G-patch domain and KOW motifs-containing protein, GPKOW; a nuclear RNA-binding protein regulated by protein kinase A
© Aksaas et al; licensee BioMed Central Ltd. 2011
Received: 29 April 2011
Accepted: 31 August 2011
Published: 31 August 2011
Post-transcriptional processing of pre-mRNA takes place in several steps and requires involvement of a number of RNA-binding proteins. How pre-mRNA processing is regulated is in large enigmatic. The catalytic (C) subunit of protein kinase A (PKA) is a serine/threonine kinase, which regulates numerous cellular processes including pre-mRNA splicing. Despite that a significant fraction of the C subunit is found in splicing factor compartments in the nucleus, there are no indications of a direct interaction between RNA and PKA. Based on this we speculate if the specificity of the C subunit in regulating pre-mRNA splicing may be mediated indirectly through other nuclear proteins.
Using yeast two-hybrid screening with the PKA C subunit Cbeta2 as bait, we identified the G-patch domain and KOW motifs-containing protein (GPKOW), also known as the T54 protein or MOS2 homolog, as an interaction partner for Cbeta2. We demonstrate that GPKOW, which contains one G-patch domain and two KOW motifs, is a nuclear RNA-binding protein conserved between species. GPKOW contains two sites that are phosphorylated by PKA in vitro. By RNA immunoprecipitation and site directed mutagenesis of the PKA phosphorylation sites we revealed that GPKOW binds RNA in vivo in a PKA sensitive fashion.
GPKOW is a RNA-binding protein that binds RNA in a PKA regulated fashion. Together with our previous results demonstrating that PKA regulates pre-mRNA splicing, our results suggest that PKA phosphorylation is involved in regulating RNA processing at several steps.
Post-transcriptional processing of pre-mRNA involves splicing, editing and polyadenylation and starts as soon as pre-mRNAs are produced at their sites of transcription. In addition to small non-coding RNAs (snRNAs) these processes require the activity of RNA-binding proteins (RBPs) [1, 2]. The discovery of the heterogeneous nuclear ribonucleoproteins (hnRNP) and other pre-mRNA/mRNA-binding proteins led to the identification of the first amino acid motifs and functional domains that confer binding to RNA . RBPs, which may contain one or multiple RNA-binding domains, are important for RNA metabolism and are involved in RNA stability, splicing, transport, cellular localization, translation and decay . The posttranscriptional RNA regulon model suggests that functionally related mRNAs are co-regulated by RBPs and snRNAs. This allows for a smooth and coordinated regulation of mRNAs and protein synthesis according to specific tasks .
Little is known about how signal transduction pathways may be involved in regulating post-transcriptional processing of pre-mRNA. For alternative splicing, it is established that reversible phosphorylation conducts some of these signals to the spliceosome . We have recently demonstrated that the C subunit of PKA is located to splicing factor compartments (SFC) where it regulates alternative pre-mRNA splicing in a cAMP-independent manner . PKA, which is a holoenzyme consisting of a regulatory (R) subunit dimer and two C subunits, is expressed in all human cells and tissues examined. There are four genes encoding the R subunits RIα, RIβ, RIIα, RIIβ, and the C subunits Cα, Cβ, Cγ and PrKX, respectively. Upon activation, the R subunit dimer binds four molecules of cAMP leading to the dissociation of the C subunits and phosphorylation of relevant substrates in the cytoplasm and the nucleus . Specificity of PKA signalling in the cell is thought to partly be maintained through targeting of the R subunits to subcellular organelles through A-kinase anchoring proteins (AKAPs) . How activity and specificity of the C subunits are regulated after dissociation from the R subunits and the corresponding AKAP, in addition to the assumption that the R subunits are absent from the nucleus is not well understood. It is however believed that temporal and spatial regulation may involve both phosphorylation and association of the C subunit with different target proteins. It is well documented that the C subunit phosphorylates and regulates the activity of a vast number of proteins including nuclear cAMP response element-binding proteins (CREBs) . Moreover, C subunit binding proteins have also been identified, and include the cytoplasmic proteins IκB , Caveolin-1  and p75 neurotrophin receptor (P75NTR)  as well as the nuclear proteins protein kinase inhibitor (PKI) , homologous to AKAP95 (HA95) , A-kinase-interacting protein (AKIP)  and heat shock factor 1 .
Using yeast two-hybrid screening with the PKA Cβ2 subunit as bait we identified GPKOW, also known as MOS2 homolog or T54 protein, as an interaction partner for Cβ2. There is currently little knowledge about GPKOW. We demonstrate that it is a nuclear protein that binds RNA in a PKA-regulated fashion in vivo; indicating that PKA may be involved in regulating multiple steps in post-transcriptional processing of pre-mRNAs.
Materials and methods
Yeast two-hybrid screening
Yeast two-hybrid screen using the PKA C subunit Cβ2 as bait was carried out by Dualsystems Biotech AG, Zurich, Switzerland. The bait construct was made by subcloning of a cDNA encoding complete Cβ2 into the pLexA-DIR (Dualsystems Biotech AG, Zurich, Switzerland). The bait construct was transformed into the strain DSY-1 (MATa his3200 trp1-901 leu2-3,112 ade2 LYS2::(lexAop)4-HIS3 URA3::(lexAop)8-lacZ GAL4) using standard procedures . Correct expression of the bait was verified by western blotting of cell extracts using a mouse monoclonal antibody directed against the LexA domain (Santa Cruz Biotechnology, Santa Cruz, California, USA). The absence of self-activation was verified by co-transformation of the bait together with a control prey and selection on minimal medium lacking the amino acids tryptophan, leucine and histidine (selective medium). For the yeast two-hybrid screen, the bait was co-transformed together with a human peripheral blood cDNA library into DSY-1. Six point four million transformants were screened yielding 22 transformants that grew on selective medium. Positive transformants were tested for β-galactosidase activity using a filter assay . Twenty one of the 22 initial positives showed β-galactosidase activity. Library plasmids were isolated from positive clones and assayed in a bait dependency test with pLexAdir with Cβ2 as bait plasmid and pLexA-p53 and pLexA-laminC plasmids as control bait encoding a LexA-laminC fusion using a mating strategy . Seventeen of the 21 positives showed β-galactosidase activity when co-expressed with the bait but not when co-expressed with the control bait, and were considered to be bait-dependent interactors. The identity of the interactors was determined by sequencing.
DNA for the native PKA subunits Cα1, Cβ1, Cβ2, Cβ4 and RIα, in addition to the C-terminal V5-tagged Cβ2, was PCR amplified from cDNA from NT2-N cells. PCR products were cloned into expression plasmids using the pENTR/D-TOPO Cloning Kit (Invitrogen 45-0218) and the mammalian expression vector pEF-DEST51 (Invitrogen 12285-011) by the LR Clonase reaction (Invitrogen 11791-019) according to the manufacturer. Full-length GPKOW was PCR-amplified from Jurkat cell cDNA using the following primers: upper GPKOW F TOPO (5'CACCATGGCTGACTCCAAAGAGGG3') and GPKOW R (5'GTCATCATCTGTGTCACTAGG3') for constructs without stop codon or GPKOW stop R (5'TCAGTCATCATCTGTGTCACTAG3') for constructs with stop codon. The GPKOW PCR products were cloned into expression plasmids using the pENTR/D-TOPO Cloning Kit (Invitrogen 45-0218) and the mammalian expression vector pEF-DEST51 (Invitrogen 12285-011) by the LR Clonase reaction (Invitrogen 11791-019) according to the manufacturer. The resulting plasmids expressed full-length GPKOW with or without a C-terminal V5-tag. The plasmids for prokaryote expression were made by PCR-amplification of Jurkat cDNA using following primers: GPKOW Nde1 F (5'TACGCATATGGCTGACTCCAAAGAGGGTGT3') and GPKOW C-His BamHI R (5'TACGGGATCCTCAGTGATGGTGATGGTGATGGTCATCATCTGTGTCACTAGG3' to introduce Nde1 and BamHI restriction sites and a C-terminal 6 × His-tag. Digested PCR products were cloned into the pET24b vector (Novagen 69750). The QuickChange mutagenesis kit (Stratagene 200524-5) was used to generate GPKOW full-length with mutations in the PKA phosphorylation sites with primers GPKOWfos176U23 (5'CACTCGCACGGCCGCACGGAGGC3') and GPKOWfos176L23 (5'GCCTCCGTGCGGCCGTGCGAGTG3') to change serine to alanine at position 27. The primers GPKOWfos2940U26 (5'CTCATCACGGAAGGCCCTCTGGAATC3') and GPKOWfos2940L26 (5'GATTCCAGAGGGCCTTCCGTGATGAG3') were used to changed threonine to alanine at position 316. All primers were bought from Sigma-Genosys and all expression plasmids were sequenced.
293T cells were maintained at 37°C in humidified air with 5% CO2 in RPMI 1640 (Sigma-Aldrich R0883) supplemented with 10% foetal bovine serum (Sigma-Aldrich F7524), 1% non-essential amino acids (GibcoBRL 11140-035), 1% L-glutamine (Sigma-Aldrich G7513), 1% sodium pyruvat (GibcoBRL 11360-039) and 1 × penicillin-streptomycin solution (Sigma-Aldrich P4458). The 293T cells were transfected with Lipofectamine 2000 (Invitrogen 11668-019) according to the manufacturer's protocol. U2OS cells were grown in DMEM (Sigma-Aldrich D6546) supplemented with 10% foetal bovine serum (Sigma-Aldrich F7524), 1% L-glutamine (Sigma-Aldrich G7513) and 1 × penicillin-streptomycin solution (Sigma-Aldrich P4458). U2OS cells were transfected with Fugene6 (Roche 11814443001) according to the manufacturer's protocol.
Four wells (35 mm) with transfected 293T cells were washed in PBS and lysed by sonication in immunoprecipitation buffer (150 mM NaCl, 50 mM Tris pH 7.5, 0.5% Triton X-100, 1 × protease inhibitor cocktail (Sigma P8340), 1 mM PMSF (Sigma P7626) and 1 mM Na3VO4 (Sigma S6508)). The lysates were cleared by centrifugation and adjusted to equal protein concentration for each experiment (between 1.5 - 3.4 μg protein/μl) by the Bradford method (BioRad 500-0006). The lysates were precleared with Dynabeads Protein G (Invitrogen 100-04D, 1:10) before input samples were collected (20 μl) and the remainder of the lysates were added one of the following antibodies; rabbit IgG (same amount μg as the positive immunoprecipitation antibody, Sigma I5006), anti-GPKOW (1.6 μg, Atlas Antibodies HPA001894), anti-PKA RIα serum (6 μl) or anti-PKA Cβ2 (12.8 μg, clone SNO103 from rabbit serum). The mixture of cell lysate and antibody were incubated at 4°C rotating over night before Dynabeads Protein G (1:10) were added the next day and incubated for another hour. The samples were washed with immunoprecipitation buffer, added SDS loading dye and boiled for 5 minutes before immune blotting. For samples treated with cAMP, the magnetic beads were after washing incubated 5 min with buffer with or without 1 mM 8-CPT (Sigma C3913) and both pellet and the supernatant were analyzed by immunoblotting.
The procedure is according to the manufacturer's recommendation (Sigma product P0114). Two wells with 293T cells were washed in PBS and lysed by sonication in immunoprecipitation buffer (150 mM NaCl, 50 mM Tris pH 7.5, 0.5% Triton X-100, 1 × protease inhibitor cocktail (Sigma P8340), 1 mM PMSF (Sigma P7626) and 1 mM Na3VO4 (Sigma S6508)). The lysates were cleared by centrifugation and adjusted to equal protein concentration (between 2.5 - 3.0 μg protein/μl) by the Bradford method (BioRad 500-0006). The lysates were precleared with Dynabeads Protein G (Invitrogen 100-04D, 1:10) and incubated over night with anti-GPKOW (0.8 μg, Atlas Antibodies HPA001894). Dynabeads Protein G (1:10) were added the next day and incubated for another hour. The samples were washed with immunoprecipitation buffer. Magnetic beads were added 100 units of alkaline phosphatase (Sigma P0114) in 5 mM Tris pH 7.9, 10 mM NaCl, 1 mM MgCl2 and 0.1 mM DTT for 30 minutes at 30°C or left untreated on ice. The samples were added SDS loading dye and boiled for 5 minutes before immune blotting.
If not otherwise stated, the cells were washed in ice cold PBS and lysed by sonication in lysis buffer (150 mM NaCl, 50 mM Tris pH 7.5, 0.5% Triton-X100, 1 mM Na3VO4, 1 mM PMSF and 1 × Protease Inhibitor Cocktail (Sigma-Aldrich P8340)). Lysates were cleared by centrifugation at 16.000 × g for 20 minutes at 4°C. Equal amounts of protein were separated by SDS-PAGE and transferred to a PVDF membrane. The membrane was blocked by drying and then rehydrated in methanol before incubation with primary antibodies; anti-GPKOW 0287 (1:250 dilution, Atlas Antibodies HPA000287), anti-GPKOW1894 (1:500 dilution, Atlas Antibodies HPA001894), anti-GPKOWB01 (1:1000 dilution, Abnova H00027238-B01), purified mouse anti-PKAc (1:250 dilution, BD Transduction Laboratories 610981), anti-PKA RIα (1:250) or anti-V5 (1:2000, Invitrogen R960-25) for one hour at room temperature (RT). The membrane was washed, before incubating with the secondary antibodies; HRP conjugated goat anti-mouse (1:2000 dilution, ICN Biomed 55563) or HRP conjugated goat anti-rabbit (1:2000 dilution, ICN Biomed 55689) for one hour at RT. After washing, immunoreactive proteins were visualized using the ECL detection system and developed using Hyperfilm or the Syngene G:BOX imaging system.
The procedure was performed as previously described . The following antibodies were used; primary antibodies: anti-GPKOW1894 (1:100), anti-V5 (1:2000) and a rabbit polyclonal antibody against a peptide of human B-type lamins (1:1000) and secondary antibodies: Alexa Fluor 488 goat anti-rabbit IgG (1:400 dilution, Invitrogen A11008) and Alexa Fluor 594 goat anti-mouse IgG (1:400, Invitrogen A11005). To check the specificity of the GPKOW-antibody, it was pre-incubated with its blocking peptide (Atlas Antibodies, PrEST antigen for GPKOW HPA001894).
The method is according to Rogne et al  with some minor modifications. For the endogenous samples, 293T cells were grown confluent in 150 cm2 petri dishes (sufficient for 2 samples), while four 10 cm2 wells were used for the transiently transfected 293T cells. Culture medium was replaced by PBS before UV irradiation (254 nm, 200 mJ/cm2, twice). Cells were harvested, washed in PBS and lysed in 300 μl IPB buffer (10 mM HEPES pH 7.5, 2 mM EDTA, 10 mM KCl, 1% TX-100, 1 mM PMSF, 1 × Protease Inhibitor Cocktail (Sigma-Aldrich P8340)) with 150 mM NaCl pr sample before sonication. Lysates were cleared by centrifugation at 15,000 × g for 20 minutes at 4°C before addition of 0.048 U/μl (final concentration) of T1 RNase (Fermentas EN0541) and incubation for 8 minutes at 37°C with 1000 rpm agitation. The lysates were adjusted to equal protein concentrations and precleared with Dynabeads Protein G (Invitrogen 100.04D) for 30 minutes at 4°C rotating. Antibody (0.8 μg anti-GPKOW 1894 or 0.8 μg rabbit IgG, Sigma 1-5006) and beads were incubated on a rotator for 2 hours at 4°C followed by three washes in IPB buffer. Supernatants were incubated with 30 μl conjugated beads for 2 hours at 4°C rotating. The immunoprecipitated samples were washed 4 times by alternating between 1 ml RIPA (1 × PBS, 0.05% SDS, 0.1% deoxycholate, 1% NP-40, 1 × Protease Inhibitor Cocktail (Sigma-Aldrich P8340)) and RIPA 1000 (1 × PBS, 1 mM EDTA, 0.05% SDS, 0.1% deoxycholate, 1 M NaCl, 1% NP-40, 1 × Protease Inhibitor Cocktail (Sigma-Aldrich P8340)). Immunoprecipitated samples were dephosphorylated (0.038 U/μl calf intestinal phosphatase for 10 min, Roche 10713023001) and washed three times with Buffer C (50 mM Tris HCl, pH 7,4, 10 mM MgCl2, 0,5% NP-40, 1 × protease inhibitor cocktail (Sigma-Aldrich P8340)), followed by labeling with γ-32P ATP (2.1 μCi, Nerliens NEG502H) by polynucleotide kinase (PNK, 0.5 U/μl NEB M0201L) phosphorylation and further washed three times with Buffer C. All samples were resolved in FA dye and separated by electrophoresis on a denaturing (7 M urea) 6% polyacrylamide (PAA) gel. Incorporated phosphate was visualized by autoradiography. Unsaturated images from the Typhoon 9410 phosphoimager (GE Healthcare Life Sciences) were quantified using the histogram function in Adobe Photoshop. The lanes were manually defined with identical frames. The statistical analysis was performed with paired students T-test in Prism GraphPad.
Plasmids were transformed into Rosetta 2(DE)pLys bacteria and grown on LB agar plates. 10-20 colonies were picked and grown in 50 ml LB-medium over night at 37°C. The bacteria were pelleted and resuspended in 500 ml TB-medium and grown to optic density between 0.5-0.7 at 600 nm at 37°C and 150 rpm, before protein expression was induced by 0.25 mM IPTG and further grown for 4 hours at 25°C at 150 rpm. The bacteria were lysed in Buffer A (50 mM sodium dihydrogen phosphate pH 7.5, 0.2 M NaCl, 5 mM Imidazole, 1 × EDTA free protease inhibitor cocktail (Roche 04693132001) and 0.4 mM betamercaptoetanol) and purified on a crude HisTrap column (GE Healthcare 11-0004-58) using Buffer A and Buffer B (50 mM sodium dihydrogen phosphate pH 7.5, 0.2 M NaCl, 500 mM Imidazole, 1 × EDTA free protease inhibitor cocktail (Roche 04693132001) and 0.4 mM betamercaptoetanol). Fractions with the highest optical density at 280 nm were pooled, dialyzed to Buffer C (20 mM Tris-HCl, pH 8) and further purified by ion exchange chromatography (Resource Q, GE Healthcare 520348) at pH 8 with buffer C and buffer D (20 mM Tris-HCl pH 8, 1 M NaCl). Fractionated proteins were dialyzed to GPKOW storage buffer (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 1 × protease inhibitor cocktail and 0.4 mM betamercaptoetanol) and stored at 4°C.
In vitro phosphorylation assay
Purified GPKOW proteins were in vitro phosphorylated as previously described . As a negative control for phosphorylation heat-inactivated PKA Cα1 was used. Unsaturated images from Syngene G-box and Typhoon 9400 phosphoimager were quantified by Genetools (Syngene) and the statistical analysis was performed with paired students T-test in GraphPad Prism. The values from the phospho blot were adjusted according to the amount of protein detected on the Coomassie Brilliant Blue (CBB)-stained gel.
Full-length GPKOW was cloned into the Gateway system for eukaryote expression with and without a C-terminal V5 tag. To identify expressed GPKOW, we applied three polyclonal GPKOW antibodies and a V5-antibody. This demonstrated that all antisera reacted against the expressed proteins of the expected theoretical sizes of 52.5 kDa (full-length) and 57.5 kDa (V5-tagged GPKOW) (Figure 1C). Anti-GPKOW1894 revealed the best titer and was reactive against both expressed and endogenous protein and was therefore primarily used.
We have characterized the protein GPKOW and demonstrated that it is a nuclear RNA-binding protein which is in vitro phosphorylated by and probably associated with the C subunit of PKA. GPKOW contains two PKA phosphorylation sites at S27 and T316, which by mutational analysis were shown to regulate RNA-binding in vivo in a PKA-dependent manner. Endogenous as well as expressed wt and mutated GPKOW were all shown to locate to the nucleus, as determined by immunofluorescence microscopy. The mechanism by which GPKOW locates to the nucleus is unknown. However, based on our results, database searches and the literature it probably does not involve PKA-dependent phosphorylation, the G-patch domain or a recognizable nuclear localization signal (NLS). The latter is supported by searches using various publicly available bioinformatics tools including PredictNLS Online, Prosite and PSORT, which all indicated that GPKOW does not contain any known NLS. This was unexpected since the GPKOW homolog, modifier of snc 1 and 2 (MOS2), identified in Arabidopsis thaliana, has been shown to be nuclear and contains a NLS . Furthermore, the assumption that nuclear localization of GPKOW do not involve the G-patch domain is supported by recent reports demonstrating that the Zebra fish Telomerase Reverse Transcriptase (zLPTS), which is nuclear, remained nuclear after deletion of its N-terminal G-patch domain . In addition, mutating three of the conserved glycines in the G-patch domain of Tuftelin-Interacting Protein 11 (TFIP11) did not change its nuclear localization [43, 44]. In the case of the PKA phosphorylation sites, we show that over-expression of single- or double-mutated GPKOW S27A and GPKOW T316A does not alter their localization.
Based on experiments using RNA immumoprecipitation we concluded that GPKOW binds RNA. However, we can not rule out that the pulled down RNA may be associated with an unknown interaction partner of GPKOW. This needs to be investigated further. We used T1 RNase treatment of the samples prior to immunoprecipitation with anti-GPKOW to obtain suitable sized RNA fragments for the electrophoresis. T1 RNase is an endoribonuclease which digests RNA at G residues. This treatment of cell extracts will therefore result in RNA species of various lengths [25, 45]. Hence, a smear of nucleotides when applying anti-GPKOW immunoprecipitation would be expected. However, GPKOW have 3 domains capable of binding nucleic acids that may bind to different but distinct RNAs. That GPKOW binds to specific RNA species finds support in e.g. the results in lane 2 in Figure 4A and lanes 2 and 4 in Figure 6Bwhere faint but distinct RNA bands of different sizes are detected. To what extent these bands represent specific RNAs and hence may imply that GPKOW have affinity for specific RNA sequences remains to be investigated. We can not exclude the possibility that GPKOW also binds DNA in addition to RNA since other G-patch domain containing proteins have been shown to be involved in DNA repair and telomere maintenance [46, 42, 47] as well as RNA-processing [48, 49]. Furthermore, the spliceosomal protein TFIP11, which affects the splicing pattern of the E1A minigene in vivo , interacts with PRP43 and in that way promotes the release of the lariat-intron . Finally, the KOW motif may also bind both RNA and DNA in that it is frequently found in ribosomal proteins and is proposed to have functions associated with translation [28, 50–53]. To this end, a study where two conserved residues were mutated in the KOW motif of UpaY in Bacteriodes fragilis revealed loss of function, suggesting a role for the KOW motif in transcriptional termination .
The way in which RNA-binding of GPKOW is regulated is not understood but may involve the two sites in GPKOW for PKA-dependent phosphorylation. We postulate these sites since they were both phosphorylated by PKA in vitro. In order to determine which site that would be preferred by PKA we performed site-directed mutagenesis. We observed that both single- and double-mutation resulted in a marked decreased phosphorylation, indicating that both S27 and T316 are phosphorylated by PKA. The sequences surrounding GPKOWs PKA phosphorylation sites are RXS27 (arginine-random-serine) and RXT316 (arginine-random-serine). These consensus sequences are estimated to be phosphorylated with low efficiency by PKA . Hence, it may be argued that these sites in GPKOW are only available for in vitro phosphorylation and not relevant in vivo. However, in support of biological relevance, several physiological substrates for PKA are identified with similar consensus phosphorylation sites. These include the Kir1.1 renal outer medullary K+ channel 1 and 2 (ROMK1/2 at LRKS200 and VRTS294) [55–57], the D1 dopamine receptor (DRD1, at KRET268) , Elongation Factor-2 kinase (eEF2K or calmodulin-dependent protein kinase III at PRRS499)  and Hormone-sensitive Lipase (HSL, at MRRS563 and PRRS659) [60–62]. Together this supports the potential PKA-phosphorylation sites in GPKOW as genuine also in vivo.
That PKA may have regulatory effects on RNA-binding in vivo finds support in that the SR-protein serine/arginine-rich splicing factor 1 (SRSF1) (Aksaas, Kvissel and Skålhegg, unpublished) and the hnRNP-protein polypyrimidine tract-binding protein (PTB)  are both phosphorylated by PKA. Moreover, we have demonstrated that the C subunit of PKA is located to SFCs and regulates alternative splice site selection in vivo . Finally, we also recently found that splicing factor arginine/serine-rich 17A (SFRS17A) is an AKAP and may be involved in targeting PKA to SFCs . In the present work we found that GPKOW interacts with Cβ2 as determined by the two-hybrid screen (five of seventeen bait-dependent clones) containing the main binding partner of Cβ2, the R subunit (twelve of seventeen bait dependent clones). Together this supported high specificity of the screen. We also could demonstrate co-immunoprecipitation between GPKOW and Cβ2. We do however note that this interaction appeared fragile as only about 30% of the experiments revealed a clear result. Despite this we considered this interaction likely since the immunoprecipitation conditions were found to be optimal, the immunoprecipitation was not influenced by cAMP and co-immunoprecipitations of GPKOW with Cβ1, Cβ4 or Cα1 were consistently negative. Since the co-immunoprecipitation of GPKOW and Cβ2 was not influenced by cAMP we suggest that the interaction is independent of the R subunit, and hence that GPKOW is not an AKAP. Rather, it should be considered a C-binding protein.
Despite that the biological role of GPKOW is unknown, silencing of its homolog in C. Elegans (R11A8.2) by RNAi revealed embryonic lethality . In addition to its importance for embryonic development this result also points to GPKOW as evolutionary conserved, which is suggestive of an important biological role. The latter assumption is also indicated by the importance of G-patch proteins in carcinogenesis [66, 67]. MOS2, which contains one G-patch domain and two KOW motifs organized in the same way as GPKOW, is involved in innate immunity via the disease resistance genes in plants . One may speculate that MOS2 may be paralleled to downstream proteins of the Toll-like receptor pathway in eukaryote cells . In immune cells, Toll-like receptors signal through NFκB, which has been shown to bind and activate the PKA C subunit in a cAMP-independent fashion . Cβ2 is an immune cell-specific PKA C subunit  and may suggest that Cβ2 is associated with PKA-dependent phosphorylation and regulation of RNA-binding of GPKOW related to immune function. To what extent this is the case remains to be investigated.
GPKOW is a nuclear protein with three nucleic acid binding domains, one G-patch domain and two KOW-motifs. We have demonstrated that GPKOW binds RNA in vivo and that GPKOW associate with Cβ2 of PKA. GPKOWs ability to bind RNA is regulated by PKA-dependent phosphorylation at two sites. This implicates that PKA phosphorylation is a regulatory factor in post-transcriptional RNA processing.
The work was funded by The Norwegian Cancer Society.
- Hui J: Regulation of mammalian pre-mRNA splicing. Sci China C Life Sci 2009, 52:253–260.PubMedView ArticleGoogle Scholar
- Glisovic T, Bachorik JL, Yong J, Dreyfuss G: RNA-binding proteins and post-transcriptional gene regulation. FEBS Lett 2008, 582:1977–1986.PubMedView ArticleGoogle Scholar
- Burd CG, Dreyfuss G: RNA binding specificity of hnRNP A1: significance of hnRNP A1 high-affinity binding sites in pre-mRNA splicing. EMBO J 1994, 13:1197–1204.PubMedGoogle Scholar
- Keene JD: Minireview: global regulation and dynamics of ribonucleic Acid. Endocrinology 2010, 151:1391–1397.PubMedView ArticleGoogle Scholar
- Keene JD: RNA regulons: coordination of post-transcriptional events. Nat Rev Genet 2007, 8:533–543.PubMedView ArticleGoogle Scholar
- Stamm S: Regulation of alternative splicing by reversible protein phosphorylation. J Biol Chem 2008, 283:1223–1227.PubMedView ArticleGoogle Scholar
- Kvissel AK, Orstavik S, Eikvar S, Brede G, Jahnsen T, Collas P, Akusjarvi G, Skalhegg BS: Involvement of the catalytic subunit of protein kinase A and of HA95 in pre-mRNA splicing. Exp Cell Res 2007, 313:2795–2809.PubMedView ArticleGoogle Scholar
- Skalhegg BS, Tasken K: Specificity in the cAMP/PKA signaling pathway. Differential expression, regulation, and subcellular localization of subunits of PKA. Front Biosci 2000, 5:D678-D693.PubMedView ArticleGoogle Scholar
- Wong W, Scott JD: AKAP signalling complexes: focal points in space and time. Nat Rev Mol Cell Biol 2004, 5:959–970.PubMedView ArticleGoogle Scholar
- Sands WA, Palmer TM: Regulating gene transcription in response to cyclic AMP elevation. Cell Signal 2008, 20:460–466.PubMedView ArticleGoogle Scholar
- Zhong H, SuYang H, Erdjument-Bromage H, Tempst P, Ghosh S: The transcriptional activity of NF-kappaB is regulated by the IkappaB-associated PKAc subunit through a cyclic AMP-independent mechanism. Cell 1997, 89:413–424.PubMedView ArticleGoogle Scholar
- Razani B, Rubin CS, Lisanti MP: Regulation of cAMP-mediated signal transduction via interaction of caveolins with the catalytic subunit of protein kinase A. J Biol Chem 1999, 274:26353–26360.PubMedView ArticleGoogle Scholar
- Higuchi H, Yamashita T, Yoshikawa H, Tohyama M: PKA phosphorylates the p75 receptor and regulates its localization to lipid rafts. EMBO J 2003, 22:1790–1800.PubMedView ArticleGoogle Scholar
- Zheng L, Yu L, Tu Q, Zhang M, He H, Chen W, Gao J, Yu J, Wu Q, Zhao S: Cloning and mapping of human PKIB and PKIG, and comparison of tissue expression patterns of three members of the protein kinase inhibitor family, including PKIA. Biochem J 2000, 349:403–407.PubMedView ArticleGoogle Scholar
- Han I, Xue Y, Harada S, Orstavik S, Skalhegg B, Kieff E: Protein kinase A associates with HA95 and affects transcriptional coactivation by Epstein-Barr virus nuclear proteins. Mol Cell Biol 2002, 22:2136–2146.PubMedView ArticleGoogle Scholar
- Sastri M, Barraclough DM, Carmichael PT, Taylor SS: A-kinase-interacting protein localizes protein kinase A in the nucleus. Proc Natl Acad Sci USA 2005, 102:349–354.PubMedView ArticleGoogle Scholar
- Murshid A, Chou SD, Prince T, Zhang Y, Bharti A, Calderwood SK: Protein kinase A binds and activates heat shock factor 1. PLoS One 2010, 5:e13830.PubMedView ArticleGoogle Scholar
- Gietz RD, Woods RA: Genetic transformation of yeast. Biotechniques 2001, 30:816–6-828.Google Scholar
- Serebriiskii IG, Golemis EA: Uses of lacZ to study gene function: evaluation of beta-galactosidase assays employed in the yeast two-hybrid system. Anal Biochem 2000, 285:1–15.PubMedView ArticleGoogle Scholar
- Kolonin MG, Zhong J, Finley RL: Interaction mating methods in two-hybrid systems. Methods Enzymol 2000, 328:26–46.PubMedView ArticleGoogle Scholar
- Skalhegg BS, Johansen AK, Levy FO, Andersson KB, Aandahl EM, Blomhoff HK, Hansson V, Tasken K: Isozymes of cyclic AMP-dependent protein kinases (PKA) in human lymphoid cell lines: levels of endogenous cAMP influence levels of PKA subunits and growth in lymphoid cell lines. J Cell Physiol 1998, 177:85–93.PubMedView ArticleGoogle Scholar
- Orstavik S, Funderud A, Hafte TT, Eikvar S, Jahnsen T, Skalhegg BS: Identification and characterization of novel PKA holoenzymes in human T lymphocytes. FEBS J 2005, 272:1559–1567.PubMedView ArticleGoogle Scholar
- Labugger R, Organ L, Collier C, Atar D, Van Eyk JE: Extensive troponin I and T modification detected in serum from patients with acute myocardial infarction. Circulation 2000, 102:1221–1226.PubMedGoogle Scholar
- Chaudhary N, Courvalin JC: Stepwise reassembly of the nuclear envelope at the end of mitosis. J Cell Biol 1993, 122:295–306.PubMedView ArticleGoogle Scholar
- Rogne M, Landsverk HB, Van EA, Beullens M, Bollen M, Collas P, Kuntziger T: The KH-Tudor domain of a-kinase anchoring protein 149 mediates RNA-dependent self-association. Biochemistry (Mosc) 2006, 45:14980–14989.View ArticleGoogle Scholar
- Gyuris J, Golemis E, Chertkov H, Brent R: Cdi1, a human G1 and S phase protein phosphatase that associates with Cdk2. Cell 1993, 75:791–803.PubMedView ArticleGoogle Scholar
- Schindelhauer D, Hellebrand H, Grimm L, Bader I, Meitinger T, Wehnert M, Ross M, Meindl A: Long-range map of a 3.5-Mb region in Xp11.23–22 with a sequence-ready map from a 1.1-Mb gene-rich interval. Genome Res 1996, 6:1056–1069.PubMedView ArticleGoogle Scholar
- Kyrpides NC, Woese CR, Ouzounis CA: KOW: a novel motif linking a bacterial transcription factor with ribosomal proteins. Trends Biochem Sci 1996, 21:425–426.PubMedView ArticleGoogle Scholar
- Aravind L, Koonin EV: G-patch: a new conserved domain in eukaryotic RNA-processing proteins and type D retroviral polyproteins. Trends Biochem Sci 1999, 24:342–344.PubMedView ArticleGoogle Scholar
- Mayr B, Montminy M: Transcriptional regulation by the phosphorylation-dependent factor CREB. Nat Rev Mol Cell Biol 2001, 2:599–609.PubMedView ArticleGoogle Scholar
- Regan JW: EP2 and EP4 prostanoid receptor signaling. Life Sci 2003, 74:143–153.PubMedView ArticleGoogle Scholar
- Svec M, Bauerova H, Pichova I, Konvalinka J, Strisovsky K: Proteinases of betaretroviruses bind single-stranded nucleic acids through a novel interaction module, the G-patch. FEBS Lett 2004, 576:271–276.PubMedView ArticleGoogle Scholar
- Silverman EJ, Maeda A, Wei J, Smith P, Beggs JD, Lin RJ: Interaction between a G-patch protein and a spliceosomal DEXD/H-box ATPase that is critical for splicing. Mol Cell Biol 2004, 24:10101–10110.PubMedView ArticleGoogle Scholar
- Frenal K, Callebaut I, Wecker K, Prochnicka-Chalufour A, Dendouga N, Zinn-Justin S, Delepierre M, Tomavo S, Wolff N: Structural and functional characterization of the TgDRE multidomain protein, a DNA repair enzyme from Toxoplasma gondii. Biochemistry (Mosc) 2006, 45:4867–4874.View ArticleGoogle Scholar
- Steiner T, Kaiser JT, Marinkovic S, Huber R, Wahl MC: Crystal structures of transcription factor NusG in light of its nucleic acid- and protein-binding activities. EMBO J 2002, 21:4641–4653.PubMedView ArticleGoogle Scholar
- Reay P, Yamasaki K, Terada T, Kuramitsu S, Shirouzu M, Yokoyama S: Structural and sequence comparisons arising from the solution structure of the transcription elongation factor NusG from Thermus thermophilus. Proteins 2004, 56:40–51.PubMedView ArticleGoogle Scholar
- le MA, Schiltz M, Stura EA, Pinon-Lataillade G, Couprie J, Moutiez M, Gondry M, Angulo JF, Zinn-Justin S: A tandem of SH3-like domains participates in RNA binding in KIN17, a human protein activated in response to genotoxics. J Mol Biol 2006, 364:764–776.View ArticleGoogle Scholar
- Shabb JB: Physiological substrates of cAMP-dependent protein kinase. Chem Rev 2001, 101:2381–2411.PubMedView ArticleGoogle Scholar
- Hoang T, Fenne IS, Cook C, Borud B, Bakke M, Lien EA, Mellgren G: cAMP-dependent protein kinase regulates ubiquitin-proteasome-mediated degradation and subcellular localization of the nuclear receptor coactivator GRIP1. J Biol Chem 2004, 279:49120–49130.PubMedView ArticleGoogle Scholar
- Xie J, Lee JA, Kress TL, Mowry KL, Black DL: Protein kinase A phosphorylation modulates transport of the polypyrimidine tract-binding protein. Proc Natl Acad Sci USA 2003, 100:8776–8781.PubMedView ArticleGoogle Scholar
- Zhang Y, Cheng YT, Bi D, Palma K, Li X: MOS2, a protein containing G-patch and KOW motifs, is essential for innate immunity in Arabidopsis thaliana. Curr Biol 2005, 15:1936–1942.PubMedView ArticleGoogle Scholar
- Sun C, Wu Z, Jia F, Wang Y, Li T, Zhao M: Identification of zebrafish LPTS: a gene with similarities to human LPTS/PinX1 that inhibits telomerase activity. Gene 2008, 420:90–98.PubMedView ArticleGoogle Scholar
- Wen X, Tannukit S, Paine ML: TFIP11 Interacts with mDEAH9, an RNA Helicase Involved in Spliceosome Disassembly. Int J Mol Sci 2008, 9:2105–2113.PubMedView ArticleGoogle Scholar
- Tannukit S, Crabb TL, Hertel KJ, Wen X, Jans DA, Paine ML: Identification of a novel nuclear localization signal and speckle-targeting sequence of tuftelin-interacting protein 11, a splicing factor involved in spliceosome disassembly. Biochem Biophys Res Commun 2009, 390:1044–1050.PubMedView ArticleGoogle Scholar
- Jensen KB, Darnell RB: CLIP: crosslinking and immunoprecipitation of in vivo RNA targets of RNA-binding proteins. Methods Mol Biol 2008, 488:85–98.PubMedView ArticleGoogle Scholar
- Dendouga N, Callebaut I, Tomavo S: A novel DNA repair enzyme containing RNA recognition, G-patch and specific splicing factor 45-like motifs in the protozoan parasite Toxoplasma gondii. Eur J Biochem 2002, 269:3393–3401.PubMedView ArticleGoogle Scholar
- Herrmann G, Kais S, Hoffbauer J, Shah-Hosseini K, Bruggenolte N, Schober H, Fasi M, Schar P: Conserved interactions of the splicing factor Ntr1/Spp382 with proteins involved in DNA double-strand break repair and telomere metabolism. Nucleic Acids Res 2007, 35:2321–2332.PubMedView ArticleGoogle Scholar
- Tsai RT, Fu RH, Yeh FL, Tseng CK, Lin YC, Huang YH, Cheng SC: Spliceosome disassembly catalyzed by Prp43 and its associated components Ntr1 and Ntr2. Genes Dev 2005, 19:2991–3003.PubMedView ArticleGoogle Scholar
- Sampson ND, Hewitt JE: SF4 and SFRS14, two related putative splicing factors on human chromosome 19p13.11. Gene 2003, 305:91–100.PubMedView ArticleGoogle Scholar
- Tselykh TV, Roos C, Heino TI: The mitochondrial ribosome-specific MrpL55 protein is essential in Drosophila and dynamically required during development. Exp Cell Res 2005, 307:354–366.PubMedView ArticleGoogle Scholar
- Bylund GO, Persson BC, Lundberg LA, Wikstrom PM: A novel ribosome-associated protein is important for efficient translation in Escherichia coli. J Bacteriol 1997, 179:4567–4574.PubMedGoogle Scholar
- Andres O, Kellermann T, Lopez-Giraldez F, Rozas J, Domingo-Roura X, Bosch M: RPS4Y gene family evolution in primates. BMC Evol Biol 2008, 8:142.PubMedView ArticleGoogle Scholar
- Guo M, Xu F, Yamada J, Egelhofer T, Gao Y, Hartzog GA, Teng M, Niu L: Core structure of the yeast spt4-spt5 complex: a conserved module for regulation of transcription elongation. Structure 2008, 16:1649–1658.PubMedView ArticleGoogle Scholar
- Chatzidaki-Livanis M, Coyne MJ, Comstock LE: A family of transcriptional antitermination factors necessary for synthesis of the capsular polysaccharides of Bacteroides fragilis. J Bacteriol 2009, 191:7288–7295.PubMedView ArticleGoogle Scholar
- Liou HH, Zhou SS, Huang CL: Regulation of ROMK1 channel by protein kinase A via a phosphatidylinositol 4,5-bisphosphate-dependent mechanism. Proc Natl Acad Sci USA 1999, 96:5820–5825.PubMedView ArticleGoogle Scholar
- MacGregor GG, Xu JZ, McNicholas CM, Giebisch G, Hebert SC: Partially active channels produced by PKA site mutation of the cloned renal K+ channel, ROMK2 (kir1.2). Am J Physiol 1998, 275:F415-F422.PubMedGoogle Scholar
- Xu ZC, Yang Y, Hebert SC: Phosphorylation of the ATP-sensitive, inwardly rectifying K+ channel, ROMK, by cyclic AMP-dependent protein kinase. J Biol Chem 1996, 271:9313–9319.PubMedView ArticleGoogle Scholar
- Jiang D, Sibley DR: Regulation of D(1) dopamine receptors with mutations of protein kinase phosphorylation sites: attenuation of the rate of agonist-induced desensitization. Mol Pharmacol 1999, 56:675–683.PubMedGoogle Scholar
- Diggle TA, Subkhankulova T, Lilley KS, Shikotra N, Willis AE, Redpath NT: Phosphorylation of elongation factor-2 kinase on serine 499 by cAMP-dependent protein kinase induces Ca2+/calmodulin-independent activity. Biochem J 2001, 353:621–626.PubMedView ArticleGoogle Scholar
- Anthonsen MW, Ronnstrand L, Wernstedt C, Degerman E, Holm C: Identification of novel phosphorylation sites in hormone-sensitive lipase that are phosphorylated in response to isoproterenol and govern activation properties in vitro. J Biol Chem 1998, 273:215–221.PubMedView ArticleGoogle Scholar
- Garton AJ, Campbell DG, Cohen P, Yeaman SJ: Primary structure of the site on bovine hormone-sensitive lipase phosphorylated by cyclic AMP-dependent protein kinase. FEBS Lett 1988, 229:68–72.PubMedView ArticleGoogle Scholar
- Stralfors P, Bjorgell P, Belfrage P: Hormonal regulation of hormone-sensitive lipase in intact adipocytes: identification of phosphorylated sites and effects on the phosphorylation by lipolytic hormones and insulin. Proc Natl Acad Sci USA 1984, 81:3317–3321.PubMedView ArticleGoogle Scholar
- Colwill K, Pawson T, Andrews B, Prasad J, Manley JL, Bell JC, Duncan PI: The Clk/Sty protein kinase phosphorylates SR splicing factors and regulates their intranuclear distribution. EMBO J 1996, 15:265–275.PubMedGoogle Scholar
- Jarnaess E, Stokka AJ, Kvissel AK, Skalhegg BS, Torgersen KM, Scott JD, Carlson CR, Tasken K: Splicing factor arginine/serine-rich 17A (SFRS17A) is an A-kinase anchoring protein that targets protein kinase A to splicing factor compartments. J Biol Chem 2009, 284:35154–35164.PubMedView ArticleGoogle Scholar
- Piano F, Schetter AJ, Morton DG, Gunsalus KC, Reinke V, Kim SK, Kemphues KJ: Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans. Curr Biol 2002, 12:1959–1964.PubMedView ArticleGoogle Scholar
- Li R, Zhang H, Yu W, Chen Y, Gui B, Liang J, Wang Y, Sun L, Yang X, Zhang Y, Shi L, Li Y, Shang Y: ZIP: a novel transcription repressor, represses EGFR oncogene and suppresses breast carcinogenesis. EMBO J 2009, 28:2763–2776.PubMedView ArticleGoogle Scholar
- Lin ML, Fukukawa C, Park JH, Naito K, Kijima K, Shimo A, Ajiro M, Nishidate T, Nakamura Y, Katagiri T: Involvement of G-patch domain containing 2 overexpression in breast carcinogenesis. Cancer Sci 2009, 100:1443–1450.PubMedView ArticleGoogle Scholar
- Takeuchi O, Akira S: Pattern recognition receptors and inflammation. Cell 2010, 140:805–820.PubMedView ArticleGoogle Scholar
- Funderud A, Henanger HH, Hafte TT, Amieux PS, Orstavik S, Skalhegg BS: Identification, cloning and characterization of a novel 47 kDa murine PKA C subunit homologous to human and bovine Cbeta2. BMC Biochem 2006, 7:20.PubMedView ArticleGoogle Scholar
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