Purification of MAP-kinase protein complexes and identification of candidate components by XL-TAP-MS.

The purification of low-abundance protein complexes and detection of in vivo protein-protein interactions in complex biological samples remains a challenging task. Here, we devised crosslinking and tandem affinity purification coupled to mass spectrometry (XL-TAP-MS), a quantitative proteomics approach for analyzing tandem affinity-purified, crosslinked protein complexes from plant tissues. We exemplarily applied XL-TAP-MS to study the MKK2-Mitogen-activated protein kinase (MPK4) signaling module in Arabidopsis thaliana. A tandem affinity tag consisting of an in vivo-biotinylated protein domain flanked by two hexahistidine sequences was adopted to allow for the affinity-based isolation of formaldehyde-crosslinked protein complexes under fully denaturing conditions. Combined with 15N stable isotopic labeling and tandem MS we captured and identified a total of 107 MKK2-MPK4 module-interacting proteins. Consistent with the role of the MPK signaling module in plant immunity, many of the module-interacting proteins are involved in the biotic and abiotic stress response of Arabidopsis. Validation of binary protein-protein interactions by in planta split-luciferase assays and in vitro kinase assays disclosed several direct phosphorylation targets of MPK4. Together, the XL-TAP-MS approach purifies low abundance protein complexes from biological samples and discovers previously unknown protein-protein interactions.

Assays for MAP Kinase Activation in Magnaporthe oryzae and Other Plant Pathogenic Fungi.

Mitogen-activated protein (MAP) kinases have the hallmark motif TXY and function in key signal transduction pathways in eukaryotic organisms. Most ascogenous plant pathogenic fungi have three MAPK pathways that regulate different developmental and infection processes. In the rice blast fungus Magnaporthe oryzae, the Pmk1 and Mps1 MAP kinases with the TEY motif are essential for appressorium formation, penetration, and invasive growth. Osm1 is the third MAP kinase that has the TGY motif and functions in osmoregulation. Although orthologs of Pmk1 and Mps1 are important for pathogenesis in all the plant pathogens studied, Osm1 orthologs have species-specific roles in stress responses and pathogenesis. Because of their functions in fungal development and pathogenesis, it is important to determine the expression and activation of MAP kinases under different growth conditions or infection stages. In this chapter, we describe methods for protein extraction and detection of the activation of the three MAP kinases in M. oryzae with the commercially available anti-TpEY or anti-TpGY phosphorylation-specific antibodies. Similar approaches can be used to monitor MAP kinase activation in other plant pathogenic fungi.

High-Throughput In Vitro Identification of Direct MAPK/Erk Substrates.

Phosphorylation mediated by cellular protein kinases is an effective mechanism employed by an organism to regulate central processes such as cell-cycle progression, metabolic pathways, cytoskeletal function, cell migration and differentiation. Thus, for example, various signaling pathways utilize sequential phosphorylation events to relay external cues from the cell surface to the nucleus, where eventually gene expression profiles are altered and, consequently, changes in cell fates and function are induced. Accordingly, recognizing the direct targets of key effector kinases is of utmost importance for understanding the cellular responses to pathway activity. Here we describe a high-throughput genome-wide proteomics approach aimed at uncovering novel nuclear targets for the single Drosophila MAPK/Erk. Briefly, pools of cDNA are transcribed and translated in vitro in the presence of [35S]Methionine, generating a library of radiolabeled protein pools which are subsequently subjected to biochemical kinase assays using recombinant, active Erk2. Phosphorylated proteins representing potential MAPK/Erk substrates are then detected due to their shifted mobility on SDS-PAGE gels. This protocol can be easily adjusted and applied toward identifying targets of other kinases for which in vitro phosphorylation assays are available.

Analytical ultracentrifugation: A versatile tool for the characterisation of macromolecular complexes in solution.

Analytical ultracentrifugation, an early technique developed for characterizing quantitatively the solution properties of macromolecules, remains a powerful aid to structural biologists in their quest to understand the formation of biologically important protein complexes at the molecular level. Treatment of the basic tenets of the sedimentation velocity and sedimentation equilibrium variants of analytical ultracentrifugation is followed by considerations of the roles that it, in conjunction with other physicochemical procedures, has played in resolving problems encountered in the delineation of complex formation for three biological systems - the cytoplasmic dynein complex, mitogen-activated protein kinase (ERK2) self-interaction, and the terminal catalytic complex in selenocysteine synthesis.

Analysis of MAPK activities using MAPK-specific antibodies.

Phosphorylation of proteins by mitogen-activated protein kinases is central to many cellular processes, including signal transduction after stress encounter. Thus, assays to identify or characterize MAP kinase activities are a key tool for research in this area. While in-gel kinase assays using isotope-labeled ATP are a powerful tool to investigate the general induction of MAPK activities in any organism, alternative methods using phospho-specific MAPK antibodies are now being established for many model organisms. However, both in-gel kinase assay and phospho-specific western blot analysis do not allow for the unambiguous identification of the activated MAPK. To obtain specificity, initial immunoprecipitation purification of the kinase of interest prior to further analysis can be performed.

Affinity-based SDS PAGE identification of phosphorylated Arabidopsis MAPKs and substrates by acrylamide pendant Phos-Tag™.

Protein phosphorylation is the most abundant and best studied protein posttranslational modification, dedicated to the regulation of protein function and subcellular localization as well as to protein-protein interactions. Identification and quantitation of the dynamic, conditional protein phosphorylation can be achieved by either metabolic labeling of the protein of interest with (32)P-labeled ATP followed by autoradiographic analysis, the use of specific monoclonal or polyclonal antibodies against the phosphorylated protein species and finally by phosphoproteome delineation using mass spectrometry.Hereby we present a fourth alternative which relies on the enforced-affinity-based-electrophoretic separation of phosphorylated from non-phosphorylated protein species by standard SDS-PAGE systems co-polymerized with Phos-Tag™ and Mn(2+) or Zn(2+) cations. Phosphate groups of phosphorylated Ser, Thr, and Tyr residues form complexes with Mn(2+) and Zn(2+) cations with polyacrylamide immobilized Phos-Tag™. Following appropriate treatment of the gels, separated proteins can be quantitatively transferred to PVDF or nitrocellulose membranes and probed with common-not phosphorylation state specific-antibodies and delineate the occurrence of a certain phosphoprotein species against its non-phosphorylated counterpart.

Rapid mutagenesis-based analysis of phosphorylation sites in mitogen-activated protein kinase substrates.

In eukaryotes, mitogen-activated protein kinases (MAPKs) are one of the best studied pathways for posttranslational modification-mediated regulation of protein functions. Here, we describe a rapid in vitro method to screen potential protein phosphorylation sites targeted by MAPKs. The method is based on PCR-mediated mutagenesis together with a type IIs restriction digest. Screening for the successfully mutated clones is further facilitated through introduction of a second diagnostic restriction site. Besides time-saving, this reduces the cost for sequencing confirmation of the positive clones, which are used for subsequent recombinant protein production and kinase assay validation.

Quantitative phosphoproteomic analysis using iTRAQ method.

The MAPK (mitogen-activated kinase) cascade plays important roles in plant perception of and reaction to developmental and environmental cues. Phosphoproteomics are useful to identify target proteins regulated by MAPK-dependent signaling pathway. Here, we introduce the quantitative phosphoproteomic analysis using a chemical labeling method. The isobaric tag for relative and absolute quantitation (iTRAQ) method is a MS-based technique to quantify protein expression among up to eight different samples in one experiment. In this technique, peptides were labeled by some stable isotope-coded covalent tags. We perform quantitative phosphoproteomics comparing Arabidopsis wild type and a stress-responsive mapkk mutant after phytotoxin treatment. To comprehensively identify the downstream phosphoproteins of MAPKK, total proteins were extracted from phytotoxin-treated wild-type and mapkk mutant plants. The phosphoproteins were purified by Pro-Q(®) Diamond Phosphoprotein Enrichment Kit and were digested with trypsin. Resulting peptides were labeled with iTRAQ reagents and were quantified and identified by MALDI TOF/TOF analyzer. We identified many phosphoproteins that were decreased in the mapkk mutant compared with wild type.

Protein kinase assays for measuring MPF and MAPK activities in mouse and rat oocytes and early embryos.

Protein phosphorylation plays a pivotal role in cell cycle regulation. MPF (M-phase Promoting Factor) and MAPK (Mitogen-activated protein kinase) are two major kinases driving oocyte maturation and early embryonic divisions. Their activities can be measured experimentally with kinase assays that use specific exogenous substrates. The activities of MPF and MAPK are measured using histone H1 kinase and MBP (Myelin Basic Protein) kinase assays, respectively. Here, we describe detailed procedures for measuring these two activities in mouse and rat oocytes and in early mouse embryos. The assays we describe can be performed using very small amounts of biological material and produce clearly discernible measurements of histone H1 and MBP kinase activities.

Molecular characterization of RsMPK2, a C1 subgroup mitogen-activated protein kinase in the desert plant Reaumuria soongorica.

Reaumuria soongorica (Pall.) Maxim. is a short woody shrub widely found in semi-arid areas of China, and can survive severe environmental stresses. To understand its potential signaling transduction pathway in stress tolerance, we investigated the participation of mitogen-activated protein kinases (MAPKs) as possible mediators of abiotic stresses. A novel MAP kinase cDNA (RsMPK2) that encodes a 374 amino acid protein was isolated from R. soongorica. RsMPK2 belongs to the C1 subgroup, which is still functionally uncharacterized compared to groups A and B; and contains all 11 of the conserved MAPK subdomains and the TEY phosphorylation motif. RsMPK2 is expressed in vegetative (root, stem, leaf and callus) and reproductive (flower) organs. The transcripts of RsMPK2 were rapidly accumulated at high levels when R. soongorica was subjected to dehydration, salinity conditions and treatment with abscisic acid or hydrogen peroxide. Growth analysis of Escherichia coli (srl::Tn10) cells transformed with pPROEXHT-RsMPK2 showed that the expression products of RsMPK2 do not act as an osmoprotectant. But, the inhibition of RsMPK2 expression by the inhibitor U0126 induced a decrease of antioxidant enzyme activity under stresses, indicating that RsMPK2 is involved in the regulation of the antioxidant defense system in the response to stress signaling.

A "molecular evolution" approach for isolation of intrinsically active (MEK-independent) MAP kinases.

Mitogen-activated protein (MAP) kinases are a large family of enzymes composed of about four subfamilies, each containing several isoforms and splicing variants. Many MAP kinases are coexpressed in each eukaryotic cell and coactivated in response to various stimuli. It is, therefore, difficult to explore the specific downstream effects of each species of MAPK. Expression of an intrinsically active variant of a MAPK, while other MAPKs are not active, allows for tracking of a specific array of substrates, target genes, and biological/pathological effects corresponding to the expressed molecule. This chapter describes a method for obtaining such intrinsically active MAPKs. Because of the unique mode of MAPK activation, which is absolutely dependent on unconventional phosphorylation (on neighboring Thr + Tyr residues), a rational design of mutations that would render the kinase intrinsically active is currently unfeasible. Our method is based, therefore, on a "Molecular Evolution" approach that uses the power of yeast genetics and is unbiased toward the mutation sites. We describe in detail how to prepare a large population of randomly mutated molecules of the desired MAPK and how to screen this library in a yeast strain lacking the relevant MAPK kinase (MAPKK). The idea is to identify MAPK variants that are fulfilling all MAPK functions and allow growth of this strain - namely, MAPK molecules that function biologically in the complete absence of their upstream activator. We further describe the details of the "plasmid-loss" assay used for distinguishing between true positive and false positive clones. Finally, we report on a new yeast strain lacking four MAPKKs that could serve as a universal target for screening for active MAPK of all subfamilies.

The pmk1-like mitogen-activated protein kinase from Lecanicillium (Verticillium) fungicola is not required for virulence on Agaricus bisporus.

In plant-pathogenic fungi, the pmk1 mitogen-activated protein kinase (MAPK) signalling pathway plays an essential role in regulating the development of penetration structures and the sensing of host-derived cues, but its role in other pathosystems such as fungal-fungal interactions is less clear. We report the use of a gene disruption strategy to investigate the pmk1-like MAPK, Lf pmk1 in the development of Lecanicillium fungicola (formerly Verticillium fungicola) infection on the cultivated mushroom Agaricus bisporus. Lf pmk1 was isolated using a degenerate PCR-based approach and was shown to be present in a single copy by Southern blot analysis. Quantitative RT-PCR showed the transcript to be fivefold upregulated in cap lesions compared with pure culture. Agrobacterium-mediated targeted disruption was used to delete a central portion of the Lf pmk1 gene. The resulting mutants showed normal symptom development as assessed by A. bisporus mushroom cap assays, sporulation patterns were normal and there were no apparent changes in overall growth rates. Our results indicate that, unlike the situation in fungal-plant pathogens, the pmk1-like MAPK pathway is not required for virulence in the fungal-fungal interaction between the L. fungicola pathogen and A. bisporus host. This observation may be of wider significance in other fungal-fungal and/or fungal-invertebrate interactions.

Identity of an ABA-activated 46 kDa mitogen-activated protein kinase from Zea mays leaves: partial purification, identification and characterization.

Mitogen-activated protein kinase (MAPK) cascades have been shown to be important components in abscisic acid (ABA) signal transduction pathway. In this study, a 46 kDa MAPK (p46MAPK) induced by ABA was partially purified from maize (Zea mays) by Q-Sepharose FF, Phenyl-Sepharose FF, Resource Q, Mono QTM 5/50 GL, poly-L-lysine-agarose, and Superdex 75 prep-grade columns, and was identified as ZmMAPK5 (gi|4239889) by the matrix-assisted laser desorption/ionization time-of-flight/time-of-flight (MALDI-TOF/TOF) mass spectrometry. Furthermore, the kinase showed optimal activity at pH 8.0, 30 degrees C, and 10 mM MgCl(2); the K(m) for myelin basic protein (MBP) substrate and ATP were 0.13 microg microl(-1) and 62 microM, respectively. MBP was the preferred substrate, of which the threonine residue was phosphorylated. Finally, the kinase was found to respond to diverse extracellular stimuli. These results enable us to further reveal the function of the ZmMAPK5 in ABA signaling.

Activation of a nuclear-localized SIPK in tobacco cells challenged by cryptogein, an elicitor of plant defence reactions.

When a plant cell is challenged by a well-defined stimulus, complex signal transduction pathways are activated to promote the modulation of specific sets of genes and eventually to develop adaptive responses. In this context, protein phosphorylation plays a fundamental role through the activation of multiple protein kinase families. Although the involvement of protein kinases at the plasma membrane and cytosolic levels are now well-documented, their nuclear counterparts are still poorly investigated. In the field of plant defence reactions, no known study has yet reported the activation of a nuclear protein kinase and/or its nuclear activity in plant cells, although some protein kinases, e.g. MAPK (mitogen-activated protein kinase), are known to be translocated into the nucleus. In the present study, we investigated the ability of cryptogein, a proteinaceous elicitor of tobacco defence reactions, to induce different nuclear protein kinase activities. We found that at least four nuclear protein kinases are activated in response to cryptogein treatment in a time-dependent manner, some of them exhibiting Ca(2+)-dependent activity. The present study focused on one 47 kDa protein kinase with a Ca(2+)-independent activity, closely related to the MAPK family. After purification and microsequencing, this protein kinase was formally identified as SIPK (salicyclic acid-induced protein kinase), a biotic and abiotic stress-activated MAPK of tobacco. We also showed that cytosolic activation of SIPK is not sufficient to promote a nuclear SIPK activity, the latter being correlated with cell death. In that way, the present study provides evidence of a functional nuclear MAPK activity involved in response to an elicitor treatment.

Characterization of PsMPK2, the first C1 subgroup MAP kinase from pea (Pisum sativum L.).

Mitogen-activated protein kinase (MAPK) cascades play a key role in plant growth and development as well as in biotic and abiotic stress responses. They are classified according to their sequence homology into four major groups (A-D). A large amount of information about MAPKs in groups A and B is available but few data of the C group have been reported. In this study, a C1 subgroup MAP kinase cDNA, PsMPK2, was isolated from Pisum sativum. PsMPK2 is expressed in vegetative (root and leaf) and reproductive (stamen, pistil and fruit) organs. Expression of PsMPK2 in Arabidopsis thaliana shows that mechanical injury and other stress signals as abscisic acid, jasmonic acid and hydrogen peroxide increase its kinase activity, extending previous results indicating that C1 subgroup MAPKs may be involved in the response to stress.

Le.MAPK and its interacting partner, Le.DRMIP, in fruiting body development in Lentinula edodes.

Development in shiitake mushroom, Lentinula edodes, is a unique process and studies of the molecular basis of this process may lead to improvement in mushroom cultivation. Previous studies have identified a number of signal transduction genes related to mushroom development, but those genes have not been well characterized. The present work characterized a developmentally regulated MAP kinase, Le.MAPK, and its interaction with a novel gene, Le.DRMIP in the signal transduction pathway. The expression profiles of these two genes reveal their importance in fruiting body initiation and development; the Le.DRMIP transcript is localized predominantly in the developing young fruiting body and gills, which further signifies its role in cell differentiation during mushroom development.

Isolation of intrinsically active mutants of MAP kinases via genetic screens in yeast.

Intrinsically active variants of a protein are powerful tools for deciphering the specific functions of that protein. Since the catalytic activity of such variants is spontaneously active in vivo, they can disclose very accurately biochemical and biological functions of the parental protein. It is particularly important to obtain intrinsically active variants of individual MAP kinases. This is because in response to extracellular signals, more than one MAPK is typically concomitantly activated making it difficult to reveal their individual functions and downstream targets. Until very recently intrinsically active variants were not available for MAP kinases because of their unusual mechanism of activation that requires dual phosphorylation on neighboring Thr and Tyr residues. It is not known how to mimic the phospho-Thr-Xaa-phospho-Tyr motif by mutagenesis. We describe here a genetic screen in yeast that we successfully used to isolate bona fide intrinsically active variants of the yeast MAP kinase Hog1 and all isoforms of the human p38 family. We further established a screen for isolation of intrinsically active ERKs. The rationale of our screening approach is to search for MAPK molecules that are active in the absence of their activators. The method could be applied to the discovery of intrinsically active variants of any MAP kinase of any organism. We describe in detail the rationale, the steps that should be taken for establishment of such a screen and a step-by-step protocol for carrying out the screen.

The expression of the homologue of the Caenorhabditis elegans lin-45 raf is regulated in the motile stages of the plant parasitic nematode Meloidogyne artiellia.

The Ras-MAPK signal transduction pathway controls multiple developmental events and is involved in the processing of olfactory information in the free living nematode Caenorhabditis elegans. We have studied the Ras-MAPK pathway in the plant parasitic nematode Meloidogyne artiellia. The genes Mt-let-60, Mt-lin-45, Mt-mek-2 and Mt-mpk-1 have been isolated and sequenced. Each of them shows a high level of sequence similarity to its presumed ortholog in C. elegans and key functional domains are structurally conserved. Furthermore, we show that the M. artiellia recombinant MEK-2 protein can phosphorylate and activate the M. artiellia recombinant MPK-1 and the recombinant MEK-2 itself can be phosphorylated and activated by immunoprecipitated mammalian Raf. Surprisingly, the Mt-lin-45 message is not detectable in freshly emerged juveniles or in male specimens, suggesting that it may be quickly degraded in these life stages.

Characterisation of EmMPK1, an ERK-like MAP kinase from Echinococcus multilocularis which is activated in response to human epidermal growth factor.

Mitogen-activated protein (MAP) kinases are key regulators of cellular signalling systems that mediate responses to a wide variety of extracellular stimuli and should also play a central role in developmental mechanisms of parasitic helminths. Until now, however, no MAP kinase orthologue has been characterised in a member of this parasite group. Here, we report the identification and characterisation of such a molecule, EmMPK1, from the human parasitic cestode Echinococcus multilocularis. Using a degenerative PCR approach, we isolated and completely sequenced the 1.2kb cDNA for EmMPK1 which displays significant homologies to known MAP kinases of different phylogenetic origin. EmMPK1 contains all amino acid residues which are characteristic for MAP kinases, including a conserved TEY motif which identifies the protein as a member of the ERK subfamily of MAP kinases. The corresponding gene, emmpk1 (6.9 kb), was characterised and contained 10 introns. Southern blot hybridisation studies showed that emmpk1 is present as single copy locus in E. multilocularis. Using RT-PCR analyses we demonstrated that emmpk1 is expressed in form of three different transcripts which derive from alternative splice acceptor site utilisation at intron 9. Using EmMPK1-specific antibodies in Western blot studies and immunohistochemistry, we detected the Echinococcus protein and its phosphorylated form in the larval stages metacestode and protoscolex during in vitro cultivation and during an infection of the intermediate host. EmMPK1, immunoprecipitated from Echinococcus lysate, was able to phosphorylate myelin basic protein in activity assays, indicating that it is a functionally active MAP kinase. Finally, we also show that phosphorylation of EmMPK1 is specifically induced in vitro-cultivated E. multilocularis metacestode vesicles in response to exogenous host serum and upon addition of human epidermal growth factor. These data indicate that the E. multilocularis metacestode is able to sense epidermal growth factor from the host which results in an activation of the parasite's MAP kinase cascade.

Identification of a 115kDa MAP-kinase activated by freezing and anoxic stresses in the marine periwinkle, Littorina littorea.

The mitogen-activated protein kinase (MAPK) cascade regulates changes in gene transcription by transmitting extracellular stimuli from the plasma membrane to the cell nucleus and has an important role to play in organismal responses to environmental stresses. The activities of MAPKs were investigated in the marine gastropod mollusk, Littorina littorea, a species that tolerates both extracellular freezing and long term oxygen deprivation. In-gel kinase assays revealed the presence of two MAPKs in foot muscle and hepatopancreas, a 42 and a 115kDa protein. Immunoblot analysis showed that both were MAPK proteins and that one was the periwinkle homologue of p42(ERK2). Size exclusion chromatography confirmed the 115kDa size of the novel snail MAPK and its role as the dominant MAPK activity in foot muscle. In-gel kinase assays, immunoblotting with phospho-specific ERK antibody, as well as kinase activity profiles from hydroxyapatite chromatography demonstrated that p115 MAPK kinase activity was increased in foot muscle in response to in vivo freezing or anoxia exposures. The results suggest a role for this novel kinase in environmental stress response.