Interactions of an Arabidopsis RanBPM homologue with LisH-CTLH domain proteins revealed high conservation of CTLH complexes in eukaryotes
© Tomastíková et al.; licensee BioMed Central Ltd. 2012
Received: 20 December 2011
Accepted: 7 June 2012
Published: 7 June 2012
RanBPM (Ran-binding protein in the microtubule-organizing centre) was originally reported as a centrosome-associated protein in human cells. However, RanBPM protein containing highly conserved SPRY, LisH, CTLH and CRA domains is currently considered as a scaffolding protein with multiple cellular functions. A plant homologue of RanBPM has not yet been characterized.
Based on sequence similarity, we identified a homologue of the human RanBPM in Arabidopsis thaliana. AtRanBPM protein has highly conserved SPRY, LisH, CTLH and CRA domains. Cell fractionation showed that endogenous AtRanBPM or expressed GFP-AtRanBPM are mainly cytoplasmic proteins with only a minor portion detectable in microsomal fractions. AtRanBPM was identified predominantly in the form of soluble cytoplasmic complexes ~230 – 500 kDa in size. Immunopurification of AtRanBPM followed by mass spectrometric analysis identified proteins containing LisH and CRA domains; LisH, CRA, RING-U-box domains and a transducin/WD40 repeats in a complex with AtRanBPM. Homologues of identified proteins are known to be components of the C-terminal to the LisH motif (CTLH) complexes in humans and budding yeast. Microscopic analysis of GFP-AtRanBPM in vivo and immunofluorescence localization of endogenous AtRanBPM protein in cultured cells and seedlings of Arabidopsis showed mainly cytoplasmic and nuclear localization. Absence of colocalization with γ-tubulin was consistent with the biochemical data and suggests another than a centrosomal role of the AtRanBPM protein.
We showed that as yet uncharacterized Arabidopsis RanBPM protein physically interacts with LisH-CTLH domain-containing proteins. The newly identified high molecular weight cytoplasmic protein complexes of AtRanBPM showed homology with CTLH types of complexes described in mammals and budding yeast. Although the exact functions of the CTLH complexes in scaffolding of protein degradation, in protein interactions and in signalling from the periphery to the cell centre are not yet fully understood, structural conservation of the complexes across eukaryotes suggests their important biological role.
KeywordsArabidopsis homologue of RanBPM CTLH-complex LisH-CTLH domain proteins
Ras-related nuclear proteins (Rans) are abundant small GTPases, associated with Ran-specific nuclear GEFs (guanine nucleotide exchange factors), cytoplasmic GAPs (GTPase activating proteins), and with RanBP1 (Ran binding protein 1) that stimulate RanGTP hydrolysis in the cytoplasm [1, 2]. The Arabidopsis genome contains three genes encoding AtRan , two genes encoding AtRanGAP related proteins  and three genes for RanBP1 isoforms – RanBP1a, RanBP1b and RanBP1c [3, 5]. Plant Ran binding proteins (RanBPs) display significant homology with yeast and mammalian RanBPs, but there is little evidence for their biological function [6, 7].
One RanBP in animal cells, RanBPM (RanBP9), was identified in a yeast two-hybrid screen with Ran as a bait. RanBPM comprises four domains – SPRY, LisH, CTLH and CRA and is homologous to the human RanBP10 protein . Although RanBPM and RanBP10 have been shown to bind the Ran protein, they do not contain a consensus Ran-binding sequence . RanBPM was defined as a member of the Scorpin family of proteins (SPRY-containing Ran binding protein) with a unique domain organization . As reviewed in Suresh et al. , numerous protein interactions described for the RanBPM protein suggest its multiple roles in the regulation of protein stability, cell cycle regulation and other as yet undefined cellular processes.
RanBPM was reported to be a part of the large CTLH (C-terminal to the LisH motif) complexes [12–14]. CTLH complexes composed of LisH, CTLH and CRA domain containing proteins, transducin/WD40 repeat proteins, and armadillo repeat proteins have been found in mammals and yeast [15, 16]. Mammalian and yeast CTLH complexes are structurally conserved but their biological function is still not fully understood. In yeast, the CTLH complex of Gid/Vid proteins plays a role in vacuole and proteasome-dependent fructose-1,6-bisphosphatase degradation . Similarly, it has been suggested that CTLH complexes partake in lysosome and proteasome-dependent proteolysis in mammalian cells . Data on proteins with SPRY, LisH, CTLH or CRA domain-containing proteins in plants are limited. In Pinus radiata, the SPRY domain containing protein, SEPR11, is the homologue of a Trithorax-group member and is involved in plant reproduction and development . In Oryza sativa, the LisH domain-containing protein, OsLIS-L1 is required for male gametophyte formation and the first internode elongation .
Here we provide data on an Arabidopsis homologue of RanBPM that belongs to the uncharacterized family of plant SPRY, LisH, CTLH and CRA domain-containing proteins. We used in silico analysis, biochemical, proteomic and microscopic analyses in vivo and in situ to characterize AtRanBPM. We found that the AtRanBPM protein is present predominantly in the form of large cytoplasmic protein complexes that are structurally homologous to the CTLH type of complexes described in mammals and budding yeast.
The Arabidopsis homologue of RanBPM is a SPRY-domain containing protein
By homology search of the Arabidopsis thaliana genome, we found a SPRY-domain containing protein AtRanBPM (At1g35470), which is a homologue of the human RanBPM (RanBP9) protein. The AtRanBPM cDNA contains a single open reading frame and consists of 467 amino acids. AtRanBPM is a member of the HOM002780 gene family that comprises 44 genes in 21 plant species, particularly from the ORTHO002658 subfamily. In Arabidopsis there are three paralogues of AtRanBPM (At4g09310, At4g09200, At4g09250) and one gene originating from the segmental duplication of chromosome 1 (At4g09340) (Plaza 2.0; A resource for plant comparative genomics, ). The products of these genes are described as SPRY domain-containing proteins but their biological roles in plants have not yet been identified.
SPRY, LisH, CTLH and CRA conserved domains are mainly involved in protein-protein interactions. The SPRY domain (SPla and the RYanodine Receptor) was originally identified as a structural motif in ryanodine receptors . Proteins with SPRY domains are involved in intracellular calcium release, as is the case for ryanodine receptors, in RNA metabolism and in regulatory and developmental processes . The LisH domain (Lissencephaly type-1-like homology motif) functions as a stable homodimerization and dimerization motif and its contribution to the dynamics of microtubules has been suggested . Located adjacent to the C-terminus of the LisH domain is a C-terminal to the LisH motif (CTLH) that has a putative α-helical structure with an as yet undescribed function. The CRA domain (CT11-RanBPM) was found to be a motif in the C-terminal part of RanBPM and RanBP10 and represents a protein-protein interaction domain often found in Ran-binding proteins .
Protein expression levels, cellular distribution and molecular forms of AtRanBPM
The AtRanBPM coding sequence [EMBL:AEE31799] was cloned into Gateway-compatible plant binary vectors for N-terminal GFP and C-terminal GFP fusion. Arabidopsis cell suspension cultures were transformed according to Mathur et al. . Transformed Arabidopsis plants were obtained through the floral-dip method .
The cellular distribution of AtRanBPM was analysed using differential centrifugation. As shown in Figure 3C, the majority of the protein was cytoplasmic and only small amounts sedimented either in low speed pellets or in the microsomal pellet (P100). The fact that AtRanBPM was also sedimented from a high-speed cytoplasmic S100 extract to pellet P200 indicated that the protein might be present in the form of higher MW complexes. The separation of S100 high speed extract by native polyacrylamide gel electrophoresis (native PAGE) confirmed cell fractionation data and suggested that AtRanBPM is a component of protein complexes with a molecular mass of around ~230 – 500 kDa (Figure 3D). Further, we immunopurified GFP-AtRanBPM using the GFP trap. Separation of purified GFP-AtRanBPM by native PAGE followed by Western blotting showed the presence of complexes of similar size as observed when high-speed supernatant S100 was analysed (Figure 3D). Altogether these data showed that AtRanBPM is present predominantly in the form of large cytoplasmic complexes.
Analysis of AtRanBPM protein complexes by mass spectrometry
Proteins copurified with AtRanBPM are members of CTLH complexes
Sequence coverage [%]
Members of CTLH complex in other organisms
RanBPM [Q96S59] Gid1/Vid30 [P53076]***
LisH and RanBPM domain-containing protein
Twa1 [Q9NWU2]**Gid8 [P40208]***
LisH/CRA/RING-U-box domain-containing protein
MAEA [Q7L5Y9]*Gid9p [P40492]***
LisH/CRA/RING-U-box domain-containing protein
RMD5 [Q9H871]*Gid2 [Q12508]***
Transducin/WD40 domain-containing protein
Transducin/WD40 domain-containing protein
Database search indicated that the proteins copurified with AtRanBPM were homologous to protein components of the human CTLH complex . The CTLH complex is annotated in CORUM (The comprehensive resource for mammalian complexes, ) as a complex with a putative function in regulating cell migration, nucleokinesis, chromosome segregation and microtubule dynamics. Components of the CTLH complex are conserved amongst animal species and their presence is predicted for other eukaryotes such as plants and fungi. A relatively lower degree of homology with individual mammalian and plant members of CTLH complexes (Figure 4B, Additional file 5) is due to the fact that part of the molecule separating highly conserved domains contains insertions and deletions of various lengths, differing among plant, mammalian and/or yeast homologues.
The LC-MALDI-MS/MS analysis also identified among proteins copurified with AtRanBPM Armadillo-repeat-containing protein (At3g08947) (Additional file 6). However, the protein was not proven to be a homologue of the human armadillo repeat ARMC8, a member of the CTLH complex [34, 35]. Further, Yippee family proteins (At5g53940, At2g40110) and Yippee-like protein (At3g08890) were copurified with AtRanBPM and identified by LC-MALDI-MS/MS (Additional file 6). Yippee-like proteins belong to the YPEL family of proteins whose members have been described as interactors of the human RanBPM . Proteins At5g08560, At5g43920, At3g55070, and At3g37880, copurified with AtRanBPM were predicted to interact within a functional network in the Aranet database (Probabilistic Functional Gene Network for Arabidopsis thaliana, ) (Table 1).
Together these data suggest that plant AtRanBPM protein, like its yeast and mammalian homologues, is a component of a cytoplasmic multiprotein complex where it interacts with LisH-CTLH domain-containing proteins and armadillo-repeat-containing proteins.
In vivo localization of GFP-AtRanBPM and AtRanBPM immunofluorescence labelling in Arabidopsis cultured cells and seedlings
Additional file 7: GFP-AtRanBPM in Arabidopsis root cells. AtRanBPM-GFP signal is dynamic and moving with the cytoplasmic stream. (MPEG 284 KB)
To determine whether the AtRanBPM protein plays a role in microtubule organization like the truncated version of human RanBPM , we studied the colocalization of AtRanBPM with the centrosomal protein, γ-tubulin. In acentrosomal plant cells, γ-tubulin is present with dispersed sites of microtubule nucleation in the cytoplasm, with nuclei, and on membranes and microtubules . We found that the Arabidopsis homologue AtRanBPM did not colocalize with γ-tubulin-positive sites either present with the nuclear envelope or on microtubular arrays (Figure 6C).
As a portion of RanBPM was reported to be associated with the Ran protein in mammalian cells  we performed double immunofluorescence labelling of AtRanBPM and Ran protein. In cultured cells of Arabidopsis, Ran was localized in the cytoplasm and in nuclei but only a small fraction of AtRanBPM colocalized with nuclear Ran.
RanBPM protein was first characterized in human cells as a centrosomal protein involved in microtubule nucleation which colocalized with γ-tubulin at centrosomes and at ectopic nucleation sites . The data on RanBPM initiated an investigation of the role of the RanGTPase pathway and its role in chromatin-mediated microtubule nucleation and spindle assembly . However, later it was found that antibody against the 55 kDa form of RanBPM that was characterized by Nakamura et al.  did not recognize the full length 90 kDa RanBPM protein. The truncated form of RanBPM (55 kDa) was shown to be an incorrectly translated product of the RanBPM gene and moreover, only the truncated version but not the whole RanBPM molecule was active in microtubule nucleation . The complete RanBPM molecule thus does not show the same properties as the truncated version and it was depicted as a scaffold protein that links and modulates interactions between cell surface receptors and their intracellular signalling pathways [11, 40]. The molecular mass of plant AtRanBPM (52 kDa) corresponds to that of the truncated RanBPM rather than to the whole human RanBPM molecule. However, the reason for the apparent discrepancy in size of the full length human and plant RanBPM molecules is an insertion of 150 amino acids between CTLH and CRA domains in the plant protein and the presence of a long stretch of proline and glutamine residues on the N-terminal part of human RanBPM molecule.
We found that AtRanBPM maintained the properties of the full length RanBPM of mammals: (i) while the truncated version of human RanBPM is present in centrosomal and ectopic microtubule nucleation sites , AtRanBPM protein in acentrosomal plant cells did not colocalize with microtubule nucleation sites positive for γ-tubulin; (ii) proteins of the γ-tubulin nucleating machinery were not identified by MALDI-MS or LC-MALDI-MS/MS among proteins interacting with AtRanBPM, nor were they found in coexpression databases and a biological role of AtRanBPM other than in processes relating to centrosomes and microtubules was thus suggested; (iii) the presence of highly conserved SPRY, LisH, CTLH and CRA domains in AtRanBPM indicated its function in mediating multiple protein interactions that were described for the whole molecule of human RanBPM [12, 14, 15].
AtRanBPM protein was not specifically enriched with microtubules in dividing cells or localized in putative microtubule nucleation sites. Subcellular localization of AtRanBPM corresponded to published data on the subcellular localization of the whole RanBPM molecule in mammalian cells [14, 41, 42]. Since a weak nuclear signal, observed for human RanBPM was suggested to be a consequence of over-expression of its tagged version , we analysed by immunofluorescence the nuclear localization for endogenous AtRanBPM protein. A smaller portion of AtRanBPM was present in nuclei and the possibility that the nuclear signal observed for GFP-AtRanBPM or AtRanBPM-GFP resulted from over expression of GFP fusions was thus excluded. We observed only partial colocalization of Ran and AtRanBPM in nuclei. It would be interesting to address the question whether transport of the AtRanBPM complex between nucleus, perinuclear area and cytoplasm might be regulated by a weak interaction between AtRanBPM and Ran as it was suggested for mammalian RanBPM . Heterogeneity in the localization of mammalian RanBPM might depend on interacting proteins . Conserved domains of RanBPM protein are responsible for interactions and complex formations with a physiologically divergent group of proteins. As reviewed by Suresh et al. , RanBPM is a modulator/protein stabilizer, a regulator of transcriptional activity, and has cell cycle and neurological functions. RanBPM interacts with a wide range of receptors , acts as a scaffolding protein [44, 45], and is involved in signal transduction pathways [44, 46], and the apoptotic pathways . Plant homologues of RanBPM belong to genes with unknown functions. We found that the product of AtRanBPM is predominantly a cytoplasmic protein that is a part of protein complexes with a molecular mass of approximately 230 – 500 kDa. A large protein complex of RanBPM was described by Nishitani et al.  and Ideguchi et al. . Later the complex was designated as a CTLH complex . Five from eleven CTLH domain-containing proteins that were identified in databases were described as being a part of the CTLH complex and an interaction within the complex via LisH-CTLH domains was suggested . In Saccharomyces cerevisiae all four CTLH domain-containing proteins present in the genome are part of the CTLH-like complex Gid. The Gid complex is suggested to be involved in proteasome-dependent glucose-induced degradation of fructose-1,6-bisphosphatase [16, 48]. There are twenty one CTLH-domain containing proteins encoded in the Arabidopsis genome and of these, six proteins were identified in our experiments to form CTLH-like complexes with AtRanBPM protein. Though we identified the same spectrum of AtRanBPM interacting proteins in several independent experiments it cannot be ruled out that the members of CTLH complexes exist and remain to be identified. We found that the antibody raised against a peptide from the AtRanBPM sequence did not work in immunopurification experiments. The immunopurifications performed with a panel of antibodies against the AtRanBPM protein might help to disclose the presence of other putative members of plant CTLH complexes. Alternatively, immunopurification of the CTLH complex or pull down experiments via proteins that copurified with AtRanBPM might extend our knowledge of the composition and protein interactions of newly identified CTLH complexes.
All the members of the CTLH complexes that we identified belong to yet uncharacterized plant LisH-CTLH domain-containing proteins. Protein At1g61150 is a homologue of the human Twa1 protein found in yeast by two-hybrid analysis to interact with RanBPM . LisH, CRA, and RING/U-box domain-containing proteins of unknown function (At3g55070, At4g37880), copurified with AtRanBPM, are homologous to human MAEA and RMD5, respectively, that are members of the CTLH complex annotated by Kobayashi et al. . Similarly, LisH and CTLH domain-containing proteins such as RanBP10 or the WD repeat domain 26 (WDR26), were suggested to be putative members of the CTLH complex . We found that uncharacterized Arabidopsis transducin/WD-40 domain-containing proteins At5g08560 and At5g43920 which copurified with AtRanBPM, are homologues of human WDR26 protein and thus belong to components of the plant CTLH complex. Corresponding to our microscopic data on cytoplasmic and nuclear localizations of AtRanBPM, the members of the human CTLH complex, proteins RanBPM, RMD5, WDR26, Twa1, and MAEA, were shown to have predominantly cytoplasmic and a weaker nuclear localization [12, 15, 49].
A component of the human CTLH complex, the armadillo repeat-containing protein ARMC8, when exogenously expressed, upregulates the proteolytic degradation of ectopically expressed α-catenin, and thus was suggested to play an important role in the ubiquitin-independent and proteasome-dependent degradation of α-catenin . α-Catenin is known to function as a link protein between cadherins and actin-containing filaments of the cytoskeleton ; thus a complex might regulate molecular adhesion. We identified Armadillo-repeat-containing protein (At3g08947) among proteins copurified with AtRanBPM but its homology with armadillo repeat ARMC8, a member of the human CTLH complex, was not proven. However, we found that expression of copurified protein At4g37880, a homologue of RMD5 protein, correlated strongly with expression of the armadillo repeat-containing protein At3g01400, one of the homologues of ARMC8, and with expression of the plant adhesion molecule RabGAP/TBC domain-containing protein At3g02460 (ATTED-II, ). It is tempting to speculate whether similar function in connecting external signals in adhesion with the cell centre analogous to the cadherin and catenin pathway in animals might exist for plant CTLH complexes. However, further experimental data are needed to prove this hypothetical function of the CTLH complexes in plants.
Besides copurification with CTLH complex proteins, we found that plant AtRanBPM interacts with Yippee proteins (At5g53940, At2g40110) and Yippee-like protein (At3g08890). It was shown in human cells that RanBPM binds members of YPEL (Yippee like) family of proteins involved in a cell division-related functions . Our data showed that binding with Yippee proteins might present one of the AtRanBPM multiple protein interactions in plant cells too.
RanBPM protein was shown to have numerous apparently functionally unrelated protein interactors, including membrane receptors, cytoplasmic and nuclear proteins [12, 15]. This suggests its role in a variety of cellular processes. Our biochemical and proteomic studies showed that AtRanBPM is a component of plant homologues of CTLH complexes. The fact that CTLH complexes are present in mammals, yeast and in plants suggests their structural conservation in evolution. CTLH complexes thus might represent a module with important but not fully understood biological functions.
Arabidopsis thaliana (L.) Heynh. plants, ecotype Columbia were used. Sterilized seeds were sown and stratified at 4 °C for 2 days, then grown under 8 h of light, 16 h of darkness at 20 °C and after 4 weeks, under 16 h of light and 8 h of darkness. Seeds were cultivated on half-strength Murashige and Skoog (MS) medium (Duchefa), supplemented with 0.25 mM MES, 1% saccharose and 1% phytoagar. Transformed seedlings were selected as described in Harrison et al. . Arabidopsis thaliana suspension cultures were cultured as described in Drykova et al. .
Molecular cloning of AtRanBPM
AtRanBPM coding sequence [EMBL:AEE31799] was obtained by PCR amplification using Arabidopsis thaliana cDNA as template and Platinum Pfx DNA Polymerase (Invitrogen). The PCR primers with attB sites (underlined) were designed according to the manufacturer’s intruction, forward 5’ – GGGGACAAGTTTGTACAAAAAAGCAGGCTTCATGAACTCTTCACCACCACCG – 3’, reverse 5' – GGGGACCACTTTGTACAAGAAAGCTGGGTCTTAGTCTCCATTCAGTGACCGCCTTTC – 3’ for N-terminal GFP fusion and for C-terminal GFP fusion forward 5' – GGGGACAAGTTTGTACAAAAAAGCAGGCTTCATGAACTCTTCACCACCACCG – 3’, reverse 5' – GGGGACCACTTTGTACAAGAAAGCTGGGTCTTAGTCTCCATTCAGTGACCGCCTTTC – 3´. PCR products were isolated using QIAquick gel extraction kit (Qiagen) and afterwards cloned by Gateway technology (Invitrogen). Gateway binary vectors pK7WGF2,0 for N-terminal GFP fusion, pMDC43 for C-terminal GFP fusion  were used.
Stable transformation of cell suspension cultures and plants
Arabidopsis suspension cultures of Landsberg erecta ecotype stably expressing GFP-AtRanBPM or transiently expressing AtRanBPM-GFP were prepared according to the protocol of Mathur et al. . Arabidopsis plants Landsberg erecta ecotype were transformed by the floral-dip method .
Preparation of protein extracts and its fractionation by differential centrifugation
Cultured suspension cells or seedlings of Arabidopsis thaliana were ground in liquid nitrogen and thawed in extraction buffer in ratio 1:1 weight to volume. Extraction buffer was 50 mM Na-Hepes, pH 7.5, 75 mM NaCl, 1 mM MgCl2, 1 mM EGTA, 1 mM DTT supplemented with inhibitors of proteases and phosphatases according to Drykova et al.  with increased concentration of 4-(2-aminoethyl)benzenesulfonyl fluoride hydrochloride to 2 mM and β-glycerophosphate to 60 mM. Crude extracts were centrifuged at 10,000 g for 10 min at 4 °C; obtained supernatants S10 were subsequently centrifuged at 20,000 g for 0.5 h at 4 °C to gain supernatants S20 and pellets P20. Supernatants S20 were then centrifuged at 100,000 g for 1 h at 4 °C when S100 were needed. Supernatants S100 were centrifuged at 200,000 g for 1.5 h at 4 °C to gain supernatants S200 and pellets P200 when needed. For differential centrifugation, pellets were resuspended in a volume of extraction buffer equal to the volume of the corresponding supernatants; equal sample volumes were loaded on SDS-PAGE gel.
Immunoprecipitation of GFP-AtRanBPM
Cell extracts S20 (~ 4 mg protein/mL) were used directly or solubilized by 1% NP-40 (Calbiochem) for 1 h at 4 °C. Immunoprecipitations of GFP-AtRanBPM protein were then performed using GFP-Trap_A (ChromoTek) according to the manufactures’ instructions. GFP immunopurification from extracts S20 of wild type Ler Arabidopsis culture was used as a negative control.
Protein digestion and mass spectrometry
The analysed protein bands were cut out of the Ag-stained SDS-PAGE gels, trypsin-digested and the proteins were identified by peptide mass mapping as described elsewhere . Alternatively, eluates from the GFP trap were denatured in 8 M urea and digested overnight using trypsin. After desalting the resulting peptides were separated using the Ultimate HPLC system (LC Packings) on a Magic C18AQ column. The eluent from the column was spotted directly onto PAC-target using a ProteineerFC spotting device (Bruker Daltonics). Automatic MALDI MS/MS analyses were performed on an Ultraflex III TOF/TOF (Bruker Daltonics) and the proteins were identified by searching MS/MS spectra against A. thaliana subset of NCBI database using the in-house Mascot program (Matrixscience). The high resolution MALDI spectra were acquired on an APEX-Qe 9.4 T FTMS instrument (Bruker Daltonics).
Electrophoresis and immunoblotting
Protein samples after addition of appropriate sample buffer were separated either on 10% SDS-PAGE gels  or on 3-10% non-denaturing PAGE gels as described previously in Drykova et al. . Proteins were transferred onto 0.45 μm polyvinylidene fluoride membranes (Millipore) by wet electroblotting and immunodetected with appropriate antibody. Anti-AtRanBPM antibody was designed against peptide of AtRanBPM amino acid sequence (CSTNPNKKDVQRS), raised in rabbits and purified with immunogenic peptide coupled to protein A sepharose beads (GeneScript) and used in dilution 1:100 for Western blotting from non-denaturating PAGE, 1:300-1:500 for Western blotting from SDS-PAGE. Anti-GFP ab290 (Abcam) was diluted 1:2,000. Secondary anti-Rabbit IgG ECL Antibody, HRP Conjugated (GE Healthcare) was diluted 1:10,000; Super Signal West Pico Chemiluminiscent Substrate (Thermal Scientific) was used according to manufacturer’s instructions. Alternatively, SDS-PAGE gels were stained with silver, and the selected protein bands analysed by MALDI-MS.
Arabidopsis thaliana suspension cultures were fixed for 30 min using 3.7% paraformaldehyde and processed for immunofluorescence labelling according to Binarová et al. . Primary antibodies used: mouse anti-α-tubulin monoclonal antibody DM1A (Sigma) diluted 1:500, mouse monoclonal anti-γ-tubulin TU-32 (kindly provided by Pavel Dráber, IMG, Prague, Czech Republic) diluted 1:10, mouse anti-GFP antibody (Abcam) diluted 1:1,000, and mouse antibody against human Ran protein (BD Transduction Laboratories) diluted 1:1,000. Anti-AtRanBPM antibody was used in a dilution 1:1,000, anti-rabbit or anti-mouse secondary antibodies DyLight 488 or DyLight 549 (Jackson Immuno Research Laboratories) were diluted 1:250. DNA was stained with DAPI.
Microscopical analysis was performed on an IX81 motorized inverted research microscope CellR (Olympus) equipped with DSU (Disk Scanning Unit) and digital monochrome CCD camera CCD-ORCA/ER. To avoid filter crosstalk, fluorescence was detected using HQ 480/40 exciter and HQ 510/560 emitter filter cubes for DyLight 488 and HQ 545/30 exciter and HQ 610/75 emitter filter cubes for DyLight 549 (both AHF AnalysenTechnique). Confocal images were taken on Olympus FluoView FV1000 based on IX81 microscope using PLAPO 100x/1.45 and UPLSAPO 60x/1.35 objectives. GFP was excited by 473 nm solid state laser and its emission was detected from 485 to 545 nm. Images were processed and analysed using CellR and FV10-ASW (Olympus). Adobe Photoshop 7.0 was used for preparation of figures.
To identify putative domains, SMART (Simple Modular Architecture Research Tool, , http://smart.embl-heidelberg.de/) and Pfam (, http://pfam.sanger.ac.uk/) databases were used. Multiple sequence alignment was performed by ClustalX2  and evaluation of similarity and identity was done by WU-BLAST (Basic Local Alignment Search Tool, , http://www.ebi.ac.uk/Tools/sss/wublast/). Schematic drawings of protein structure were prepared in DOG (Domain Graph, ) and MyDomains (Prosite, http://prosite.expasy.org/cgi-bin/prosite/mydomains/). Search for putative interaction sites in AtRanBPM amino acid sequence was done in ELM (The eukaryotic linear motif resource for functional sites in proteins, , http://elm.eu.org/) and SumoSP 2.0 (Sumoylation sites prediction , http://sumosp.biocuckoo.org/). Phylogenetic relationships were analysed in MEGA 5.02 (Molecular evolutionary genetic analysis, ). Genes with similar expression pattern to AtRanBPM were identified in publically available databases ATTED-II (, http://atted.jp/) and AraNet (, http://www.functionalnet.org/aranet/). Putative interactors were analysed by Arabidopsis eFP browser (, http://bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi) and Genevestigator (, https://www.genevestigator.com/gv/plant.jsp). The information and phylogenetic relationships of human CTLH complex with similar complexes from other species were found in CORUM (, http://mips.helmholtz-muenchen.de/genre/proj/corum/).
C-terminal to LisH
GTPase activating protein
Guanine nucleotide exchange factor
Green fluorescent protein
- Gid/Vid proteins:
Glucose-induced degradation/vacuole-induced degradation proteins
Lissencephaly type-1-like homology
Ran binding protein
Ran binding protein1
Ran binding protein in microtubule organizing centre
SPIa and Ryanodine receptor
- Scorpin family:
SPRY-containing Ran binding protein family.
We thank Dr. Tomáš Takáč for preliminary confocal analyses. This work was supported by grants 204/07/1169, 204/09/P155, and P501/12/2333 from the Grant Agency of the Czech Republic, grant No. CZ.1.05/2.1.00/01.0007 Centre of the Region Haná for Biotechnological and Agricultural Research for ET and BP, IGA UP PrF/2012/001 for ET, grants LC06034 and LC545 from Ministry of Education, Youth and Sports of Czech Republic, and grant IAA500200719 from Grant Agency of the Czech Academy of the Sciences.
- Vetter IR, Wittinghofer A: The guanine nucleotide-binding switch in three dimensions. Science. 2001, 294: 1299-1304. 10.1126/science.1062023.PubMedView Article
- Weis K: Nucleocytoplasmic transport: cargo trafficking across the border. Curr Opin Cell Biol. 2002, 14: 328-335. 10.1016/S0955-0674(02)00337-X.PubMedView Article
- Haizel T, Merkle T, Pay A, Fejes E, Nagy F: Characterization of proteins that interact with the GTP-bound form of the regulatory GTPase Ran in Arabidopsis. Plant J. 1997, 11: 93-103. 10.1046/j.1365-313X.1997.11010093.x.PubMedView Article
- Pay A, Resch K, Frohnmeyer H, Fejes E, Nagy F, Nick P: Plant RanGAPs are localized at the nuclear envelope in interphase and associated with microtubules in mitotic cells. Plant J. 2002, 30: 699-709. 10.1046/j.1365-313X.2002.01324.x.PubMedView Article
- Kim SH, Roux SJ: An Arabidopsis Ran-binding protein, AtRanBP1c, is a co-activator of Ran GTPase-activating protein and requires the C-terminus for its cytoplasmic localization. Planta. 2003, 216: 1047-1052.PubMed
- Baloğlu MC, Zakharov FN, Öktem HA, Yücel AM: Molecular cloning, characterization, and expression analysis of a gene encoding a Ran binding protein (RanBP) in Cucumis melo L. Turk J Biol. 2011, 35: 387-397.
- Cho HK, Park JA, Pai HS: Physiological function of NbRanBP1 in Nicotiana benthamiana. Mol Cells. 2008, 26: 270-277.PubMed
- Wang D, Li Z, Schoen SR, Messing EM, Wu G: A novel MET-interacting protein shares high sequence similarity with RanBPM, but fails to stimulate MET-induced Ras/Erk signaling. Biochem Biophys Res Commun. 2004, 313: 320-326. 10.1016/j.bbrc.2003.11.124.PubMedView Article
- Dansereau D, Lasko P: RanBPM regulates cell shape, arrangement, and capacity of the female germline stem cell niche in Drosophila melanogaster. J Cell Biol. 2008, 182: 963-977. 10.1083/jcb.200711046.PubMedPubMed CentralView Article
- Hosono K, Noda S, Shimizu A, Nakanishi N, Ohtsubo M, Shimizu N, Minoshima S: YPEL5 protein of the YPEL gene family is involved in the cell cycle progression by interacting with two distinct proteins RanBPM and RanBP10. Genomics. 2010, 96: 102-111. 10.1016/j.ygeno.2010.05.003.PubMedView Article
- Suresh B, Ramakrishna S, Baek KH: Diverse roles of the scaffolding protein RanBPM. Drug Discov Today. 2012, 17: 379-387. 10.1016/j.drudis.2011.10.030.PubMedView Article
- Umeda M, Nishitani H, Nishimoto T: A novel nuclear protein, Twa1, and Muskelin comprise a complex with RanBPM. Gene. 2003, 303: 47-54.PubMedView Article
- Ideguchi H, Ueda A, Tanaka M, Yang J, Tsuji T, Ohno S, Hagiwara E, Aoki A, Ishigatsubo Y: Structural and functional characterization of the USP11 deubiquitinating enzyme, which interacts with the RanGTP-associated protein RanBPM. J Biochem. 2002, 367: 87-95. 10.1042/BJ20011851.View Article
- Nishitani H, Hirose E, Uchimura Y, Nakamura M, Umeda M, Nishii K, Mori N, Nishimoto T: Full-sized RanBPM cDNA encodes a protein possessing a long stretch of proline and glutamine within the N-terminal region, comprising a large protein complex. Gene. 2001, 272: 25-33. 10.1016/S0378-1119(01)00553-4.PubMedView Article
- Kobayashi N, Yang J, Ueda A, Suzuki T, Tomaru K, Takeno M, Okuda K, Ishigatsubo Y: RanBPM, Muskelin, p48EMLP, p44CTLH, and the armadillo-repeat proteins ARMC8α and ARMC8β are components of the CTLH complex. Gene. 2007, 396: 236-247. 10.1016/j.gene.2007.02.032.PubMedView Article
- Regelmann J, Schutz T, Josupeit FS, Horak J, Rose M, Entian K, Thumm M, Wolf DH: Catabolite Degradation of Fructose-1, 6-bisphosphatase in the Yeast Saccharomyces cerevisiae: A Genome-wide Screen Identifies Eight Novel GID Genes and Indicates the Existence of Two Degradation Pathways. Mol Biol Cell. 2003, 14: 1652-1663. 10.1091/mbc.E02-08-0456.PubMedPubMed CentralView Article
- Tomaru K, Ueda A, Suzuki T, Kobayashi N, Yang J, Yamamoto M, Takeno M, Kaneko T, Ishigatsubo Y: Armadillo Repeat Containing 8alpha Binds to HRS and Promotes HRS Interaction with Ubiquitinated Proteins. Open Biochem J. 2010, 4: 1-8. 10.2174/1874091X01004010001.PubMedPubMed CentralView Article
- Aquea F, Matte JP, Gutiérrez F, Rico S, Lamprecht M, Sánchez C, Arce-Johnson P: Molecular characterization of a Trithorax-group homologue gene from Pinus radiata. Plant Cell Rep. 2009, 28: 1531-1538. 10.1007/s00299-009-0752-9.PubMedView Article
- Gao X, Chen Z, Zhang J, Li X, Chen G, Li X, Wu C: OsLIS-L1 encoding a lissencephaly type-1-like protein with WD40 repeats is required for plant height and male gametophyte formation in rice. Planta. 2012, 354: 713-727.View Article
- Proost S, Van Bel M, Sterck L, Billiau K, Van Parys T, Van de Peer Y, Vandepoele K: PLAZA: a comparative genomics resource to study gene and genome evolution in plants. Plant Cell. 2009, 21: 3718-3731. 10.1105/tpc.109.071506.PubMedPubMed CentralView Article
- Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, Radenbaugh A, Singh S, Swing V, Tissier C, Zhang P, Huala E: The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res. 2008, 36: D1009-14.PubMedPubMed CentralView Article
- Lopez R: WU-Blast2 server at the European Bioinformatics Institute. Nucleic Acids Res. 2003, 31: 3795-3798. 10.1093/nar/gkg573.PubMedPubMed CentralView Article
- Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol. 2011, 28: 2731-2739. 10.1093/molbev/msr121.PubMedPubMed CentralView Article
- Ponting C, Schultz J, Bork P: SPRY domains in ryanodine receptors (Ca2 + -release channels). Trends Biochem Sci. 1997, 5: 2-3.
- Rhodes D, de Bono B, Trowsdale J: Relationship between SPRY and B30.2 protein domains. Evolution of a component of immune defence?. Immunology. 2005, 116: 411-417.PubMedPubMed Central
- Emes RD, Ponting CP: A new sequence motif linking lissencephaly, Treacher Collins and oral-facial-digital type 1 syndromes, microtubule dynamics and cell migration. Hum Mol Genet. 2001, 10: 2813-2820. 10.1093/hmg/10.24.2813.PubMedView Article
- Menon RP, Gibson TJ, Pastore A: The C Terminus of Fragile X Mental Retardation Protein Interacts with the Multi-domain Ran-binding Protein in the Microtubule-organising Centre. J Mol Biol. 2004, 43-53.
- Puntervoll P: ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res. 2003, 31: 3625-3630. 10.1093/nar/gkg545.PubMedPubMed CentralView Article
- Ren J, Gao X, Jin C, Zhu M, Wang X, Shaw A, Wen L, Yao X, Xue Y: Systematic study of protein sumoylation: Development of a site-specific predictor of SUMOsp 2.0. Proteomics. 2009, 9: 3409-3412. 10.1002/pmic.200800646.View Article
- Mathur J, Csaba K: Establishment and Maintenance of Cell SuspensionCultures. In Methods in Molecular Biology. Volume 82. Arabidopsis protocols.Edited by Martinéz-Zapater J, Salinas J. Totowa: Humana Press;1997:27–30.
- Clough SJ, Bent F: Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 1998, 16: 735-743. 10.1046/j.1365-313x.1998.00343.x.PubMedView Article
- Winter D, Vinegar B, Nahal H, Ammar R, Wilson GV, Provart NJ: An “Electronic Fluorescent Pictograph” browser for exploring and analyzing large-scale biological data sets. PLoS One. 2007, 2: e718-10.1371/journal.pone.0000718.PubMedPubMed CentralView Article
- Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W, Zimmermann P: Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Advances in bioinformatics. 2008, 2008: 420747.PubMedPubMed CentralView Article
- Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, Mewes HW: CORUM: the comprehensive resource of mammalian protein complexes-2009. Nucleic Acids Res. 2010, 38: D497-501. 10.1093/nar/gkp914.PubMedPubMed CentralView Article
- Suzuki T, Ueda A, Kobayashi N, Yang J, Tomaru K, Yamamoto M, Takeno M, Ishigatsubo Y: Proteasome-dependent degradation of alpha-catenin is regulated by interaction with ARMc8alpha. J Biochem. 2008, 411: 581-591. 10.1042/BJ20071312.View Article
- Lee I: Ambaru Bi, Thakkar P, Marcotte EM, Rhee SY: Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nature Biotechnol. 2010, 28: 149-156. 10.1038/nbt.1603.View Article
- Nakamura M, Masuda H, Horii J, Kuma KI, Yokoyama N, Ohba T, Nishitani H, Miyata T, Tanaka M, Nishimoto T: When overexpressed, a novel centrosomal protein, RanBPM, causes ectopic microtubule nucleation similar to gamma-tubulin. J Cell Biol. 1998, 143: 1041-1052. 10.1083/jcb.143.4.1041.PubMedPubMed CentralView Article
- Dryková D, Cenklová V, Sulimenko V, Volc J, Dráber P, Binarová P: Plant gamma-Tubulin Interacts with alpha-Tubulin Dimers and Forms Membrane-Associated Complexes. Plant Cell. 2003, 15: 465-480. 10.1105/tpc.007005.PubMedPubMed CentralView Article
- Heald R, Weis K: Spindles get the Ran around. Cell. 2000, 8924: 1-4.
- Murrin LC, Talbot JN: RanBPM, a scaffolding protein in the immune and nervous systems. J Neuroimmune Pharm. 2007, 2: 290-295. 10.1007/s11481-007-9079-x.View Article
- Zou Y, Lim S, Lee K, Deng X, Friedman E, Chem JB: Serine/Threonine Kinase Mirk/Dyrk1B Is an Inhibitor of Epithelial Cell Migration and Is Negatively Regulated by the Met Adaptor Ran-binding Protein M. J Biol Chem. 2003, 278: 49573-49581. 10.1074/jbc.M307556200.PubMedView Article
- Denti S, Sirri A, Cheli A, Rogge L, Innamorati G, Putignano S, Fabbri M, Pardi R, Bianchi E: RanBPM Is a Phosphoprotein That Associates with the Plasma Membrane and Interacts with the Integrin LFA-1. J Biol Chem. 2004, 279: 13027-13034.PubMedView Article
- Poirier MB, Laflamme L, Langlois MF: Identification and characterization of RanBPM, a novel coactivator of thyroid hormone receptors. J Mol Endocrinol. 2006, 36: 313-325. 10.1677/jme.1.01891.PubMedView Article
- Talbot JN, Skifter DA, Bianchi E, Monaghan DT, Toews ML, Murrin LC, Myron LT: Neuroscience Letters Regulation of mu opioid receptor internalization by the scaffold protein RanBPM. Neurosci Lett. 2009, 466: 154-158. 10.1016/j.neulet.2009.09.048.PubMedPubMed CentralView Article
- Puverel S, Barrick C, Dolci S, Coppola V, Tessarollo L: RanBPM is essential for mouse spermatogenesis and oogenesis. Development. 2011, 138: 2511-2521. 10.1242/dev.062505.PubMedPubMed CentralView Article
- Cheng L, Lemmon S, Lemmon V: RanBPM is an L1-interacting protein that regulates L1-mediated mitogen-activated protein kinase activation. J Neurochem. 2005, 94: 1102-1110. 10.1111/j.1471-4159.2005.03254.x.PubMedPubMed CentralView Article
- Atabakhsh E, Bryce DM, Lefebvre KJ, Schild-Poulter C: RanBPM has proapoptotic activities that regulate cell death pathways in response to DNA damage. Mol Cancer Res. 2009, 7: 1962-1972. 10.1158/1541-7786.MCR-09-0098.PubMedView Article
- Santt O, Pfirrmann T, Braun B, Juretschke J, Kimmig P, Scheel H, Hofmann K, Thumm M, Wolf DH: The Yeast GID Complex, a Novel Ubiquitin Ligase (E3) Involved in the Regulation of Carbohydrate Metabolism. Mol Biol Cell. 2008, 19: 3323-3333. 10.1091/mbc.E08-03-0328.PubMedPubMed CentralView Article
- Zhu Y, Wang Y, Xia C, Li D, Li Y, Zeng W, Yuan W, Liu H, Zhu C, Wu X, Liu M: WDR26: a novel Gbeta-like protein, suppresses MAPK signaling pathway. J Cell Biochem. 2004, 93: 579-87. 10.1002/jcb.20175.PubMedView Article
- Kobielak A, Pasolli HA, Fuchs E: Mammalian formin-1 participates in adherens junctions and polymerization of linear actin cables. Nature Cell Biol. 2004, 6: 21-30. 10.1038/ncb1075.PubMedPubMed CentralView Article
- Obayashi T, Nishida K, Kasahara K, Kinoshita K: ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. Plant Cell Physiol. 2011, 52: 213-219. 10.1093/pcp/pcq203.PubMedPubMed CentralView Article
- Harrison SJ, Mott EK, Parsley K, Aspinall S, Gray JC, Cottage A: A rapid and robust method of identifying transformed Arabidopsis thaliana seedlings following floral dip transformation. Plant Methods. 2006, 2: 19-25. 10.1186/1746-4811-2-19.PubMedPubMed CentralView Article
- Karimi M, Inzé D, Depicker A: GATEWAY vectors for Agrobacterium-mediated plant transformation. Trends Plant Sci. 2002, 7: 193-195. 10.1016/S1360-1385(02)02251-3.PubMedView Article
- Halada P, Man P, Grebenova D, Hrkal Z, Havlicek V: Identification of HL60 proteins affected by 5-aminolevulinic acid-based photodynamic therapy using mass spectrometric approach. Collect Czech Chem Commun. 2001, 66: 1720-1728. 10.1135/cccc20011720.View Article
- Laemmli UK: Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970, 227: 680-685. 10.1038/227680a0.PubMedView Article
- Binarová P, Cenklová V, Procházková J, Doskočilová A, Volc J, Vrlík M, Bogre L: gamma-Tubulin Is Essential for Acentrosomal Microtubule Nucleation and Coordination of Late Mitotic Events in Arabidopsis. Plant Cell. 2006, 18: 1199-1212. 10.1105/tpc.105.038364.PubMedPubMed CentralView Article
- Letunic I, Doerks T, Bork P: SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res. 2011, 1-4.
- Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A: The Pfam protein families database. Nucleic Acids Res. 2008, 36: D281-8. 10.1093/nar/gkn226.PubMedPubMed CentralView Article
- Larkin M, Blackshields G, Brown NP, Chenna R, McGettigan P, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG: Clustal W and Clustal X version 2.0. Bioinformatics. 2007, 23: 2947-2958. 10.1093/bioinformatics/btm404.PubMedView Article
- Xao X, Xue Y: DOG 1.0: illustrator of protein domain structures. Cell Res. 2009, 19: 271-273. 10.1038/cr.2009.6.View Article
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.