Preparation of raf-oncogene-specific antiserum with raf protein produced in E. coli

Analysis of RAS and drug induced homo- and heterodimerization of RAF and KSR1 proteins in living cells using split Nanoluc luciferase

The dimerization of RAF kinases represents a key event in their activation cycle and in RAS/ERK pathway activation. Genetic, biochemical and structural approaches provided key insights into this process defining RAF signaling output and the clinical efficacy of RAF inhibitors (RAFi). However, methods reporting the dynamics of RAF dimerization in living cells and in real time are still in their infancy. Recently, split luciferase systems have been developed for the detection of protein-protein-interactions (PPIs), incl. proof-of-concept studies demonstrating the heterodimerization of the BRAF and RAF1 isoforms. Due to their small size, the Nanoluc luciferase moieties LgBiT and SmBiT, which reconstitute a light emitting holoenzyme upon fusion partner promoted interaction, appear as well-suited to study RAF dimerization. Here, we provide an extensive analysis of the suitability of the Nanoluc system to study the homo- and heterodimerization of BRAF, RAF1 and the related KSR1 pseudokinase. We show that KRAS^G12V promotes the homo- and heterodimerization of BRAF, while considerable KSR1 homo- and KSR1/BRAF heterodimerization already occurs in the absence of this active GTPase and requires a salt bridge between the CC-SAM domain of KSR1 and the BRAF-specific region. We demonstrate that loss-of-function mutations impairing key steps of the RAF activation cycle can be used as calibrators to gauge the dynamics of heterodimerization. This approach identified the RAS-binding domains and the C-terminal 14-3-3 binding motifs as particularly critical for the reconstitution of RAF mediated LgBiT/SmBiT reconstitution, while the dimer interface was less important for dimerization but essential for downstream signaling. We show for the first time that BRAF^V600E, the most common BRAF oncoprotein whose dimerization status is controversially portrayed in the literature, forms homodimers in living cells more efficiently than its wildtype counterpart. Of note, Nanoluc activity reconstituted by BRAF^V600E homodimers is highly sensitive to the paradox-breaking RAFi PLX8394, indicating a dynamic and specific PPI. We report the effects of eleven ERK pathway inhibitors on RAF dimerization, incl. third-generation compounds that are less-defined in terms of their dimer promoting abilities. We identify Naporafenib as a potent and long-lasting dimerizer and show that the split Nanoluc approach discriminates between type I, I^1/2 and II RAFi. Video Abstract.

Neuronal expression of Raf protooncogene in the brain stem of adult guinea pig

The Raf protooncogenes encode for cytoplasmic serine/threonine-specific protein kinases which can be activated via growth factor receptors by phosphorylation. Immunohistochemical and Western blotting studies have proven the existence of Raf protein kinases in neurons of the cerebral cortex of rats and guinea pigs. The aim of the present study was to map the immunohistochemical distribution of Raf kinase-like staining in the brain stem of guinea pig. Polyclonal antibodies were used that were raised against a recombinant viral protein in combination with the avidin-biotin-peroxidase system for detection of immunoreactivity. Specificity of the antibodies was tested in Western blotting experiments. Cytoplasmic immunostaining was observed in motor nuclei of hypoglossal, accessory, vagus, facial, trigeminal, abducent, oculomotor and trochlear nerves, and in the nucleus ambiguus, nucleus retroambigualis, lateral vestibular nucleus, mesencephalic nucleus of the trigeminal nerve, the red nucleus, raphe nuclei and reticular formation. Scattered neurons were stained in other sensory nuclei, such as solitary tract nuclei, medial, dorsal and ventral vestibular nuclei and cochlear nuclei. The spinal trigeminal nucleus and the main sensory nucleus of the trigeminal nerve contained few medium-sized immunoreactive cells. In general, staining was mainly somatodendritic; the axonal plexus was not positive. It is concluded, that the widespread neuronal appearance of cytoplasmic Raf kinase suggests an important role in transmission of trophic and growth factor signals in these neurons.

Expression of the raf protooncogene in glial cells of the adult rat cerebral cortex, brain stem and spinal cord

The raf protooncogenes encode cytoplasmic serine/threonine-specific protein kinases which can be activated from different growth factor receptors by phosphorylation. Our previous immunohistochemical studies proved that raf kinases are present in neurons of the mammalian central nervous system. The present study describes the immunohistochemical localization of raf kinases in glia-like cells of the rat cerebral cortex, spinal cord and brain stem. Small glia-like cells measuring 8-12 microns were observed in the neocortex, the entorhinal and prepiriform allocortical areas and the subcortical white matter. In the hippocampus, the immunoreactive cells were most numerous in the fimbria, the alveus and the molecular layer of the dentate fascia. Ultrastructural studies following preembedding immunohistochemistry revealed that in the cerebral cortex only astrocytes contained raf-protein-like immunoreactivity. Our immunofluorescence studies showed, that the white matter of the spinal cord, the pyramids of the medulla and the basis of the pons contained small glia-like cells, too. No electron microscopic investigations were performed, but the location (white matter tracts) and size (6-12 microns) of these cells suggested their glial nature. On the basis of data from other cell systems we expect that raf kinases participate in growth factor- and cytokine-regulated glial functions of the mammalian central nervous system.

Immunohistochemical detection of raf protein kinase in cerebral cortical areas of adult guinea pigs and rats

The raf protooncogenes are the cellular counterparts of the v-raf oncogene expressed by a murine sarcoma virus. The raf protooncogenes encode cytoplasmic serine/threonine-specific protein kinases which can be activated from different growth factor receptors by phosphorylation. The mRNAs of raf protooncogenes are found in a large variety of normal adult tissues, including the central nervous system. As concerns the distribution and localization of their protein products (the raf kinases), very few data are to be found in the literature. This is the first detailed description of their light microscopic localization in neocortical and allocortical areas of rodents. Preembedding immunohistochemical studies were performed on vibratome sections from the brains of adult guinea pigs and albino rats. The localizations of two isoenzymes, raf-1 kinase and B-raf kinase, were studied with the help of isoenzyme-specific polyclonal antibodies. Both of the antibodies detected raf protein-like immunoreactivity in many neurons and scattered glial cells of the sensory neocortex, and the cingular, pyriform, perirhinal and entorhinal allocortical areas. Pyramidal and non-pyramidal cells of Ammon's horn, granule cells of the dentate fascia and the large neurons in the hilar region were immunoreactive, too. The findings indicated that B-raf protein kinase and raf-1 kinase are present almost ubiquitously in the neurons of the investigated cortical structures. The intensity of staining obtained with serial dilutions of the antibodies indicated that the cytoplasmic concentration of B-raf kinase is tended to be higher than that of raf-1 kinase. The present findings suggested that the raf kinases are localized in postsynaptic structures, mainly in dendrites and cell bodies. Their cytosolic localization and their ability to undergo intracellular translocation during activation and phosphorylation raise the possibility that they play a pivotal role in the intracellular signaling of neurons.

Neuronal expression of the RAF protooncogene in the spinal cord of adult guinea pigs

The cellular raf oncogenes encode cytoplasmic serine/threonine specific protein kinases. Since there are some indications that they are involved in neuronal plasticity, we investigated the localization of raf protein kinases immunohistochemically. The spinal cord of adult guinea pigs was fixed by means of transcardial perfusion, transverse sections were cut from each segment and stained with monoclonal and polyclonal antibodies, raised against synthetic raf peptide and recombinant raf protein, respectively. The motor neurons of the ventral horn and the large- and medium sized neurons of laminae I, IV, V, VI, VII and VII were stained in every segment of the spinal cord. The widespread occurrence of raf kinases in the spinal cord and the literature data indicating their participation in growth factor mediated processes, raise the possibility that the raf protooncogenes play a fundamental role in the regulation of transmembrane signalling of these neurons.

Immunohistochemical localization of raf protein kinase in dendritic spines and spine apparatuses of the rat cerebral cortex

The ultrastructural localization of raf protein (product of the raf protooncogene) in the neocortex, pyriform cortex and hippocampus of the rat has been investigated by means of pre-embedding immunohistochemistry. Specificity of the antiserum was tested with Western blotting. Besides the immunoreactivity of the dendrites, remarkably strong immunostaining of the dendritic spines and spine apparatuses was noted in each of the investigated areas. The postsynaptic densities were also stained. Since raf proteins are serine/threonine-specific protein kinases, our findings could be important steps toward the understanding of dendritic spine plasticity.

Epidermal growth factor (EGF) stimulates association and kinase activity of Raf-1 with the EGF receptor

Raf-1 serine- and threonine-specific protein kinase is transiently activated in cells expressing the epidermal growth factor (EGF) receptor upon treatment with EGF. The stimulated EGF receptor coimmunoprecipitates with Raf-1 kinase and mediates protein kinase C-independent phosphorylation of Raf-1 on serine residues. Hyperphosphorylated Raf-1 has lower mobility on sodium dodecyl sulfate gels and has sixfold-increased activity in immunocomplex kinase assay with histone H1 or Raf-1 sequence-derived peptide as a substrate. Raf-1 activation requires kinase-active EGF receptor; a point mutant lacking tyrosine kinase activity in inactive in Raf-1 coupling and association. It is noteworthy that tyrosine phosphorylation of c-Raf-1 induced by EGF was not detected in these cells. These observations suggest that Raf-1 kinase may act as an important downstream effector of EGF signal transduction.

Epidermal growth factor (EGF) stimulates association and kinase activity of Raf-1 with the EGF receptor

Raf-1 serine- and threonine-specific protein kinase is transiently activated in cells expressing the epidermal growth factor (EGF) receptor upon treatment with EGF. The stimulated EGF receptor coimmunoprecipitates with Raf-1 kinase and mediates protein kinase C-independent phosphorylation of Raf-1 on serine residues. Hyperphosphorylated Raf-1 has lower mobility on sodium dodecyl sulfate gels and has sixfold-increased activity in immunocomplex kinase assay with histone H1 or Raf-1 sequence-derived peptide as a substrate. Raf-1 activation requires kinase-active EGF receptor; a point mutant lacking tyrosine kinase activity in inactive in Raf-1 coupling and association. It is noteworthy that tyrosine phosphorylation of c-Raf-1 induced by EGF was not detected in these cells. These observations suggest that Raf-1 kinase may act as an important downstream effector of EGF signal transduction.

Transient increase of raf protein kinase-like immunoreactivity in the rat dentate gyrus during long-term potentiation

Altered levels of cellular raf proteins (products of the raf protooncogenes) have been shown in the neurons of the dentate fascia of rats in response to high-frequency stimulation, with light microscopic immunohistochemistry by using polyclonal antibodies. No raf-1-like staining was seen in unstimulated tissue, while the pan-raf antibodies revealed immunoreactivity in the cytoplasm of neurons in the Ammon's horn and dentate fascia of rats and guinea pigs. The induction of long-term potentiation in the dentate fascia of freely-moving rats triggered the appearance of raf-1-like staining and increased the number of granule cells with pan-raf-like immunoreactivity. Since these proteins are serine/threonine-specific protein kinases, their appearance in long-term potentiation may indicate the activation of important cell membrane - nucleus transduction pathways.

Mutational activation of c-raf-1 and definition of the minimal transforming sequence

A series of wild-type and mutant raf genes was transfected into NIH 3T3 cells and analyzed for transforming activity. Full-length wild-type c-raf did not show transforming activity. Two types of mutations resulted in oncogenic activity similar to that of v-raf: truncation of the amino-terminal half of the protein and fusion of the full-length molecule to gag sequences. A lower level of activation was observed for a mutant with a tetrapeptide insertion mapping to conserved region 2 (CR2), a serine- and threonine-rich domain located 100 residues amino-terminal of the kinase domain. To determine essential structural features of the transforming region of raf, we analyzed point and deletion mutants of v-raf. Substitutions of Lys-56 modulated the transforming activity, whereas mutation of Lys-53, a putative ATP binding residue, abolished it. Deletion analysis established that the minimal transforming sequence coincided precisely with CR3, the conserved Raf kinase domain. Thus, oncogenic activation of the Raf kinase can be achieved by removal of CR1 and CR2 or by steric distortion and requires retention of an active kinase domain. These findings are consistent with a protein structure model for the nonstimulated enzyme in which the active site is buried within the protein.

Mutational activation of c-raf-1 and definition of the minimal transforming sequence

A series of wild-type and mutant raf genes was transfected into NIH 3T3 cells and analyzed for transforming activity. Full-length wild-type c-raf did not show transforming activity. Two types of mutations resulted in oncogenic activity similar to that of v-raf: truncation of the amino-terminal half of the protein and fusion of the full-length molecule to gag sequences. A lower level of activation was observed for a mutant with a tetrapeptide insertion mapping to conserved region 2 (CR2), a serine- and threonine-rich domain located 100 residues amino-terminal of the kinase domain. To determine essential structural features of the transforming region of raf, we analyzed point and deletion mutants of v-raf. Substitutions of Lys-56 modulated the transforming activity, whereas mutation of Lys-53, a putative ATP binding residue, abolished it. Deletion analysis established that the minimal transforming sequence coincided precisely with CR3, the conserved Raf kinase domain. Thus, oncogenic activation of the Raf kinase can be achieved by removal of CR1 and CR2 or by steric distortion and requires retention of an active kinase domain. These findings are consistent with a protein structure model for the nonstimulated enzyme in which the active site is buried within the protein.

Expression of human c-raf-1 oncogene proteins in E. coli

Full length and truncated versions of the human c-raf-1 cDNA were cloned into the inducible E. coli expression vector pJL6. C-raf proteins of 73 kD, 57 kD and 39 kD were produced upon induction. p73 differs from normal p73 c-raf by deletion of the two first N-terminal amino acids and their replacement by 16 amino acids encoded by the vector. The p57 and p39 represent N-terminal deletions which leave the transforming protein kinase domain intact. These proteins could be readily purified from E. coli lysates by immunoprecipitation with raf-specific antisera.