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Human T-cell leukemia virus type 2 (HTLV-2) Rex is a transacting regulatory protein required for efficient cytoplasmic expression of the unspliced and incompletely spliced viral mRNA transcripts encoding the structural and enzymatic proteins. Previously, it was demonstrated that phosphorylation of Rex-2, predominantly on serine residues, is correlated with an altered conformation, as observed by a gel mobility shift and the detection of two related protein species (p24Rex and p26Rex). Rex-2 phosphorylation is required for specific binding to its viral-mRNA target sequence and inhibition of mRNA splicing and may be linked to subcellular compartmentalization. Thus, the phosphorylation-induced structural state of Rex in the infected cell may be a switch that determines whether HTLV exists in a latent or productive state. We conducted a phosphoryl and functional mapping of both structural forms of mammalian-cell-expressed Rex 2 using affinity purification, liquid chromatography-tandem mass spectrometry, and site-directed substitutional mutational analysis. We identified two phosphorylation sites in p24Rex at Ser-117 and Thr-164. We also identified six phosphorylation sites in p26Rex at Thr-19, Ser-117, Ser-125, Ser-151, Ser-153, and Thr-164. We evaluated the functional significance of these phosphorylation events and found that phosphorylation on Thr-164, Ser-151, and Ser-153 is critical for Rex-2 function in vivo and that phosphorylation of Ser-151 is correlated with nuclear/nucleolar subcellular localization. Overall, this work is the first to completely map the phosphorylation sites in Rex-2 and provides important insight into the phosphorylation continuum that tightly regulates Rex-2 structure, cellular localization, and function.
Human T-cell leukemia virus types 1 and 2 (HTLV-1 and HTLV-2) are closely related complex retroviruses that have the ability to transform primary human T cells in culture and are associated with leukemia and a variety of human diseases (57). HTLV-1 is causally associated with adult T-cell leukemia, an aggressive CD4+ T-cell malignancy, and a chronic neurodegenerative disorder, HTLV-associated myelopathy/tropical spastic paraparesis (14, 50). Disease association with HTLV-2 is less clear, with only a few cases of leukemia and neurological diseases reported (20, 39, 40). The difference in pathogenesis between the two related viruses has yet to be elucidated but likely results from the activities of the regulatory and accessory proteins, as well as their distinct Env cell surface molecule interaction profiles (11, 22, 23, 53).
In addition to the archetypal structural and enzymatic retroviral genes gag, pol, and env, HTLV carries two trans-regulatory genes, tax and rex, which are essential for efficient viral replication/transformation, as well as several accessory genes important for viral infection and persistence in vivo (27). The viral oncoprotein Tax acts to trans-activate transcription from the viral long terminal repeat (7, 10) and modulates the transcription/functions of numerous cellular genes involved in cell growth, cell cycle control, DNA repair, and cell differentiation (6, 30, 35, 36, 43). The pleiotropic affects of Tax on these numerous cellular processes are critical for its ability to induce cellular transformation and oncogenesis (11, 13, 38, 41).
HTLV Rex is a positive trans-acting regulator of viral replication. Rex is a nuclear-localizing and shuttling phosphoprotein that acts posttranscriptionally by binding and selectively exporting the unspliced and incompletely spliced viral mRNAs from the nucleus to the cytoplasm, thus controlling the expression of the viral gene products that are essential for viral progeny production (19, 26). Therefore, it has been proposed that Rex is critical for the transition from the early, latent phase to the late, productive phase of HTLV infection. Rex binds viral mRNAs via a cis-acting viral RNA structure termed the Rex response element (RxRE) located in the R region of the viral long terminal repeat (3, 33, 48). Previous analysis of HTLV-1 Rex (Rex-1), HTLV-2 Rex (Rex-2), and their RxREs revealed structural homologies and showed that they are functionally interchangeable (55, 56). Rex mutational analysis has defined several domains that are critical for its functions, including an arginine-rich N-terminal sequence that functions as an RNA binding domain (RBD), which also overlaps with a nuclear localization signal, a leucine-rich central core activation domain that contains a nuclear export signal, and two flanking Rex-Rex multimerization domains (4, 5, 18, 21, 32, 34, 37, 45, 51). More recently, it has been reported that Rex-2 contains a novel C-terminal inhibitory/stability functional domain that is positively regulated through phosphorylation (31, 32, 54).
Phosphorylation is a well-documented regulatory event with a pivotal role in controlling the activities/functions of proteins (47). Earlier studies demonstrated that both Rex-1 and Rex-2 are phosphoproteins and that this modification is critical to their function (1, 2, 17). In HTLV-2-infected T cells and cell lines transfected with Rex-2 expression plasmids, two species of Rex-2 (p24Rex and p26Rex) are detected. Both Rex-2 species have the same amino acid backbone and differ by a charge-induced conformational change due to a serine/threonine phosphorylation (15, 16, 31). This altered gel mobility is unique to Rex-2, since Rex-1 presents as a single 27-kDa phosphoprotein. We reported the identification of important Rex-2 phosphorylation sites using targeted serine- or threonine-to-alanine substitution mutational analysis. That study identified at least one critical phosphorylation site at serine 151 (31). A serine-to-alanine substitution at this residue (S151A) resulted in reduced phosphorylation, impaired RNA binding capability, diffused cytoplasmic localization, and decreased functional activity. In contrast, replacement of the serine with an aspartic acid (S151D) resulted in detection of only the p26Rex species in cells. The S151D mutant was found to be more active than wild-type (wt) Rex-2 and displayed enhanced RNA binding capacity and intense localization to the nucleus (31, 32).
Our earlier studies suggested a linear relationship between phosphorylation, conformational changes, and Rex-2 function, implicating phosphorylation as a key regulatory event within the productive life cycle of the virus (31). To understand the regulation of Rex-2 function by phosphorylation, we performed complete phosphorylation mapping of both p24Rex and p26Rex. In this study, we combined liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis (28) of affinity-purified Rex-2 protein with substitution mutational analysis to identify and functionally characterize key phosphorylation sites. We achieved 100% coverage of both p24Rex and p26Rex. We identified two phosphorylation sites in p24Rex and six total phosphorylation sites in p26Rex. We also determined three specific amino acid phosphorylation events that were found to be critical for Rex-2 function in vivo (Ser-151, Ser-153, and Thr-164). Phosphorylation at Ser-151 and Ser-153 is the major switch event for the conformational change between p24Rex and p26Rex. Phosphorylation of one of these sites (Ser-151) was critical for nuclear subcellular localization of the Rex-2 protein. Taken together, our data support a model in which a phosphorylation continuum of Rex-2 at the carboxy terminus regulates its biological properties and, ultimately, viral replication.
293T and HeLa-Tat cells were maintained in Dulbecco's modified Eagle's medium at 37°C in a humidified atmosphere of 5% CO2 in air. The medium was supplemented with 10% fetal bovine serum, 2 mM glutamine, penicillin (100 U/ml), and streptomycin (100 μg/ml).
The Rex-2 expression vector BC20.2, which contains the HTLV-2 tax/rex cDNA expressed from the cytomegalovirus (CMV) immediate-early gene promoter, was described previously (16, 55). The S-tagged expression vector S-Rex-2 was constructed by inserting the HTLV-2 rex open reading frame from BC20.2 into pTriEx4-Neo (Novagen, Madison, WI) in frame with the amino-terminal His tag and S tag via SmaI and BamHI. All generated rex expression vectors contained a previously described mutation in the overlapping tax reading frame (F4Term), which had no effect on the Rex amino acid sequence but severely truncated Tax, completely knocking out its expression and function (42). The various rex-2 targeted mutations were generated using the QuikChange site-directed mutagenesis kit (Stratagene, La Jolla, CA). All mutations were confirmed by DNA sequence analysis, and vector expression was verified by transfection and Western blot analysis. The human immunodeficiency virus type 1 (HIV-1) Tat expression vector, pcTat; Rex-2 reporter plasmid (pCgagRxRE-II); and CMV-luciferase (firefly) (CMV-luc) were described previously (31).
The Rex-2 functional assay was performed as described previously with slight modifications (31). Briefly, 0.1 μg Rex-2 cDNA expression plasmids were cotransfected into 293T cells with 0.05 μg of CMV-luc, 0.25 μg of pcTat, and 0.5 μg of Rex reporter plasmid pCgag-RxRE-II using Lipofectamine reagent (Invitrogen, Carlsbad, CA). Cell lysates were prepared at 24 h posttransfection in Passive Lysis Buffer (Promega, Madison, WI) with a protease inhibitor mixture (Roche Applied Science, Indianapolis, IN) on ice for 30 min. Luciferase activity was determined and used as a transfection efficiency control. HIV-1 p24 Gag levels in the cellular lysates were determined by enzyme-linked immunosorbent assay (ZeptoMetrix, Buffalo, NY). All transfection experiments were performed in triplicate in three independent experiments.
Cell lysates were prepared at 24 h posttransfection in Passive Lysis Buffer (Promega, Madison, WI) with a protease inhibitor mixture (Roche Applied Science, Indianapolis, IN) on ice for 30 min. After centrifugation, total protein concentrations were determined by Bradford protein assay (Bio-Rad). The cell lysates were subjected to 12% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to nitrocellulose (Schleicher & Schuell Biosciences, Keene, NH). Western blots were performed as recommended by the manufacturer, and proteins were visualized using an enhanced-chemiluminescence-Western blot analysis system (Santa Cruz Biotechnology, Santa Cruz, CA). Rex-2 was detected using protein-specific rabbit polyclonal antisera. Subcellular localization of Rex-2 was performed as previously described (49) with slight modifications. HeLa-Tat cells were transfected with 2 μg of vector control plasmid, wt Rex-2, or various Rex-2 mutants. At 24 h posttransfection, the cells were washed and fixed in phosphate-buffered saline containing 2% paraformaldehyde and permeabilized in phosphate-buffered saline containing 0.2% Triton X-100 and 0.5% fetal bovine serum for 15 min at 4°C. The cells were incubated in blocking buffer (0.5% fetal bovine serum and 2 mg/ml human immunoglobulin G) for 30 min at room temperature. Staining was conducted in blocking buffer with rabbit Rex-2-specific antisera, followed by incubation with secondary antibody conjugated to fluorescein isothiocyanate Alexa Fluor 488 (Molecular Probes, Eugene, OR). Nuclear staining was performed using 4′6-diamidino-2-phenylindole (DAPI) Slow Fade Gold (Invitrogen, Carlsbad, CA). Fluorescence was visualized on an epifluorescence microscope (Olympus, Melville, NY), and digital images were taken using an Optronics (Goleta, CA) imaging system.
Protein purification was performed as described previously with slight modifications (9). Briefly, the cell lysate (1.5-ml volume) was incubated with a 75-μl bed volume of S protein-agarose (Novagen, Gibbstown, NJ) overnight at 4°C and washed twice with a high-salt modified RIPA buffer (0.05 M Tris-HCl, pH 8.0, 0.1% SDS, 1% Triton X-100, 1.0 M NaCl, 0.01 M EDTA) and twice with a low-salt modified RIPA buffer (0.05 M Tris-HCl, pH 8.0, 0.1% SDS, 1% Triton X-100, 150 mM NaCl). The S protein-agarose beads were resuspended in 100 μl SDS loading dye containing β-mercaptoethanol and subsequently boiled for 2 min. Samples were electrophoresed in a 12% SDS one-dimensional polyacrylamide gel and visualized by Coomassie blue staining. Both the p24Rex and p26Rex bands were excised from the gel separately for further proteomic analysis.
LC-MS/MS analysis was performed as described previously with slight modifications (9). Briefly, p24Rex and p26Rex excised gel slices were cut into 1- to 2-mm cubes, washed three times with 500 μl ultrapure water, and incubated in 100% acetonitrile for 45 min. Samples were reduced with 50 mM dithiothreitol at 56°C for 45 min and then alkylated with 55 mM iodoacetamide for 1 h at room temperature. The material was dried in a speed-vac, rehydrated in a 12.5-ng/μl modified sequencing-grade trypsin solution (Promega, Madison, WI), and incubated in an ice bath for 40 to 45 min. The trypsin solution was removed and replaced with 40 to 50 μl of 50 mM ammonium bicarbonate and 10% acetonitrile (pH 8.0), and the mixture was incubated overnight at 37°C. Elastase digestions were performed as described for trypsin at an enzyme concentration of 15 ng/μl in the absence of acetonitrile in the reaction buffer. Peptides were extracted two times with 25 μl 50% acetonitrile, 5% formic acid and dried in a speed-vac. The digests were resuspended in 20 μl buffer A (5% acetonitrile, 0.1% formic acid, 0.005% heptafluorobutyric acid), and 3 to 6 μl was loaded onto a 12-cm by 0.075-mm fused silica capillary column packed with 5 μm-diameter C18 beads (The Nest Group, Southboro, MA) using an N2 pressure vessel at 1,100 lb/in2. The peptides were eluted over 55 min by applying a 0 to 80% linear gradient of buffer B (95% acetonitrile, 0.1% formic acid, 0.005% heptafluorobutyric acid) at a flow rate of 150 μl/min with a precolumn flow splitter, resulting in a final flow rate of ~200 nl/min directly into the source. In some cases, the gradient was extended to 150 min to acquire more MS/MS spectra. An LTQ Linear Ion Trap (ThermoFinnigan, San Jose, CA) was run in automated collection mode with an instrument method composed of a single segment and five data-dependent scan events with a full MS scan followed by four MS/MS scans of the highest-intensity ions. The normalized collision energy was set at 35, and activation quadrupole was 0.250 with minimum full scan signal intensity at 1 × 105, with no minimum MS/MS intensity specified. Dynamic exclusion was turned on, utilizing a 3-minute repeat count of 2, with the mass width set at 1.0 m/z. Sequence analysis was performed with TurboSEQUEST (ThermoFinnigan, San Jose, CA) or MASCOT (Matrix Sciences, London, United Kingdom) using an indexed human subset database of the nonredundant protein database from the National Center for Biotechnology Information website (http://www.ncbi.nlm.nih.gov).
Two species of Rex-2 (p24Rex and p26Rex) are detected in virus-infected cells. The two Rex-2 species have the same amino acid backbone and differ by a charge-induced conformational change due to a serine/threonine phosphorylation (15, 16, 31). The p24Rex species is incapable of binding target mRNA and is found primarily in the cytoplasm, whereas the p26Rex species is localized primarily to the nucleus, and its presence is correlated with Rex-2-specific RxRE target RNA binding (17, 56). Mutational analysis permitted the assignment of functional properties to distinct domains of the Rex-2 protein (Fig. (Fig.1).1). In addition to the nuclear localization signal/RBD, central core activation domain/nuclear export signal, and multimerization domains that were also shared with the functionally homologous HTLV-1 Rex (32), we also reported that Rex-2 contained a unique C-terminal inhibitory/stability domain that was found to be important for proper nucleocytoplasmic shuttling, subcellular localization, and function (32, 54). This domain also encompasses at least one phosphorylated serine residue (S151), identified by substitutional mutational and peptide phosphoamino acid analysis, that is critical for Rex-2 function in vivo (31, 32). Replacement of this serine with aspartic acid to mimic phosphorylation (S151D) resulted in detection of only the p26Rex species in cells. The S151D mutant was more functionally active than wt Rex-2 and was locked in a p26Rex conformation, since in vitro phosphatase treatment failed to alter its mobility. Therefore, since phosphorylation of Rex-2 may be a key regulatory event, a complete analysis of Rex-2 phosphorylation is well justified.
To determine the distinct phosphorylation events present in both p24Rex and p26Rex that occur in vivo, we used a tandem affinity-tagged Rex-2 construct that was expressed in and purified from mammalian cells. The Rex-2 vector (S-Rex-2) expresses full-length Rex-2 protein fused to amino-terminal His6 and S tags (Fig. (Fig.2A).2A). Since the HTLV regulatory proteins Tax and Rex are translated from the same mRNA in partially overlapping reading frames, we utilized a cDNA mutant sequence containing an amino-terminal stop codon in the Tax reading frame, leaving the Rex-2 reading frame unchanged (41). This mutation abrogated Tax protein expression (data not shown). The S-Rex-2 and the wt Rex-2 expression constructs were transiently transfected into 293T cells, and protein expression was determined by Western blot analysis using rabbit polyclonal anti-Rex antisera (Fig. (Fig.2B).2B). As expected, the wt-Rex-2-transfected cells produced both p24Rex and p26Rex species. S-Rex-2-transfected cells also produced two distinct species of increased molecular weight, consistent with the addition of the tags. We performed further analyses to confirm that the S-tagged Rex-2 species had properties similar to those of wt Rex-2 (p24Rex and p26Rex). Pro Q diamond staining, a fluorescence method for detection of phosphoproteins in polyacrylamide gels, as well as protein phosphatase treatment, indicated that the upper band was a phosphorylated form of the lower band, consistent with what had been reported previously for wt Rex-2 (reference 17 and data not shown). We then tested S-Rex-2 for its ability to function in our quantitative reporter bioassay, in which HIV-1 p24 Gag production was measured and used as a readout of Rex functional activity (31). As shown in Fig. 2C, S-Rex-2 displayed significant functional activity, although slightly lower than that of wt Rex-2. We hypothesize that this reduced activity is likely due to the proximity of the amino-terminal tag to the RBD. Taken together, these data demonstrate the proper and efficient expression of a functionally active S-tagged Rex-2 from mammalian cells.
We successfully purified S-tagged Rex-2 protein from transfected 293T cells using S protein-agarose beads as described in Materials and Methods. This purification procedure is based on the strong affinity between the 15-amino-acid S tag and the S protein that is immobilized on the agarose beads, both of which are derived from RNase S (25). The affinity-purified Rex-2 protein was resolved by SDS-PAGE, in which both species of S-tagged Rex-2, equivalent to wt p24Rex and p26Rex, were detected by Coomassie blue staining (Fig. (Fig.2D).2D). This purification process produced adequate quantities of highly purified Rex-2 protein from mammalian cells and allowed the subsequent posttranslational modification analysis by LC-MS/MS.
Multiple strategies were employed to identify the phosphorylation sites within Rex-2. The two species of S-tagged Rex-2 were excised and treated separately. This ensured that we could determine the specific phosphorylation maps of each species independently in an effort to better understand how phosphorylation alters Rex-2 conformation and regulates its function. Initially, the proteins were subjected to trypsin enzymatic digestion. The tryptic peptides that were too large to detect were either further digested with elastase or independently digested with elastase. This combined analytical approach allowed us to obtain a detailed physical map covering 100% of the polypeptide for both species of S-tagged Rex-2 (Fig. (Fig.3A).3A). Our analysis identified two phosphorylation sites, Ser-117 and Thr-164, in the lower species (p24Rex equivalent). In addition to Ser-117 and Thr-164, we also identified four additional residues (Thr-19, Ser-125, Ser-151, and Ser-153) that are phosphorylated in the upper S-tagged species (p26Rex equivalent). Figure Figure3B3B shows a representative MS/MS spectrum of the tryptic phosphopeptide that identified phosphorylation at Ser-151. Furthermore, phosphorylation of Ser-151 was previously shown to be important for Rex-2 subcellular localization, RNA binding, and Rex-2 function in vivo (31).
To determine possible regulatory roles of the six identified phosphorylation sites, we generated single alanine amino acid substitutions and tested these Rex-2 mutants for the ability to function in our quantitative reporter bioassay. The Rex-2 mutants were transiently cotransfected into 293T cells with pcTat and pCgagRxRE-II, along with a CMV-luc transfection efficiency control. We identified three mutants, S151A, S153A, and T164A, within the C-terminal domain of Rex-2 that displayed significantly reduced function (Fig. (Fig.4A).4A). Further mutational analysis of these three residues by converting them to aspartic acid (S151D, S153D, and T164D), which mimics a phosphoserine or threonine, restored functional activity to wt Rex-2 levels, indicating that phosphorylation plays a positive functional role (Fig. (Fig.4A).4A). Aspartic acid substitution for Thr-19, Ser-117, or Ser-125 had no effect on protein function, consistent with the conclusion that phosphorylation of these three residues does not negatively regulate function but is silent (data not shown). The steady-state expression levels of the wt and mutant Rex-2 proteins were determined by Western blot analysis using rabbit polyclonal anti-Rex antisera (Fig. (Fig.4B).4B). All of the Rex-2 mutants were stably expressed. With the exception of S151D and S153D, detected only as p26Rex, all of the mutants displayed both the p26Rex and p24Rex forms. We previously reported that the p26Rex/p24Rex ratio of wt Rex in transfected cells is greater than or equal to 1 (31). One exception was mutant S151A, which showed a reduction in the amount of p26Rex relative to p24Rex, implying a role for phosphorylation of this residue in altering the conformation/mobility of the protein. It is notable that T164A displayed a similar reduction in p26Rex, indicating that phosphorylation of both Thr-164 and Ser-151 is correlated with p26Rex expression. Moreover, replacing threonine with aspartic acid (T164D) resulted in an increase in p26Rex and the restoration of function to wt levels (Fig. (Fig.4A),4A), which also is consistent with the conclusion that p26Rex is the active form of the protein. Taken together, our results help further define a critical functional domain that is regulated via phosphorylation of three key amino acids, Ser-151, Ser-153, and Thr-164. Since p24Rex was already found to contain phosphorylated Thr-164, we hypothesize that the altered ratio of p24Rex to p26Rex found in the T164A mutant and previously reported for S151A is indicative of an important role for this residue in the Rex-2 phosphorylation continuum.
We next wanted to determine if the phosphorylation of key Rex-2 residues identified in the carboxy terminus regulates subcellular localization of the protein. It has been documented that p26Rex is found primarily in the nucleus and nucleolus, whereas the inactive p24Rex is diffusely dispersed throughout the cytoplasm and nucleus (32, 56). We utilized indirect immunofluorescence to assess whether the three phosphor acceptor residues (Ser-151, Ser-153, and Thr-164) that were critical for function in our bioreporter assay were important for nuclear localization. HeLa-Tat cells were transiently transfected with wt Rex-2 and each of the alanine or aspartic acid substitutional mutants. Wt Rex, as well as all three phosphomimetic mutants (S151D, S153D, and T164D), localized predominantly to the nucleus with the detection of very minimal cytoplasmic staining (Fig. (Fig.5).5). Mutant S151A was widely diffused throughout the cell with significant cytoplasmic staining (Fig. (Fig.5).5). Mutants S153A and T164A showed significant nuclear staining, similar to wt Rex, but also displayed moderate cytoplasmic staining. Taking the data together, we conclude that although phosphorylation of Ser-151, Ser-153, and Thr-164 is pivotal for Rex-2 function, only the substitution of the Ser-151 phosphor acceptor residue for alanine resulted in a significant change in subcellular localization to the cytoplasm.
Combining the results from this study with previous published work suggests that phosphorylation of the carboxy terminus of Rex-2 triggers a protein conformation change that is correlated with nuclear localization, protein stability, and function. Since individual mutations at the carboxy terminus still maintain partial function and p24Rex shows Thr-164 phosphorylation, we hypothesized that phosphorylation occurs on a continuum and that phosphorylation of all three residues is required for optimal biological activity. To test this hypothesis and to determine if there is a functional relationship between Ser-151, Ser-153, and Thr-164, we generated and characterized a combination of Rex-2 alanine mutants for function and protein species expression. As shown in Fig. Fig.6,6, the two double mutants S151A T164A and S153A T164A display similar but significantly reduced functional activity compared to wt Rex-2. However, their functional activity was comparable to single-alanine-substitution mutants at either of those residues (compare Fig. Fig.2A2A and Fig. Fig.6).6). As seen with the S151A and T164A single mutants, Western blot analysis of the double mutants revealed a reduction of p26Rex relative to p24Rex, and the functional activity was directly correlated with the levels of p26Rex detected. The function of the S151A S153A T164A triple mutant was knocked down even further, but some activity over background levels was observed. Western blot analysis revealed a significant and nearly complete loss of the p26Rex species (Fig. (Fig.6).6). Some p26Rex was detected on longer exposure, which was correlated with the residual functional activity. Taken together, these data allow us to formulate a new, more complex Rex-2 phosphorylation continuum model that initiates with phosphorylation of Thr-164, followed by subsequent phosphorylation of Ser-151 and Ser-153, thus tightly regulating Rex-2 function and, ultimately, virus production.
Phosphorylation is a well-known regulatory event that plays a key role in controlling the functions of cellular and viral proteins (1, 24, 29, 46, 47, 52). The modulation of protein function can occur by multiple mechanisms, including regulation of subcellular localization, protein-protein interactions, protein stability, and protein-nucleic acid binding. Previously, it was demonstrated that phosphorylation of HTLV-2 Rex, predominantly on serine residues, was correlated with an altered conformation, as observed by a gel mobility shift and the detection of p24Rex and p26Rex protein species (16, 31). Rex-2 phosphorylation and the presence of the p26Rex species were correlated with functional activity, including specific binding to its viral mRNA target sequence, cytoplasmic export, and translation of the target mRNA (31, 32). Moreover, we recently reported that the carboxy terminus of Rex-2 contains a stability/inhibitory domain that is positively regulated through phosphorylation (54). However, a complete map of site-specific phosphorylation of Rex-2 is lacking, and the precise role it plays in protein function remains unclear. The goal of this study was to use affinity purification and LC-MS/MS to identify all phosphorylation sites in both p24Rex and p26Rex to provide insight into a possible phosphorylation continuum and the mechanism that controls Rex-2 function and ultimately the “on/off” switch that regulates productive viral replication. Consistent with previous reports, we confirmed that Rex-2 is phosphorylated predominantly on serine residues and some threonine residues, and although the p26Rex species is heavily phosphorylated, p24Rex contains minimal phosphorylation. We reported the phosphorylation of p24Rex at two sites, Ser-117 and Thr-164. We also reconfirmed phosphorylation of Ser-151 in p26Rex (31) and identified five additional phosphorylation sites, Thr-19, Ser-117, Ser-125, Ser-153, and Thr-164.
Using mutational analysis replacing the identified phosphor acceptor residues in Rex-2 with alanine or aspartic acid (which mimics phosphoserine or threonine), we showed that (i) the site-specific phosphorylations at Ser-151, Ser-153, and Thr-164 all positively contributed to Rex-2 function; (ii) the phosphorylation of Ser-151, Thr-164, and, to a lesser extent, Ser-153 dictate the p24Rex/p26Rex ratio and thus Rex conformational switching; and (iii) the phosphorylation of Ser-151 regulates the ability to efficiently localize to the nucleus. Both p24Rex and p26Rex are phosphorylated at Ser-117 and Thr-164, but only phosphorylation at Thr-164 is functionally significant. Thus, since we do not have evidence that Ser-151 or Ser-153 is phosphorylated without prior phosphorylation of Thr-164, a logical conclusion is that phosphorylation occurs on a continuum, with phosphorylation of Thr-164 an earlier initiating event that likely facilitates subsequent phosphorylation of Ser-151 and/or Ser-153 and Rex function. In Fig. Fig.7,7, we present a model, consistent with the published literature and our data, showing how phosphorylation regulates Rex-2 function. The initial translation product of Rex-2, p24Rex, is located primarily in the cytoplasm. It is an inactive species in a structural conformation in which the C terminus is configured in such a way that it prevents efficient phosphorylation of Ser-151 and Ser 153 and generation of an active p26Rex mRNA binding protein. We propose that the phosphorylation continuum starts with the phosphorylation of Thr-164, which begins the rotation of the C-terminal inhibitory domain, exposing Ser-151 and/or Ser-153 and making them available to be phosphorylated. This is also consistent with the phenotype of a previously characterized Rex-2 truncation mutant (S158Term) in which the 13 carboxy-terminal amino acids, including the Thr-164 phosphor acceptor, are deleted; Rex S158Term, although less stable, is functionally more active than the wt Rex-2 (54). However, since proteins are dynamic and not fixed in space, as long as one or more key phosphor acceptor sites are available within the C terminus, a hierarchical phosphorylation pattern could be sidestepped at a low frequency in mutant Rex proteins. This is consistent with the functional and Western blot results of our single (S151A or T164A) and double (S151A T164A or S153A T164A) alanine mutants, which maintain some function, and the expression of the active p26Rex. However, the triple alanine mutant (T164A S151A S153A), which contains none of the identified key phosphor acceptor residues, shows minimal functional activity and very little detection of the active p26Rex species. We have yet to experimentally identify the cellular kinase(s) that phosphorylates Rex on these key functional residues. However, using bioinformatics analyses, we previously reported (31) that Ser-151 falls in a predicted consensus site for phosphorylation by casein kinase 1 (Sp/Tp-X2-3-S/T-X). Ser-153 also shows high homology to the casein kinase 1 consensus sequence, and Thr-164 is predicted to be phosphorylated by either GSK3β or casein kinase 1 (data not shown).
Typically, stable protein conformational changes require bond rotations. Interestingly, using proteomic protein identification (mudpit) analysis, we recently identified the association of the cellular protein Pin1 in the Rex-2 pulldown complex (data not shown). Pin1 is a peptidylproline cis-trans isomerase of Ser/Thr peptide bonds N-terminal to proline residues. Pin1 is known to induce conformational changes that can affect enzymatic activities, phosphorylation status, subcellular localization, protein stability, and protein/protein interactions (8, 12, 24, 29, 44, 46, 58). One hypothesis consistent with our data is that once Thr-164 is phosphorylated, Pin1 could bind and cause a structural conformational change, rotating the inhibitory C-terminal domain and allowing access of the cellular kinase to phosphorylate Ser-151. The single mutants alone only hinder the ability of the kinase to reach its target consensus sequence. For example, S151A or S153A could still be phosphorylated at Thr-164, facilitating subsequent phosphorylation of either Ser-153 or Ser-151, respectively, resulting in the formation of p26Rex and modest function. In the case of the mutant T164A, the C-terminal domain is not efficiently dislocated, and since a biological protein is not static, a minimal amount of phosphorylation can occur on both Ser-151 and Ser-153. Whereas in the double mutant we not only inhibit Thr-164 phosphorylation, and thus the conformational change of the C terminus, but also block any phosphorylation of Ser-151, with this mutant we detected a greater increase in the amount of p24Rex, which correlates with the reduced function of the mutant protein, with the only possible phosphorylation being Ser-153.
The question arises as to whether this C-terminal phosphorylation domain is unique to Rex-2 or if it is also contained in the closely related Rex-1. Although the carboxy termini of the two related proteins at the amino acid level are quite divergent with no apparent Ser-151, Ser-153, and Thr-164 counterpart in Rex-1 (31, 32), we have previously shown that, like that of Rex-2, the carboxy terminus of Rex-1 does contain a stability domain (54). Rex-1 is known to be phosphorylated (1, 2), but further studies are needed to determine whether Rex-1 site-specific phosphorylation has a significant functional role.
Taken together, the data presented in this study provide a wealth of knowledge about the cellular signaling controlling Rex-2 protein function, structure, and localization. Further studies will be aimed at identifying the cellular proteins, including the kinase(s), involved in the regulation of Rex-2 function.
We thank Tim Vojt for preparation of the figures and Kate Hayes-Ozello for editorial comments.
This work was supported by a grant from the National Institutes of Health (CA100730) to P.L.G.
Published ahead of print on 24 June 2009.