Proteomic identification of heterogeneous nuclear ribonucleoprotein L as a novel component of SLM/Sam68 Nuclear Bodies
- Prabhakar Rajan†1, 2,
- Caroline Dalgliesh†1,
- Cyril F Bourgeois3, 4, 5, 6,
- Monika Heiner7,
- Kaveh Emami8,
- Emma L Clark9,
- Albrecht Bindereif7,
- James Stevenin3, 4, 5, 6,
- Craig N Robson9,
- Hing Y Leung2Email author and
- David J Elliott1Email author
© Rajan et al; licensee BioMed Central Ltd. 2009
Received: 9 July 2009
Accepted: 13 November 2009
Published: 13 November 2009
Active pre-mRNA splicing occurs co-transcriptionally, and takes place throughout the nucleoplasm of eukaryotic cells. Splicing decisions are controlled by networks of nuclear RNA-binding proteins and their target sequences, sometimes in response to signalling pathways. Sam68 (Src-associated in mitosis 68 kDa) is the prototypic member of the STAR (Signal Transduction and Activation of RNA) family of RNA-binding proteins, which regulate splicing in response to signalling cascades. Nuclear Sam68 protein is concentrated within subnuclear organelles called SLM/Sam68 Nuclear Bodies (SNBs), which also contain some other splicing regulators, signalling components and nucleic acids.
We used proteomics to search for the major interacting protein partners of nuclear Sam68. In addition to Sam68 itself and known Sam68-associated proteins (heterogeneous nuclear ribonucleoproteins hnRNP A1, A2/B1 and G), we identified hnRNP L as a novel Sam68-interacting protein partner. hnRNP L protein was predominantly present within small nuclear protein complexes approximating to the expected size of monomers and dimers, and was quantitatively associated with nucleic acids. hnRNP L spatially co-localised with Sam68 as a novel component of SNBs and was also observed within the general nucleoplasm. Localisation within SNBs was highly specific to hnRNP L and was not shared by the closely-related hnRNP LL protein, nor any of the other Sam68-interacting proteins we identified by proteomics. The interaction between Sam68 and hnRNP L proteins was observed in a cell line which exhibits low frequency of SNBs suggesting that this association also takes place outside SNBs. Although ectopic expression of hnRNP L and Sam68 proteins independently affected splicing of CD44 variable exon v5 and TJP1 exon 20 minigenes, these proteins did not, however, co-operate with each other in splicing regulation of these target exons.
Here we identify hnRNP L as a novel SNB component. We show that, compared with other identified Sam68-associated hnRNP proteins and hnRNP LL, this co-localisation within SNBs is specific to hnRNP L. Our data suggest that the novel Sam68-hnRNP L protein interaction may have a distinct role within SNBs.
Alternative splicing is regulated in part by a network of signalling pathways which respond to extracellular stimuli . One molecule with a key role linking signalling and splicing is Sam68 (Src-associated in mitosis 68 kDa). Sam68 is the prototypic member of the STAR (Signal Transduction and Activation of RNA) family of RNA-binding proteins . Sam68-dependent splicing events impact upon important cellular decisions such as choices between cell survival and cell death . Sam68 has also been recently shown to play an important role in neurogenesis through splicing regulation of specific pre-mRNAs important for neural development . Homozygous null Sam68 mice have pleiotropic defects in bone morphogenesis, spermatogenesis and motor coordination suggesting widespread anatomical functions for the encoded protein [5, 6].
Sam68 has been reported to be associated with a number of different proteins involved in RNA processing, transcription, and cell signalling. Sam68 induces ERK (extracellular signal-regulated kinase)-mediated inclusion of CD44 variable exon v5 in response to Ras activation . Activation of CD44 exon v5 splicing by Sam68 involves interactions with U2AF65 to facilitate v5 exon definition . Sam68 also interacts with the splicing repressor hnRNP A1  and nuclear transcriptional regulators [9, 10]. The amino acid sequence of Sam68 protein contains several consensus motifs that mediate protein-protein and protein-RNA interactions in response to different stimuli . In most somatic cells, Sam68 protein is exclusively nuclear, but Sam68 can also interact with cytoplasmic signalling molecules . Sam68 protein has also been observed in the cytoplasm of secondary spermatocytes, where it is associated with polysomes and is involved in translational regulation [11, 12].
In cancer cells, Sam68 protein exhibits a general nucleoplasmic distribution but is also concentrated within subnuclear structures called SLM/Sam68 Nuclear Bodies (SNBs) . Although the exact function of SNBs is unknown, they have been shown to contain some other splicing regulators, signalling components and nucleic acids. Although Sam68 has a number of reported interacting protein partners, its major associated proteins are not yet known. In this study, we searched by proteomics for the major interacting protein partners of nuclear Sam68. Our data reveal hnRNP (heterogeneous nuclear ribonucleoprotein) L as a novel Sam68-associated nuclear protein and a novel component of SNBs.
hnRNP L is a novel Sam68-interacting protein
Identities of Sam68-interacting proteins.
Swiss-Prot entry name
Nominal mass Mr
Calculated pI value
p = 0.036
p < 0.001
p < 0.001
p < 0.001
p < 0.001
To further verify the novel Sam68-hnRNP L detected interaction, HEK293 cells were transiently transfected with expression constructs encoding FLAG-tagged Sam68 and GST-tagged hnRNP L proteins. Anti-FLAG M2 agarose was used to immunoprecipitate FLAG-tagged proteins from HEK293 cells, and co-immunoprecipitated GST fusion proteins were detected using antisera specific to GST. Consistent with the observed interactions of endogenous proteins, hnRNP L-GST was efficiently co-immunoprecipitated with Sam68-FLAG (Figure 2B, compare lanes 1 and 3), but could not be co-immunoprecipitated in cells transfected with an empty FLAG vector (Figure 2B, compare lanes 2 and 4).
Note that all immunoprecipitations of both endogenous (Figure 2A) and FLAG-tagged proteins (Figure 2B) were carried out in the presence of Benzonase nuclease to ensure that the detected associations were mediated by protein-protein interactions and not bridged by nucleic acids.
Sam68 and hnRNP L are both present in small protein complexes which are quantitatively associated with nucleic acids
Sam68 is quantitatively associated with small nuclear protein complexes of a size compatible with either monomers or dimers . In order to investigate and compare the size ranges of any endogenous nuclear complexes containing hnRNP L protein, we analysed velocity gradient fractions of HEK293 cell nuclear extracts prepared either without pretreatment or after prior micrococcal nuclease (MNase) treatment to eliminate any nucleic acid dependent complexes (Figures 2C and ). Similarly to previously published data for Sam68, following MNase treatment, hnRNP L (monomeric molecular weight ~70 kDa) protein was mainly present in small stable protein complexes (of less than 158 kDa) corresponding to the expected size of monomeric or dimeric molecular complexes (Figure 2C, upper panel). Also like Sam68, hnRNP L protein was quantitatively associated with nucleic acids since it migrated with much larger complexes without prior MNase digestion (Figure 2C, lower panel).
hnRNP L uniquely co-localises with Sam68 as a novel component of SNBs
Only a small number of molecules have been identified as SNB components, and each of these share a role in cell signalling and/or RNA processing. hnRNP L has a closely-related homolog within the cell called hnRNP LL (hnRNP L-like), which also regulates signal-dependent splicing. We carried out further experiments to test if hnRNP LL protein would be also found within SNBs. Surprisingly, these experiments indicated that hnRNP LL protein exhibits a nucleoplasmic distribution outside SNBs (Figure 3D and Additional File 2). The observed hnRNP LL distribution was punctate and somewhat reminiscent to that of splicing speckles. We compared the localisation of hnRNP LL protein with SC35, but found that the speckled distribution of hnRNP LL is in fact distinct from the SC35-containing splicing speckles (Figure 3E).
Sam68 and hnRNP L proteins associate in a cell line which exhibits a low frequency of SNBs
The Sam68-hnRNP L protein interaction does not significantly impact on splicing regulation of two known target exons
The above experiments indicate that Sam68 and hnRNP L proteins interact and are both present within SNBs. Although SNBs contain some splicing regulators and RNA, they do not detectably contain key spliceosome components . Hence SNBs are not thought to be sites for active pre-mRNA splicing, which takes place in the general nucleoplasm . Both Sam68 and hnRNP L proteins are independently implicated in the regulation of distinct alternative splicing events during which exon inclusion can be either activated or repressed depending on the target transcript [4, 21]. Although active splicing of Sam68 and hnRNP L target pre-mRNAs is unlikely to take place within SNBs, we also detected significant nucleoplasmic populations of both Sam68 and hnRNP L proteins outside SNBs, and protein interactions between Sam68 and hnRNP L occurred equally well in a cell line which exhibits a low frequency of SNBs. These observations raise the question as to whether the Sam68-hnRNP L interaction might have a co-operative effect on pre-mRNA splicing in the general nucleoplasm.
Although Sam68 has been associated with a number of proteins, our proteomics screen identified hnRNP A1, hnRNP A2/B1, hnRNP G and hnRNP L as its four major nuclear interacting protein partners in LNCaP cells. The stoichiometry of the Sam68-associated proteins recovered by immunoprecipitation, their spatial localisations, and analysis of endogenous complexes using velocity gradient centrifugation analysis  are most consistent with a number of distinct small Sam68-containing protein complexes (predominantly monomeric and dimeric-sized), rather than a single large complex containing each of the identified Sam68-interacting proteins. Like Sam68 and the Sam68-interactor hnRNP G, but not hnRNP A1, hnRNP L protein was quantitatively associated with nucleic acids since it migrated with much larger complexes without prior MNase digestion before velocity gradient centrifugation.
hnRNP L protein has previously been described in discrete perinucleolar structures , which we here now identify as SNBs. Although the exact functions of SNBs are not fully understood, they are known to contain other STAR proteins (SLM-1 and SLM-2) , the splicing factor YT521B , Scaffold Attachment Factors SAFB1 and SAFB2  and the protein kinase BRK/Sik (Breast Tumour Kinase/Src-related Intestinal Kinase) . SNBs also contain nucleic acids including RNA, and on heat-shock additionally recruit hnRNP A1 and other splicing factors including arginine-serine-rich (SR) proteins . Like Sam68, hnRNP L is implicated in coupling signaling and splicing: hnRNP L regulates signal-dependent splicing of CD45 exon v4  and STREX (stress axis-regulated exon) . Despite the spatial and physical associations of Sam68 and hnRNP L detected in our study, Sam68 and hnRNP L proteins did not either co-operate or antagonize each others' splicing activity on target exons. In contrast, the generally nucleoplasmic Sam68-associated protein hnRNP G potently inhibited Sam68-mediated splicing of CD44 exon v5 ( and Additional File 3). Our protein interaction analyses indicated that the interaction between Sam68 and hnRNP L is independent of nucleic acids. Using a directed yeast two-hybrid system, a direct protein-protein interaction has been demonstrated between the STAR-family protein rSLM-2 and hnRNP L , suggesting, by analogy, that the Sam68-hnRNP L interaction may also be direct. However, we were unable to detect such an interaction by directed yeast two hybrid analysis (unpublished observations).
Amongst all the Sam68-associated proteins we investigated in this study, the subnuclear distribution of hnRNP L protein is specifically within SNBs. Consistent with the known nuclear functions of hnRNP L, SNBs have been suggested as potential nuclear sites for the regulation of RNA processing by signalling pathways. However, we found that the homologous hnRNP LL protein which is also implicated in signal-dependent CD45 splicing [28–30], did not localize to SNBs. Hence SNBs are not a default location for all nuclear RNA-binding proteins involved in signaling and RNA processing. hnRNP LL protein lacks some proline- and glycine-rich regions present within the hnRNP L amino acid sequence, and by analogy with Sam68, it is possible that these motifs are required for interactions with signaling molecules and SNB localization. The distinct nuclear localization we observe for hnRNP LL may suggest somewhat diverged functions and so provide some explanation for the evolutionary maintenance of both hnRNP L and LL proteins within cells.
We have identified hnRNP L as a novel Sam68-interacting protein partner and component of SNBs. Despite hnRNP L and Sam68 proteins also localizing to the general nucleoplasm, where pre-mRNA splicing occurs, we did not observe a role for the novel Sam68-hnRNP L protein interaction on splicing of known target exons for these RNA-binding proteins. The spatial localization of hnRNP L protein within SNBs further implicates a role for these organelles in coupling signaling to RNA processing.
Cell Culture and DNA transfection
LNCaP cells were cultured in RPMI-1640 (PAA Laboratories) supplemented with 10% foetal calf serum (FCS) (PAA Laboratories). HEK293, HeLa, NIH3T3, and Saos-2, and cells were cultured in Dulbecco's Modified Eagle Media (D-MEM) with glutamax-1 (PAA Laboratories) with 10% FCS. Plasmid transfections were performed as previously described  using Genejammer (Stratagene) according to manufacturer's instructions.
Antibodies and plasmids
The following antibodies were used: normal rabbit IgG sc-2027 and anti-Sam68 sc-333 rabbit antisera (Santa Cruz Biotechnology); anti-hnRNP A1 9H10, anti-hnRNP L 4D11, anti-SC35 SC-35, and anti-β-actin AC15 mouse monoclonal antibodies (Sigma); anti-hnRNP A2/B1 DP3B2 mouse monoclonal antibody (Abcam); anti-hnRNP LL rabbit antisera (Aviva Systems Biology); anti-GST (glutathione S-transferase) goat antisera (GE Healthcare).
The following plasmids have been described previously: FLAG-Sam68 ; pGFP3-Sam68 ; pETv5  (from Stefan Stamm, University of Kentucky, USA). The following plasmids were made using standard cloning procedures, the details of which are available on request: pcDNA-GST, pcDNA-hnRNP L-GST, and pcDNA-hnRNP LL-GST encode full-length GST, hnRNP L , and hnRNP LL with a C-terminal GST tag, respectively. pcDNA-hnRNP G encodes full-length hnRNP G. pcDNA3-TJP1-wWT contains exon 19, 20 and 21 of TJP1 with intervening intronic sequence.
Peptide mass fingerprinting and mass spectrometry (MS)
Immunoprecipitated proteins were resolved on NuPAGE Novex 10% Bis-Tris gels (Invitrogen) and stained with Coomassie blue (GE Healthcare). Excised bands were digested with trypsin, and identified by peptide mass fingerprinting. Mass spectra were obtained using the Ultraflex II MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometer (Bruker Daltonics) in standard MALDI-TOF mass spectrometry (MS) mode. The peak lists were searched against the non-redundant Swiss-Prot protein sequence database using the Mascot  search engine version 2.2 (Matrix Science). Probability-based MOWSE (Molecular Weight Search)  scores greater than 55 were considered as significant (p < 0.05).
LNCaP cell nuclear extracts were obtained using the CelLytic NuCLEAR Extraction Kit (Sigma) according to manufacturer's instructions. Benzonase nuclease (Sigma) was used at 100 units/ml where indicated. Immunoprecipitations were performed using Dynabeads Protein A (Invitrogen) or anti-FLAG M2 agarose (Sigma) according to manufacturers' instructions. Where indicated, antibodies were cross-linked to Dynabeads Protein A according to manufacturer's instructions. Recovered material was resolved by SDS-PAGE and subjected to Western analysis as previously described .
Velocity gradient centrifugation
Sucrose gradients were run using HEK293 cell nuclear extract, pre-treated or not with micrococcal nuclease (MNase), and recovered material resolved by SDS-PAGE and subjected to Western analysis as previously described .
Indirect immunofluorescence microscopy
LNCaP, HeLa, and Saos-2 cells were grown and transfected on glass coverslips (VWR International), and stained with primary and secondary antibodies as previously described . All images were captured using the LSM510 (Zeiss) or SP2 MP (Leica) confocal microscopes and associated software.
Minigene splicing assays
HEK293 cells were grown in 6-well plates (Asahi Techno Glass), and transfected with DNA as detailed in figure legends. RNA was extracted using TRIzol (Invitrogen) and RT-PCR was performed using the One-Step RT-PCR kit (Qiagen) as previously described . Densitometric band quantification was performed as previously described . All experiments shown are the mean of at least three independent experiments ± standard error.
We thank Colin Nixon, Rosie Morland (Beatson Institute) and Agata Rozanska (Newcastle University) for technical assistance, and Helen Arthur and Soulmaz Boroumand (Newcastle University) for assistance with proteomics. We are grateful to Sheila Graham (University of Glasgow) and Kim Moran-Jones (Beatson Institute) for antibodies, and Stefan Stamm for the CD44 variable exon v5 minigene. This work was supported by a Medical Research Council Clinical Research Training Fellowship (G0500482 to P.R.); A ssociation for I nternational C ancer R esearch project grant (06-705 to DJE and HYL); a Wellcome Trust project grant (WT080368 MA to DJE); a Royal Society Joint International Grant (to DJE and JS); and the European Commission-funded Network of Excellence EURASNET (AB and JS).
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