the RAP promoter, and we found that transfection of C/EBP{alpha} alone at the lowest dose resulted in 19-fold activation of the RAP promoter-driven reporter gene in Vero cells, 27-fold activation in HeLa cells, and 14-fold activation in DG75 cells. Again, the level of RAP promoter activation was proportional to the amount of C/EBP{alpha} DNA used, with 56-fold activation in Vero cells, 48-fold activation in HeLa cells, and 37-fold activation in DG75 cells being observed at the highest doses used (Fig. 1).

When both C/EBP{alpha} and RTA were added together to the cotransfection mixture, we observed an overall 4- to 5-fold increase; levels reached 88-, 152-, or 147-fold activation of the RAP promoter in Vero, HeLa, or DG75 cells, respectively, with 0.25 µg of each (2.5 µg in DG75 cells) and 155-, 265-, and 222-fold activation in the same cell types, respectively, with 0.5 µg of each (5 µg in DG75 cells) (Fig. 1). These data indicated that in addition to KSHV RTA, C/EBP{alpha} is another potent up-regulator of the KSHV RAP promoter in cotransfection assays and that the two transcriptional activators together produce 2.5- to 3-fold additional cooperativity over simple additive effects.

The RAP promoter contains a C/EBP{alpha} binding site that binds C/EBP{alpha} strongly in vitro. Because C/EBP{alpha} itself activated the KSHV RAP promoter, we decided to investigate whether any C/EBP DNA binding sites exist in the RAP promoter. Careful inspection revealed two putative oppositely oriented core C/EBP{alpha} binding sites in the RAP promoter region between positions -89 and -67. These two sites, designated C/EBP-I and C/EBP-II (Fig. 2A), contain the ACAAT consensus sequence that is homologous to a half-site of several known palindromic C/EBP{alpha} binding sites, although in this case they are located 13 bp apart (perhaps equivalent to one full turn of the helix) and may constitute a double ACAAT palindromic C/EBP binding site. To test the functionality of these putative C/EBP binding sites in binding to C/EBP{alpha} in vitro, we performed an EMSA with in vitro-translated C/EBP{alpha} and a 33-bp 32P-radiolabeled oligonucleotide probe (RAP-PWT) that encompasses both motifs (C/EBP-I and C/EBP-II). Indeed, with added C/EBP{alpha}, we found a single strongly gel-shifted band, suggesting that C/EBP{alpha} can bind to this probe very efficiently (Fig. 2B, lane 2). The specificity of this binding by C/EBP{alpha} was further confirmed by a supershift of the DNA-protein complex with anti-C/EBP{alpha} PAb (Fig. 2B, lane 3).





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  		FIG. 2. C/EBP{alpha} binds to a proximal region on the KSHV RAP promoter and transactivates RAP expression. (A) Diagram showing the locations of the two putative C/EBP binding sites, C/EBP-I and C/EBP-II, as well as site-specific mutations (underlined, bold) within these two motifs. (B) EMSA experiment showing that in vitro-translated C/EBP{alpha} bound strongly to a synthetic 32P-labeled oligonucleotide probe containing the C/EBP-II motif but only weakly to the more distal C/EBP-I motif and that double mutation of both motifs abolished C/EBP{alpha} binding. SS, supershifts; S, shifts; NS, nonspecific shifts. (C) Transient LUC reporter gene assay showing that the C/EBP-II motif was essential for C/EBP{alpha}-mediated transactivation and synergy. Effector plasmids encoding C/EBP{alpha}, RTA, or both were cotransfected into HeLa cells with target reporter plasmids containing either the intact RAP(-190/+10)-LUC reporter gene or its site-specific mutant derivatives RAP-(PM1)-LUC, RAP-(PM2)-LUC, and RAP-(PM1 + 2)-LUC. Numbers on the y axis show fold activation.

 
To evaluate the contributions of the two potential half-sites individually, we generated three mutant probes by selectively destroying one or both of the ACAAT sites. When RAP-PM1 (containing a mutation of C/EBP-I), RAP-PM2 (containing a mutation of C/EBP-II), and RAP-PM1 + 2 (containing both half-site mutations) were used for EMSAs (Fig. 2A), we found that only RAP-PM1 still bound C/EBP{alpha} strongly (Fig. 2B, lanes 5 and 6), whereas RAP-PM2 lost 90% of C/EBP{alpha} binding ability compared to RAP-PWT (Fig. 2B, lanes 8 and 9). RAP-PM1 + 2, which lacks both the C/EBP-I and the C/EBP-II motifs, failed to bind to C/EBP{alpha} at all (Fig. 2B, lanes 11 and 12). Therefore, the concept of a novel palindromic site seems unlikely. Instead, the C/EBP-II motif is the most critical site for binding to C/EBP{alpha}, whereas the C/EBP-I motif is bound only weakly and may be nonessential but may still contribute toward overall C/EBP{alpha} activity at high protein concentrations.

To test the functionality of these C/EBP binding sites in terms of the ability of C/EBP{alpha} to activate the RAP promoter, we generated three mutant RAP(-190/+10)-LUC reporter genes that contained the same sequence mutations as those found in the RAP-PM1, RAP-PM2, and PAP-PM1 + 2 oligonucleotides (Fig. 2A). LUC assays were performed with HeLa cells to evaluate the responsiveness of these individual target mutant RAP promoter genes to transfected effector plasmids expressing C/EBP{alpha}, RTA, or both. In comparison to the wild-type RAP(PWT)-LUC reporter, RAP(PM1)-LUC, which contains a mutated C/EBP-I motif, showed only a slight decrease in C/EBP{alpha} activation, from 33- to 23-fold, whereas RTA activation increased from 66- to 96-fold; the cooperativity between RTA and C/EBP{alpha} was not seriously affected (Fig. 2C). However, activation by C/EBP{alpha} alone was reduced from 33- to 11-fold when RAP(PM2)-LUC, lacking the C/EBP-II motif, was used (Fig. 2C). Furthermore, the cooperativity between RTA and C/EBP{alpha} was completely abolished for RAP(PM2)-LUC, with activation dropping from 265-fold in the wild type to 22-fold. Interestingly, activation by RTA alone was also impaired with RAP(PM2)-LUC, dropping from 66-fold for the wild type to 23-fold (Fig. 2C). Finally, the double mutant RAP(PM1 + 2)-LUC also showed reduced C/EBP{alpha} and RTA activation, and the C/EBP{alpha}-RTA synergy was completely abolished (Fig. 2C). These results showed that the C/EBP-II binding site not only is important for both C/EBP{alpha} and RTA to activate transcription of the RAP gene but also is essential for the cooperativity between RTA and C/EBP{alpha}. The considerable residual C/EBP{alpha} and RTA activation of RAP(PM2)-LUC and RAP-(PM1 + 2)-LUC suggests that there may also be weaker but noncooperative target sites for both proteins elsewhere in the RAP promoter. Indeed, we found that deletion of additional upstream sequences, from -190 to -140, in the wild-type RAP promoter-LUC reporter gene reduced RTA responsiveness nearly twofold (data not shown).

RTA and the RRE. KSHV RTA was previously reported to target a 16-bp region on the KSHV RAP promoter known as the RAP RRE (25, 45), but unexpectedly this site proved to overlap the critical C/EBP-II motif that we identified above. The defined RAP RRE contains the sequence GTGAAACAATAATGATT, of which the underlined portion (AAACAAT) represents the core C/EBP-II motif (Fig. 3A). When the C/EBP-II motif was mutated in the RAP promoter reporter gene (RAP-PM2), not only did the promoter show reduced responses to both C/EBP{alpha} and RTA transactivation, but also the synergy exhibited between C/EBP{alpha} and RTA was completed abolished (Fig. 2B). Therefore, our data suggested that direct RTA activation of the RAP promoter is at least partially dependent upon the integrity of the AAACAAT C/EBP{alpha} binding sequence and raised questions about a possible physical interaction between C/EBP{alpha} and RTA. However, because Lukac et al. have also reported that RTA transactivates the RAP promoter through direct binding of RTA to the RRE (25), we decided to further address these observations by exploring the physical interactions among RTA, C/EBP{alpha}, and both type I and type II RRE DNA sequences.



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  		FIG. 3. The C/EBP binding site in the RAP promoter overlaps the KSHV RAP promoter type I RRE sequence, which has only weak affinity for in vitro-translated RTA, compared to the high-affinity type II RRE sequence from the KSHV PAN promoter. (A) (Upper panel) Sequence of the 49-bp oligonucleotide probe (RAP-PWT) containing both of the C/EBP binding sites and overlapping the RTA type I RRE sequence from the RAP promoter (RAP-RRE). (Lower panel) EMSA with 32P-labeled probe RAP-RRE and in vitro-translated proteins. Lane 1, control reticulocyte lysate (2 µl) alone did not bind to probe RAP-RRE. Lanes 2 and 3, binding of in vitro-translated C/EBP{alpha} (2 µl) to probe RAP-RRE and supershifting of the C/EBP{alpha} gel shift with anti-C/EBP{alpha} PAb (0.5 µl). Lanes 4 to 7, C/EBP{alpha} (2 µl) binding could be competed away with unlabeled oligonucleotides (100-fold excess) containing the wild-type C/EBP-II motif (RAP-PM1 and RAP-PWT) but not with RAP-PM2 or RAP-(PM1 + 2), each of which contains the mutant C/EBP-II motif. Lanes 8 to 10, dose-response assay showing that in vitro-translated RTA (2, 4, and 6 µl, respectively) failed to bind to probe RAP-RRE even with increasing amounts of RTA. Lane 11, loss of the C/EBP{alpha} (2 µl) complex bound to the RAP RRE after the addition of in vitro-translated RTA (1 µl) (compare with lane 2), suggesting a physical interaction between the two proteins. SS, supershifts; S, shifts; NS, nonspecific bands. (B) (Upper panel) Sequences of the 41-bp oligonucleotide probe (PAN-RRE) containing the RTA type II RRE from the PAN promoter and of a mutated version of the RRE (PAN-PM1). Underlining and bold type indicate mutations. (Lower panel) EMSA with 32P-labeled PAN RRE probes and in vitro-translated proteins. Lane 1, control reticulocyte lysate (2 µl) did not harbor any probe PAN-RRE binding activity. Lane 2, in vitro-translated RTA (4 µl) bound to probe PAN-RRE. Lane 3, unlabeled oligonucleotide RAP-PWT (100-fold excess) did not compete away RTA binding to labeled probe PAN-RRE. Lane 4, unlabeled oligonucleotide PAN-RRE (100-fold excess) completely competed away RTA binding to labeled probe PAN-RRE. Lane 5, supershift of the DNA-bound RTA band with anti-RTA PAb (1 µl), confirming the identity of the RTA shifts. Lane 6, negative control showing that C/EBP{alpha} (2 µl) did not bind to probe PAN-RRE. Lanes 7 and 8, neither the negative control reticulocyte lysate (2 µl) nor RTA (4 µl) bound to mutant probe PAN-PM1.

 
To investigate binding to RAP RRE DNA by both C/EBP{alpha} and RTA, a 49-bp oligonucleotide probe encompassing the entire RRE but also containing both potential C/EBP binding sites was tested in EMSA experiments. We found that in vitro-translated C/EBP{alpha} was able to bind to probe RAP-RRE very strongly, as expected (Fig. 3A, lanes 2 and 3). To further confirm this phenomenon, unlabeled competitor oligonucleotides (RAP-PWT, RAP-PM1, RAP-PM2, and RAP-PM1 + 2) were added to binding reaction mixtures containing C/EBP{alpha} and radiolabeled probe RAP-RRE at a 200-fold excess (Fig. 3A, lanes 6 to 9). Consistent with our previous EMSA results obtained with those mutant oligonucleotides as direct radiolabeled probes, we found that the RAP-PWT and RAP-PM1 oligonucleotides competed efficiently for C/EBP{alpha} interactions against labeled probe RAP-RRE, whereas the RAP-PM2 oligonucleotide showed much weaker competition. The RAP-PM1 + 2 oligonucleotide did not interfere at all with C/EBP{alpha} binding to probe RAP-RRE.

Surprisingly, we were unable to observe any interaction between in vitro-translated wild-type RTA and the RAP RRE sequence in our EMSA system (Fig. 3A, lanes 8 to 10). Conceivably, this form of RTA binds to probe RAP-RRE very weakly, and the interaction was not obvious with the low concentrations of RTA obtained by in vitro translation. Therefore, to confirm the functional viability of our in vitro-translated RTA in binding to other target DNA sequences with an affinity for RTA, we tested a different RTA consensus sequence (type II RRE), which was found in the KSHV PAN promoter and which was reported to bind to RTA very strongly (36). A 41-bp oligonucleotide (PAN-RRE) that contained the 32-bp RRE region from the KSHV PAN promoter was used for an EMSA under the same binding conditions. In this experiment, the in vitro-translated wild-type RTA sample bound to probe PAN-RRE and formed two shifted bands (upper band, RTA shift; lower band, degradation products of RTA shift) that could in turn be supershifted by RTA antiserum (Fig. 3B, lanes 2 and 5). The same RTA sample failed to bind to mutant probe PAN-PM1 (Fig. 3B, lane 8).

LUC reporter gene assays with a cotransfected target PAN promoter (positions -261 to +14) as a control showed that the PAN promoter can be strongly activated by RTA, as expected (see (Fig. 12C). However, despite the ability of C/EBP{alpha} to bind to probe RAP-RRE, C/EBP{alpha} was unable to recognize the RRE in the PAN promoter and thus was unable to bind to probe PAN-RRE at all in our EMSA experiments (Fig. 3B, lane 6). Furthermore, when probe RAP-RRE, which could not bind to in vitro-translated RTA, and probe PAN-PM1 (Fig. 3B, lane 8), which contained mutations abolishing RTA binding (36), were used as competitors, neither of them was able to interfere with the formation of the RTA complex bound to probe PAN-RRE (Fig. 3B, lane 3, and data not shown). As a positive control, when we used the same amounts of probe PAN-RRE as an unlabeled excess competitor, formation of the bound RTA gel shift complex was abolished (Fig. 3B, lane 4). These results suggested that probe RAP-RRE has only low if any affinity for RTA, whereas probe PAN-RRE has very high affinity, and also proved that our in vitro-translated RTA was capable of binding efficiently to a DNA sequence that contains a type II RRE.



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  		FIG. 12. The RTA({Delta}151-167) deletion mutant fails to interact with C/EBP{alpha}, to bind RRE DNA, to cooperate with C/EBP{alpha}, or to transactivate RRE containing target promoters. (A) GST affinity assay showing the absence of an interaction between GST-C/EBP{alpha} and 35S-labeled RTA({Delta}151-167). Lanes 1 and 2, lack of RTA({Delta}151-167) binding to either GST or a GST-C/EBP{alpha} fusion. Lane 3, control showing input in vitro-translated 35S-labeled RTA({Delta}151-167). Numbers at left indicate mass in kilodaltons. (B) EMSA showing the absence of binding of in vitro-translated RTA({Delta}151-167) to probe PAN-RRE. Lane 1, reticulocyte lysate used as a negative control; lane 2, positive control showing in vitro-translated full-length RTA; lane 3, in vitro-translated RTA({Delta}151-167); lane 4, in vitro-translated RTA({Delta}151-167) plus anti-RTA PAb. S, shifts; NS, nonspecific shifts. (C) Histograms comparing the results of transient LUC reporter assays in which the target (RAP-C/EBP-II)3-A10-LUC reporter, RAP promoter-LUC reporter, and PAN promoter-LUC reporter genes were transiently expressed in HeLa cells either alone or in the presence of mammalian expression plasmids encoding full-length C/EBP{alpha}, RTA({Delta}151-167), a combination of both C/EBP{alpha} and RTA({Delta}151-167), or full-length RTA as a positive control.

 
We next examined whether RTA could bind to probe RAP-RRE in EMSA experiments in the presence of C/EBP{alpha}. However, when both C/EBP{alpha} and RTA were added to a binding mixture containing labeled probe RAP-RRE, C/EBP{alpha} binding to probe RAP-RRE was diminished, but no new complexes were observed (Fig. 3A, lane 11). Furthermore, the inhibitory effect was both dose responsive and specific for C/EBP{alpha}, in contrast to EBV ZTA, whose DNA binding was not affected by the addition of RAP (data not shown). These results implied either of two possibilities: (i) RTA inhibits C/EBP{alpha} binding to the RRE, or (ii) RTA and C/EBP{alpha} bind to the RRE cooperatively; however, the RTA-C/EBP{alpha}-DNA complex either is too large or is not stably maintained in the in vitro system, leading to the failure to observe a supershift. Assays with target RAP promoter-LUC reporter genes showed that there is cooperativity between RTA and C/EBP{alpha} in transactivating the RAP promoter; therefore, unless they both act by removing inhibitory binding proteins, it seems more likely that a DNA-bound RTA-C/EBP{alpha} supercomplex is formed in vivo but cannot be maintained stably during in vitro EMSA experiments. Note that the addition of either RAP or EBV ZTA to C/EBP{alpha} in EMSA experiments also led to abolition of the C/EBP{alpha} gel-shifted band without the formation of detectable stable supershifted bands (49; Wu et al., unpublished).

Responsiveness of minimal C/EBP binding sites to RTA activation. To evaluate the possibility that just the core C/EBP binding site or another consensus C/EBP binding site in a heterologous background would also confer RTA responsiveness, we constructed two additional target LUC reporter genes in a minimal simian virus 40 promoter background (pA10-LUC). The (RAP-C/EBP-II)3-A10-LUC gene contained three inserted tandem copies of the minimal C/EBP-II motif (AAACAAT) found in the RAP promoter but without the adjacent segment of the previously defined RRE sequence (AATGATT) (Fig. 4A), and the (C/EBP-wt)3-A10-LUC gene contained three inserted tandem copies of a consensus palindromic C/EBP binding site (ATTGCGCAAT) (43) (Fig. 4A). The minimal construct pA10-LUC, used as a negative control, showed no significant responsiveness to either C/EBP{alpha} or RTA (Fig. 4B). However, C/EBP{alpha} activated (RAP-C/EBP-II)3-A10-LUC 12-fold, and RTA activated the same promoter in a dose-responsive manner up to 7-fold, although in the presence of both RTA and C/EBP{alpha} the activation level was only an additive 18-fold (Fig. 4B). Similarly, C/EBP{alpha} activated (C/EBP-wt)3-A10-LUC 11-fold, and RTA also activated the consensus palindromic C/EBP binding site in a dose-responsive manner up to 5-fold; however, in the presence of both effectors, the response was increased only additively to 14-fold (Fig. 4B). Obviously, in this heterologous context, compared to in the RAP promoter context, both C/EBP{alpha} responsiveness and RTA responsiveness declined greatly. However, the basal level of activity of our A10 minimal promoter was considerably higher than that of the wild-type RAP promoter-LUC reporter gene (data not shown). Therefore, RTA appeared to retain some ability to activate all C/EBP binding sites after transfer to a heterologous context in the absence of the additional specific RAP RRE motif, although the level of activation was much lower than that for the intact RRE itself in the wild-type RAP promoter.



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  		FIG. 4. Transfer of RTA responsiveness by minimal C/EBP binding sites inserted into a heterologous reporter gene background. (A) Schematic showing the inserted 20-bp C/EBP motif oligonucleotides and sequences (bold type) in the target (RAP-C/EBP-II)3-A10-LUC and (C/EBP-wt)3-A10-LUC reporter genes, compared to the wild-type type I RRE motif in the RAP promoter-LUC reporter gene. (B) Histograms plotting the results of dose-response LUC assays in which the target (RAP-C/EBP-II)3-A10-LUC, (C/EBP-wt)3-A10-LUC, and parent A10-LUC reporter genes were transiently expressed in HeLa cells either alone or in the presence of mammalian expression plasmids encoding full-length C/EBP{alpha}, RTA, or both.

 
RTA and C/EBP{alpha} bind to the RAP RRE cooperatively in vivo, as shown by a ChIP assay. To attempt to confirm our model that an RAP RRE-bound RTA-C/EBP{alpha} supercomplex forms in vivo, we performed an in vivo ChIP assay with lytically induced JSC-1 PEL cells. First, we immunoprecipitated RTA, C/EBP{alpha}, and RAP from the cross-linked DNA-protein cell lysates; after the removal of all proteins, the recovered DNA was ethanol precipitated and amplified by PCR with primers specific for the RAP promoter (LGH4361 and LGH4362). RAP promoter DNA was indeed found to be associated with each of the RTA, C/EBP{alpha}, and RAP immunoprecipitates (Fig. 5B, lanes 1 to 3). The negative controls with anti-EBV ZTA antibody or with PBS failed to precipitate any RAP promoter DNA (within basal levels) (Fig. 5B, lanes 4 and 5). To address the question of whether RTA and C/EBP{alpha} may bind to RAP RRE DNA cooperatively, we precleared C/EBP{alpha} from lysates with anti-C/EBP{alpha} PAb overnight and then reimmunoprecipitated RTA with RTA antiserum in a second round. The results showed that RAP promoter DNA could still be recovered from the RTA immunoprecipitate in the second round (Fig. 5B, lane 7), although at a level more than threefold lower (ratio of 3.5 versus 12.5) than that obtained when C/EBP{alpha} was present in lysates. A parallel control second immunoprecipitation with C/EBP{alpha} confirmed that over 95% of the C/EBP{alpha}-bound DNA was removed (data not shown). These results suggested that, although the removal of C/EBP{alpha} significantly impaired the ability of RTA to bind to RAP promoter DNA, some RTA was still able to associate with the RAP promoter, although much less efficiently. Furthermore, the removal of RTA by antibody preclearing did not significantly affect the association of C/EBP{alpha} with RAP promoter DNA (Fig. 5B, lane 8). These results suggested that, although C/EBP{alpha} contributed to the binding of RTA to the RAP RRE, RTA did not seem to play a major reciprocal role in mediating the binding of C/EBP{alpha} to the RAP RRE. This conclusion is consistent with our earlier EMSA data which showed that, in contrast to RTA alone, in vitro-translated C/EBP{alpha} alone bound to probe RAP-RRE very efficiently. Therefore, our ChIP assay data support the model that most of the RTA binding to RAP RRE DNA requires a cooperative interaction with C/EBP{alpha}.



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  		FIG. 5. ChIP assay with JSC-1 cell extracts after 40 h of TPA treatment showing that C/EBP{alpha}, RTA, and RAP all associate with the RAP promoter and that C/EBP{alpha} is required for RTA and RAP to associate efficiently. (A) Schematic of the 164-bp region of the RAP promoter encompassing both of the C/EBP binding sites and the RRE that was targeted for detection via PCR amplification with two specific primers, LGH4361 and LGH4362. (B) (Upper panel) Lanes 1 to 5, ChIP assay results showing that RAP promoter DNA could be recovered from immunoprecipitates containing either RTA, C/EBP{alpha}, or RAP but not from immunoprecipitates with ZTA or a negative control antibody. Lanes 6 and 7, removal of C/EBP{alpha} from lysates (preclearing) abolished the association of RAP with the RAP promoter and weakened the association of RTA. Lane 8, association of C/EBP{alpha} with RAP promoter DNA was not affected by the removal of RTA. Lane 9, PCR amplification products obtained from the RAP promoter expression plasmid (pFYW41) with the same primers, indicating the expected correct sizes of the PCR products. (Lower panel) Negative control. ChIP assay results showing that nonpromoter DNA fragments were not coprecipitated nonspecifically with these antibodies. Lanes 1 to 9, primers (LGH4929 and LGH4930) specific for the detection of RTA coding region DNA (300 bp) failed to detect any positive signals above the basal level, except from the cDNA plasmid control (lane 9).

 
Unexpectedly, we also observed an association of RAP with RAP promoter DNA (Fig. 5B, lane 3), although the level was relatively weak compared to those obtained with RTA and C/EBP{alpha} (ratio of 4.7 versus 12.5 and 13.5, respectively). Because RAP interacts with C/EBP{alpha}, the ChIP assay data suggested that RAP may become associated with DNA indirectly through binding to DNA-bound C/EBP{alpha}. To address the question of whether any RAP would still be associated with RAP promoter DNA in the absence of C/EBP{alpha}, we precleared C/EBP{alpha} from cell lysates with anti-C/EBP{alpha} antibody and protein A-protein G-Sepharose and used the supernatants for a second round of immunoprecipitation with anti-RAP PAb. Indeed, after the removal of C/EBP{alpha}, we failed to recover any RAP promoter DNA with anti-RAP PAb (similar to the basal level) (Fig. 5B, lane 6). This result suggested that RAP interacts here only with DNA-bound C/EBP{alpha} and that, after the removal of C/EBP{alpha} in the preclearing step, no additional RAP was associated with RAP promoter DNA.

A negative control PCR assay with a pair of primers that specifically detected only coding region DNA sequences from within the KSHV RTA gene (LGH4929 and LGH4930) failed to yield any positive signals beyond the background level (Fig. 5B, lower panel). This result confirmed that our ChIP assay was specific and recovered only promoter region DNA sequences specifically bound by the immunoprecipitated proteins.

Expression of C/EBP{alpha} induces endogenous RAP mRNA and RAP protein in PEL cells. We have shown by LUC reporter gene assays and by EMSA studies that C/EBP{alpha} indeed binds to and transcriptionally activates the RAP promoter in vitro. Therefore, we next examined whether exogenously introduced C/EBP{alpha} may be capable of triggering the expression of the RAP gene in infected cells. Total cell mRNA was harvested from BCBL-1 cells latently infected with KSHV after transfection with either a mammalian expression plasmid encoding C/EBP{alpha} or an empty vector as a negative control. As a positive control, we also harvested mRNA from TPA-treated BCBL-1 cells, where RAP expression is known to be induced. RT-PCR was then performed to detect changes in the levels of RAP cDNA.

Functional RAP mRNA is the product of differential splicing and consists of three different exons (52). A pair of primers spanning positions 75252 to 75271 (LGH3771) and positions 75774 to 75791 (LGH3774) was designed for PCR of the total cDNA to distinguish the 540-bp RAP genomic DNA fragment from the spliced 310-bp RAP cDNA fragment (Fig. 6A). As expected, in nontransfected BCBL-1 cells (negative control), the 540-bp genomic DNA fragment of RAP was readily apparent, but the cDNA form was barely detectable (Fig. 6B, lane 1); however, in TPA-treated BCBL-1 cells (positive control), both the 540-bp genomic DNA fragment and the 310-bp cDNA fragment of RAP were present at high levels as a result of KSHV lytic-cycle induction and viral DNA replication (Fig. 6B, lane 2). In comparison, cells transfected with the C/EBP{alpha} expression plasmid showed significantly induced RAP mRNA expression, as exemplified by the increased level of the RAP cDNA fragment (Fig. 6B, lane 4); however, in cells transfected with the empty expression vector, there was no evidence for the induction of RAP mRNA (Fig. 6B, lane 3). RT-PCR products of glyceraldehyde-3-phosphate dehydrogenase mRNA showed that equal amounts of mRNA were used in the RT-PCR (Fig. 6B, lower panel).



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  		FIG. 6. RT-PCR showing that an exogenously introduced C/EBP{alpha} expression vector can trigger RAP transcription in BCBL-1 cells latently infected with KSHV. (A) Schematic showing the splicing pattern for the full-length KSHV RAP mRNA. (B) (Upper panel) RT-PCR performed with mRNA harvested from C/EBP{alpha}-transfected BCBL-1 cells and with primers specific for the RAP gene. Lane 1, lack of detectable RAP cDNA in untreated BCBL-1 cells. Lane 2, increased RAP cDNA level in TPA-treated BCBL-1 cells undergoing lytic-cycle induction. Lane 3, lack of detectable RAP cDNA in BCBL-1 cells transfected with empty vector DNA. Lane 4, induction of RAP cDNA in C/EBP{alpha}-transfected BCBL-1 cells. Lane 5, positive size marker control showing the PCR products from the RAP cDNA expression plasmid (pFYW01). (Lower panel) Loading and amplification control experiment showing that equal concentrations of template mRNA were used, as illustrated by the uniform levels of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA RT-PCR products.

 
To visually confirm that the expression of RAP was induced specifically only in C/EBP{alpha}-positive BCBL-1 cells, we performed IFA experiments. Latently infected BCBL-1 cells were transfected with either a Flag-tagged C/EBP{alpha} expression plasmid or a Flag-tagged RTA expression plasmid as a positive control, and RAP expression was monitored by double-stain IFA with anti-RAP rabbit antiserum and anti-Flag MAb. In RTA-transfected BCBL-1 cells, 82% of the Flag-RTA-positive cells were also positive for RAP expression (Fig. 7A to C), confirming that RTA strongly induced RAP expression (25, 45). Similarly, in C/EBP{alpha}-transfected BCBL-1 cells, 74% of the Flag-C/EBP{alpha}-positive cells were also positive for RAP expression (Fig. 7D to F). Therefore, although this percentage was slightly lower than that for Flag-RTA-positive cells, C/EBP{alpha} was clearly also a potent transcriptional activator of the RAP gene in the context of the latent viral genome in PEL cells. Furthermore, in BCBL-1 cells doubly transfected with both untagged RTA and Flag-tagged C/EBP{alpha}, 98% of the Flag-positive cells became positive for RAP expression (Fig. 7G to I), suggesting that cooperativity between RTA and C/EBP{alpha} contributed to even greater levels of activation of the RAP promoter. As a negative control, BCBL-1 cells transfected with the empty Flag vector produced no increase in RAP expression beyond the low level of the spontaneously lytic population (<2%) (Fig. 7J to L).



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  		FIG. 7. Both exogenously introduced Flag-RTA and Flag-C/EBP{alpha} trigger RAP expression in DNA-transfected BCBL-1 cells. (A to C) Double-label IFA illustrating the expression of Flag-RTA (in SV2-Flag-RTA-transfected cells), as detected with anti-Flag MAb (A, rhodamine, red), and enhanced expression of RAP, as detected in the same cell population with anti-RAP PAb (B, fluorescein isothiocyanate, green). (C) DAPI nuclear staining (blue) showing all cells in the same field. (D to F) Double-label IFA showing the expression of Flag-C/EBP{alpha} (in Flag-C/EBP{alpha}-transfected cells), as detected with anti-Flag MAb (D, red), and enhanced expression of RAP, as detected in the same cell population with anti-RAP PAb (E, green). (F) DAPI (blue) showing the whole cell population. (G to I) Double-label IFA showing that the cotransfection of both untagged RTA and Flag-tagged C/EBP{alpha}, as detected by anti-Flag MAb (G, red), greatly enhanced the induction of endogenous RAP expression (H, green). (I) DAPI (blue) showing the whole cell population. (J to L) Double-label IFA showing the lack of expression from the empty Flag vector (J, red) and the absence of RAP expression (K, green) in the same infected cell population. (L) DAPI (blue) showing the whole cell population. Note that spontaneous background RAP expression occurred in approximately 1% of untreated BCBL-1 cells.

 
C/EBP{alpha} physically interacts with KSHV RTA. Because of the cooperativity observed between C/EBP{alpha} and RTA in transient reporter gene assays, we examined whether the two proteins could physically interact with each other. We initially examined this interaction by performing a coimmunoprecipitation experiment with KSHV-positive BCBL-1 cells. RTA expression in BCBL-1 cells was induced by TPA-treatment. Nuclear extracts of BCBL-1 cells were prepared 30 h after induction, and an immunoprecipitation experiment was performed with anti-C/EBP{alpha} goat PAb. Because both C/EBP{alpha} and RTA can bind to DNA, we also included DNase I incubation and added ethidium bromide to the immunoprecipitation reaction to destroy double-stranded DNA and prevent nonspecific protein-protein linking via DNA binding. The immunoprecipitate was analyzed by SDS-PAGE and Western blotting, which detected a 120-kDa band of coprecipitating RTA, indicating that endogenous C/EBP{alpha} and RTA strongly interacted with each other in BCBL-1 cells (Fig. 8A, lane 2). A negative control experiment performed with preimmune goat serum yielded no RTA signal (Fig. 8A, lane 3). RTA present in the input nuclear extract yielded at least two distinct bands, but the upper one (150 kDa) was not detected in the immunoprecipitate, perhaps indicating the existence of a modified form of RTA that does not bind to C/EBP{alpha} (Fig. 8A, lane 1).




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  		FIG. 8. C/EBP{alpha} interacts with KSHV RTA both in vivo and in vitro. (A) Coimmunoprecipitation of KSHV RTA with C/EBP{alpha} in KSHV-positive BCBL-1 cells undergoing KSHV lytic-cycle induction by TPA. Detection was carried out by Western immunoblotting with anti-RTA PAb. Lane 1, positive control showing RTA in the input cell lysate (10 µl, 10% of input sample). NE, nuclear extract. Lane 2, recovery of RTA by immunoprecipitation (IP) with anti-C/EBP{alpha} PAb. Lane 3, negative control showing that immunoprecipitation with control preimmune goat serum failed to recover RTA. (B) In vitro interaction between C/EBP{alpha} and RTA. (Left panel) GST affinity assay showing the interaction between GST-C/EBP{alpha} and 35S-labeled RTA. Lane 1, negative control showing the absence of RTA binding to GST alone. Lane 2, RTA binding to GST-C/EBP{alpha}. Lane 3, input in vitro-translated 35S-labeled RTA. (Middle panel) Reciprocal interaction between GST-RTA and 35S-labeled C/EBP{alpha}. Lanes 4, 5, and 7, C/EBP{alpha} binding to both GST-C/EBP{alpha} and GST-RTA DBD but not to GST alone. Lane 6, input in vitro-translated 35S-labeled C/EBP{alpha}. (Right panel) Lanes 8 to 11, negative control showing that 35S-labeled LUC protein does not interact with either GST, the GST-C/EBP{alpha} fusion, the EST-RTA fusion, or the GST-RTA DBP fusion. Lane 12, input 35S-labeled LUC protein. Arrowheads indicate reactive bands, and numbers at left indicate mass in kilodaltons.

 
The interaction between RTA and C/EBP{alpha} was further confirmed by GST affinity assays with bacterially expressed GST-C/EBP{alpha} or GST-RTA recombinant fusions. [35S]methionine-labeled in vitro-translated RTA or C/EBP{alpha} samples were added to reaction mixtures containing either GST-C/EBP{alpha} or GST-RTA immobilized on glutathione beads. After extensive washing of the beads, bound 35S-labeled C/EBP{alpha} or RTA was recovered from the beads, suggesting that a strong interaction occurred between C/EBP{alpha} and RTA (Fig. 8B, left and middle panels). In contrast, 35S-labeled in vitro-translated LUC protein used as a negative control failed to interact with either GST-C/EBP{alpha} or GST-RTA (Fig. 8B, right panel). Furthermore, a GST-RTA DBD fragment that contained only the N-terminal 377 amino acids of RTA still interacted with C/EBP{alpha}, but at a somewhat lower affinity (Fig. 8B, middle panel), suggesting that the interaction with C/EBP{alpha} was mediated by the RTA DBD only (see below).

RTA associates with C/EBP{alpha} through a basic domain mapping between positions 151 and 170 in RTA. To further confirm and map the RTA domain that interacts with C/EBP{alpha}, extensive mutagenesis was performed, and a series of RTA deletion mutants were constructed (Fig. 9A). The expression of all of the RTA deletion mutants was confirmed by [35S]methionione-labeled in vitro translation (Fig. 9B). After testing the abilities of these mutants to interact with GST-C/EBP{alpha} by GST affinity assays, we identified a region of RTA, between amino acids 151 and 272 and encompassing a basic domain, that is crucial for the binding of RTA to C/EBP{alpha} (Fig. 9C). All RTA deletion mutants containing the first 273 amino acids from the N terminus were able to interact with C/EBP{alpha}, and several RTA mutants harboring various deletions in front of position 151 were also able to associate with C/EBP{alpha}. However, all deletions that removed amino acids between positions 151 and 272 totally abolished the in vitro interaction of RTA with C/EBP{alpha} (Fig. 9C).




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  		FIG. 9. C/EBP{alpha} interacts with a domain of RTA mapping between amino acids 151 and 273. (A) Diagram of wild-type RTA and RTA deletion mutants used. aa, amino acid; NLS, nuclear localization sequence; LZ, leucine zipper domain; AD, activation domain; N/A, not tested. (B) Relative sizes and abundances of the 10 35S-labeled in vitro-translated (IVT) proteins used as inputs for GST affinity assays. (C) Results of in vitro GST affinity assays showing the relative levels of different RTA deletion mutants recovered after binding to purified GST-C/EBP{alpha} fusion beads. Numbers at left indicate mass in kilodaltons.

 
To further characterize the region between positions 151 and 272 that interacted with C/EBP{alpha}, a number of site-specific amino acid substitutions were introduced into the N-terminal basic segment of that region (Fig. 10A). Using as a parent the deletion protein RTA(151-548), paired Lys or Arg basic residues K152 and K154, R160 and R161, or R166 and R167 were targeted for mutation to Glu or Gly. The ability of all three K152/K154, R160/R161, and R166/R167 mutants to interact with GST-C/EBP{alpha} was significantly impaired compared to that of wild-type RTA(151-548). Double mutations of the above sites, as in mutants RTA(151-548KR1), RTA(151-548KR2), and RTA(151-548RR), led to an even lower affinity for GST-C/EBP{alpha}; the triple mutation of the above sites, as in mutant RTA(151-548KRR), completely abolished the interaction with GST-C/EBP{alpha} (Fig. 10B). Therefore, the six basic amino acids at positions 152, 154, 160, 161, 166, and 167 (at the end of the N-terminal basic domain) are crucial for the ability of RTA to interact with C/EBP{alpha}.



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  		FIG. 10. Basic amino acid residues mapping between amino acids 151 and 170 of RTA are required for interaction with C/EBP{alpha}. (A) Schematic showing the amino acid sequences of positions 151 to 170 of RTA and the seven site-specific RTA mutant versions of RTA(151-548) that harbor specific mutations of basic residues. Underlining and bold type indicate mutations. (B) (Upper panel) Relative sizes and abundances of the 35S-labeled in vitro-translated (IVT) RTA mutants synthesized in vitro. (Lower panel) Results of in vitro GST affinity binding assays showing the relative levels of the different RTA mutan