Quantitative Analysis of Yeast Checkpoint Protein Kinase Activity by Combined Mass Spectrometry Enzyme Assays.

Virtually all eukaryotic cell functions and signaling pathways are regulated by protein phosphorylation. The Rad53 kinase plays crucial roles in the DNA damage response in Saccharomyces cerevisiae and is widely used as a surrogate marker for DNA damage checkpoint activation by diverse genotoxic agents. Most currently available assays for Rad53 activation are based on either electrophoretic mobility shifts or semiquantitative in situ autophosphorylation activity on protein blots. Here, we describe direct quantitative measures to assess Rad53 activity using immunoprecipitation kinase assays and quantitative mass spectrometric analysis of Rad53 activation loop autophosphorylation states. Both assays employ a highly specific Rad53 antibody, and thus enable the analysis of the untagged endogenous protein under physiological conditions. The principles of these assays are readily transferable to other protein kinases for which immunoprecipitation-grade antibodies are available, and thus potentially applicable to a wide range of eukaryotic signaling pathways beyond yeast.

Role of the N-terminal forkhead-associated domain in the cell cycle checkpoint function of the Rad53 kinase.

Forkhead-associated (FHA) domains are multifunctional phosphopeptide-binding modules and are the hallmark of the conserved family of Rad53-like checkpoint protein kinases. Rad53-like kinases, including the human tumor suppressor protein Chk2, play crucial roles in cell cycle arrest and activation of repair processes following DNA damage and replication blocks. Here we show that ectopic expression of the N-terminal FHA domain (FHA1) of the yeast Rad53 kinase causes a growth defect by arresting the cell cycle in G(1). This phenotype was highly specific for the Rad53-FHA1 domain and not observed with the similar Rad53-FHA2, Dun1-FHA, and Chk2-FHA domains, and it was abrogated by mutations that abolished binding to a phosphothreonine-containing peptide in vitro. Furthermore, replacement of the RAD53 gene with alleles containing amino acid substitutions in the FHA1 domain resulted in an increased DNA damage sensitivity in vivo. Taken together, these data demonstrate that the FHA1 domain contributes to the checkpoint function of Rad53, possibly by associating with a phosphorylated target protein in response to DNA damage in G(1).

FHA domain boundaries of the dun1p and rad53p cell cycle checkpoint kinases.

Dun1p and Rad53p of the budding yeast Saccharomyces cerevisiae are members of a conserved family of cell cycle checkpoint protein kinases that contain forkhead-associated (FHA) domains. Here, we demonstrate that these FHA domains contain 130-140 residues, and are thus considerably larger than previously predicted by sequence comparisons (55-75 residues). In vivo, expression of the proteolytically defined Dun1p FHA domain, but not a fragment containing only the predicted domain boundaries, inhibited the transcriptional induction of repair genes following replication blocks. This indicates that the non-catalytic FHA domain plays an important role in the transcriptional function of the Dun1p protein kinase.

Synapsins as major neuronal Ca2+/S100A1-interacting proteins.

The mammalian S100A1 protein can activate the invertebrate myosin-associated giant protein kinase twitchin in a Ca(2+)-dependent manner by more than 1000-fold in vitro; however, no mammalian S100-dependent protein kinases are known. In an attempt to identify novel mammalian Ca(2+)/S100A1-regulated protein kinases, brain extracts were subjected to combined Ca(2+)-dependent affinity chromatography with S100A1 and an ATP analogue. This resulted in the purification to near-homogeneity of the four major synapsin isoforms Ia, Ib, IIa and IIb. All four synapsins were specifically affinity-labelled with the ATP analogue 5'-p-fluorosulphonylbenzoyladenosine. S100A1 bound to immobilized synapsin IIa in BIAcore experiments in a Ca(2+)-dependent and Zn(2+)-enhanced manner with submicromolar affinity; this interaction could be competed for with synthetic peptides of the proposed S100A1-binding sites of synapsin. Double-labelling confocal immunofluorescence microscopy demonstrated that synapsins and S100A1 are both present in the soma and neurites of PC12 cells, indicating their potential to interact in neurons in vivo.

Expression of the AMP-activated protein kinase beta1 and beta2 subunits in skeletal muscle.

A heterotrimeric member of the AMP-activated protein kinase (AMPK) isoenzyme family was purified from rat skeletal muscle by immunoaffinity chromatography, consisting of an alpha2 catalytic and two non-catalytic subunits, beta2 and gamma1. The AMPK beta2 cDNA (271 amino acids (aa), molecular weight (MW)=30¿ omitted¿307, pI 6. 3) was cloned from skeletal muscle and found to share an overall identity of 70% with beta1 (270 aa, MW=30¿ omitted¿475, pI 6.0). In the liver AMPK beta1 subunit, Ser-182 is constitutively phosphorylated whereas in skeletal muscle beta2 isoform, we find that Ser-182 is only partially phosphorylated. In addition, the autophosphorylation sites Ser-24, Ser-25 found in the beta1 are replaced by Ala-Glu in the beta2 isoform. beta2 contains seven more Ser and one less Thr residues than beta1, raising the possibility of differential post-translational regulation. Immunoblot analysis further revealed that soleus muscle (slow twitch) contains exclusively beta1 associated with alpha2, whereas extensor digitorum longus muscle alpha2 (EDL, fast twitch) associates with beta2 as well as beta1. Sequence analysis revealed that glycogen synthase, a known AMPK substrate, co-immunoprecipitated with the AMPK alpha2beta2gamma1 complex.

Interaction of the recombinant S100A1 protein with twitchin kinase, and comparison with other Ca2+-binding proteins.

The giant myosin-associated twitchin kinase, a member of the Ca2+-regulated protein kinase superfamily, is activated by the EF-hand protein S100A1 in a Ca2+-dependent and Zn2+-enhanced manner. We used recombinant S100A1 to further characterize the interaction between the two proteins. Zn2+ enhanced the binding of Ca2+/S100A1 to twitchin kinase fragments (Kd < 50 nM) in assays using a BIAcore biosensor by reducing the S100A1 off rate. Other Ca2+-binding proteins (S100A6, calmodulin, and the calmodulin-like domain of Ca2+-dependent protein kinase alpha) bound to the kinase but did not activate it. These results indicate that binding of Ca2+-binding proteins alone is insufficient to trigger the intramolecular rearrangement of kinase autoinhibitory contacts required for twitchin kinase activation that is specifically elicited by the S100A1 protein. Kinase fragments that contained only the autoinhibited catalytic sequence or an additional immunoglobulin-like domain had very similar properties, indicating that the tethered immunoglobulin-like domain does not modulate kinase regulation.

Expression of neural BC1 RNA: induction in murine tumours.

BC1 RNA is a small cytoplasmic RNA polymerase III transcript that is expressed in the rodent nervous system. The RNA is selectively expressed in neurons where it is located in somatodendritic domains. BC1 RNA is not normally detectable in non-neuronal somatic cells; it is however expressed in germ cells and in cultured immortal cell lines of various non-neural origins. We therefore sought to establish whether the neuron-specific regulation of BC1 expression is altered in non-neural tumour cells. Oncogen and chemical carcinogen induced mouse tumours were analysed for the presence of BC1 RNA, using Northern transfer and in situ hybridisation. Here we report that BC1 RNA is selectively expressed in tumour cells, but not in corresponding normal tissues. These results indicate that neural-specific regulation of BC1 expression is lacking in murine tumour cells of non-neural origin.

Giant protein kinases: domain interactions and structural basis of autoregulation.

The myosin-associated giant protein kinases twitchin and titin are composed predominantly of fibronectin- and immunoglobulin-like modules. We report the crystal structures of two autoinhibited twitchin kinase fragments, one from Aplysia and a larger fragment from Caenorhabditis elegans containing an additional C-terminal immunoglobulin-like domain. The structure of the longer fragment shows that the immunoglobulin domain contacts the protein kinase domain on the opposite side from the catalytic cleft, laterally exposing potential myosin binding residues. Together, the structures reveal the cooperative interactions between the autoregulatory region and the residues from the catalytic domain involved in protein substrate binding, ATP binding, catalysis and the activation loop, and explain the differences between the observed autoinhibitory mechanism and the one found in the structure of calmodulin-dependent kinase I.

Substrate specificity and inhibitor sensitivity of Ca2+/S100-dependent twitchin kinases.

Myosin-associated giant protein kinases of the titin/witchin-like superfamily have previously been implicated in the regulation of muscle function, based on genetic and physiological studies. We find that recombinant constitutively active Caenorhabditis elegans and Aplysia twitchin kinase fragments differ in their catalytic activities and peptide-substrate specificities, as well as in their sensitivities to the naphthalene sulfonamide inhibitors 1-(5-chloronaphthalenesulfonyl)-1H-hexahydro-1,4-diazepine (ML-7) and 1-(5-iodonaphthalenesulfonyl)-1H-hexahydro-1,4-diazepine (ML-9). The constitutively active Aplysia twitchin kinase fragment has a remarkably high activity (Vmax > 100 mumol.min-1.mg-1) towards some substrate peptides. The autoinhibited forms of these twitchin kinases can be activated in a Ca(2+)-dependent manner by the dimeric form of the S100A1 protein (S100A1(2)). The twitchin kinase S100A1(2)-binding site can also bind Ca2+/calmodulin but neither kinase is activated by calmodulin. The data provide a functional basis for the ongoing crystallographic study of twitchin kinase fragments.

Ca2+/S100 regulation of giant protein kinases.

Protein phosphorylation by protein kinases plays a central regulatory role in cellular processes and these kinases are themselves tightly regulated. One common mechanism of regulation involves Ca2+-binding proteins (CaBP) such as calmodulin (CaM). Here we report a Ca2+-effector mechanism for protein kinase activation by demonstrating the specific and >1,000-fold activation of the myosin-associated giant protein kinase twitchin by Ca2+/S100A1(2). S100A1(2) is a member of a large CaBP family that is implicated in various cellular processes, including cell growth, differentiation and motility, but whose molecular actions are largely unknown. The S100A1(2)-binding site is a part of the autoregulatory sequence positioned in the active site that is responsible for intrasteric autoinhibition of twitchin kinase; the mechanism of autoinhibition based on the crystal structures of two twitchin kinase fragments is described elsewhere. Ca2+/S100 represents a likely physiological activator for the entire family of giant protein kinases involved in muscle contractions and cytoskeletal structure.

Studies of the calmodulin-binding site of twitchin with synthetic peptides using fluorescence and CD spectroscopy.

The calcium-dependent interaction of two synthetic peptides derived from the putative calmodulin-binding site in the protein kinase autoinhibitory region of twitchin was studied by fluorescence and CD spectroscopy. The peptides interacted with dansylcalmodulin in the presence of Ca2+ as shown by a change in the fluorescence emission spectra. Fluorescence titration of dansylcalmodulin with the peptides was used to quantify this interaction. The peptides appeared to assume a helical conformation in a non-polar environment as seen by CD spectroscopy. The ellipticity of Ca2+ calmodulin was enhanced in the presence of peptides compared with that of Ca2+ calmodulin and peptides alone, indicating that the peptides had formed a complex with calmodulin. These results support the assignment of the twitchin calmodulin-binding site.

Phosphorylation of myosin regulatory light chains by the molluscan twitchin kinase.

The unusually large (approximately 600 to > 3000 kDa) myosin-associated proteins of the titin/twitchin superfamily are considered to be important cytoskeletal rulers for thick filament assembly in muscle. This function is maintained by approximately 60-240 modular fibronectin-type-III and immunoglobulin-C2 repeats in these proteins which further contain a protein serine/threonine kinase domain of unknown function. In this study, the bacterially expressed kinase domain of Aplysia twitchin was used in order to identify a potential physiological substrate. Addition of the recombinant kinase to Aplysia actomyosin preparations resulted in the specific phosphorylation of the 19-kDa myosin regulatory light chains. The twitchin kinase phosphorylated purified light chains on Thr15 in a region which shared a high degree of similarity with the phosphorylation site for vertebrate smooth muscle myosin light chain kinase. Peptide analogs of the twitchin substrate sequence and the similar sequence in vertebrate smooth muscle myosin light chains were phosphorylated with good kinetic properties. These data reveal the first potential substrate for any of the giant protein kinases and support a dual role of twitchin in molluscan muscle as a cytoskeletal protein as well as a myosin light chain kinase.

Autophosphorylation of molluscan twitchin and interaction of its kinase domain with calcium/calmodulin.

An approximately 750-kDa member of the family of giant titin/twitchin-like myosin-associated proteins was highly purified from muscle of the marine mollusc Aplysia californica. Purified twitchin was able to autophosphorylate on threonine, which demonstrates its protein serine/threonine kinase activity. cDNA sequence analysis of the cloned kinase domain of molluscan twitchin revealed that it is most closely related with the kinase domains of Caenorhabditis elegans twitchin (62% identity) and vertebrate myosin light chain kinases (45% average identity). Analysis of the cDNA sequence further suggested the presence of a potential calmodulin-binding site in a putative autoinhibitory region. The functional activity of this site was demonstrated by the calcium-dependent binding of purified twitchin to immobilized calmodulin and the fact that this interaction could be competed with synthetic peptides deduced from the cDNA sequence. Furthermore, biotinylated calmodulin bound to immobilized twitchin in gel-overlay assays with nanomolar affinity (EC50 approximately equal to 70 nM). The potential regulation of twitchin by calcium/calmodulin indicates that titin-like molecules may serve dynamic functions during contraction-relaxation cycles in muscle in addition to their functions as cytoskeletal proteins.

cAMP-dependent phosphorylation of Aplysia twitchin may mediate modulation of muscle contractions by neuropeptide cotransmitters.

Acting through a cAMP-cAMP-dependent protein kinase (cAPK) cascade, members of two neuropeptide families, the small cardioactive peptides and myomodulins, modulate contraction amplitude and relaxation rate in the accessory radula closer (ARC) muscle of the marine mollusc Aplysia californica. An approximately 750-kDa phosphoprotein was identified in the ARC muscle as the major substrate for cAPK activated either by application of neuropeptides or by peptides released by motorneuron stimulation at physiological frequencies. Immunoblot and immunoelectron microscopy experiments revealed the widespread presence of this protein in Aplysia muscles and its colocalization with contractile filaments in the ARC muscle. Sequence analysis of proteolytic peptide fragments derived from the protein indicated that it is structurally related to the muscle protein twitchin. Finally, the level of neuropeptide-induced phosphorylation of the protein correlated well with peptidergic modulation of the relaxation rate of the muscle. We propose that twitchin in Aplysia, and perhaps in other species, may mediate the modulation of the relaxation rate of muscle contractions.

Structure, function, and phylogeny of [Arg8]vasotocin receptors from teleost fish and toad.

[Arg8]Vasotocin (AVT) is considered to be the most primitive known vertebrate neurohypophyseal peptide of the vasopressin/oxytocin hormone family and may thus be ancestral to all the other vertebrate peptide hormones. The molecular evolution of the corresponding receptor family has now been studied by cloning an AVT receptor, consisting of 435 amino acid residues, from the teleost fish, the white sucker Catostomus commersoni. Frog oocytes injected with the AVT receptor-encoding cRNA respond to the application of AVT, but not to its structural and functional counterpart isotocin, by an induction of membrane chloride currents indicating the coupling of the AVT receptor to the inositol phosphate/calcium pathway. The pharmacological properties of the expressed AVT receptor show that it represents, or is closely related to, an ancestral nonapeptide receptor: oxytocin, aspargtocin, mesotocin, and vasopressin activated the receptor, but other members of the vasopressin/oxytocin family tested showed little or no potency; antagonists of the mammalian vasopressin V1 and oxytocin receptors blocked the AVT response. Comparison of AVT receptor sequences spanning transmembrane domains two to five, deduced by cloning cDNAs from the Pacific salmon Oncorhynchus kisutch, the cave-dwelling fish Astyanax fasciatus, and the anuran Xenopus laevis, with those of their mammalian counterparts emphasizes amino acid residues that are involved in hormone binding. The presence of a 5.0-kb transcript in various teleost tissues (pituitary, liver, gills, swim bladder, and lateral line) points to a physiological role for the fish AVT receptor in metabolic, osmoregulatory, and sensory processes.

Physiology and biochemistry of peptidergic cotransmission in Aplysia.

The marine mollusc Aplysia, whose simple nervous system facilitates study of the neural basis of behavior, was used to investigate the role of peptidergic cotransmission in feeding behavior. Several novel modulatory neuropeptides were purified and localized to identified cholinergic motoneurons. Physiological and biochemical studies demonstrated that these peptides are released when the motoneurons fire at frequencies that occur during normal behavior, and that the peptides modify the relationship between muscle contraction amplitude and relaxation rate so as to maintain optimal motor output when the intensity and frequency of feeding behavior change.

Presence of a member of the Tc1-like transposon family from nematodes and Drosophila within the vasotocin gene of a primitive vertebrate, the Pacific hagfish Eptatretus stouti.

Molecular cloning of the vasotocin gene of a cyclostome, the Pacific hagfish Eptatretus stouti, reveals, in contrast to other known members of the vertebrate vasopressin/oxytocin hormone gene family, an unusual exon-intron organization. Although the location of three exons and two introns is conserved, an additional intron is present 5' of the coding region of the hagfish gene. The third intron, which is greater than 14 kilobase pairs in size, contains on the opposite DNA strand to that encoding vasotocin an open reading frame exhibiting striking similarity to the putative transposase of Tc1-like nonretroviral mobile genetic DNA elements, so far reported only from nematodes and Drosophila. The hagfish element, called Tes1, is flanked by inverted terminal repeats representing an example of the existence of a typical inverted terminal-repeat transposon within vertebrates. The presence of Tc1-like elements in nematodes, Drosophila, and cyclostomes indicates that these genetic elements have a much broader phylogenetic distribution than hitherto expected.

Vasotocin genes of the teleost fish Catostomus commersoni: gene structure, exon-intron boundary, and hormone precursor organization.

cDNA clones encoding two members of the vasotocin hormone precursor gene family have been isolated from the white sucker Catostomus commersoni. The hormone is encoded by at least two distinct genes, both of which are expressed, as indicated by Northern blot analysis. Genomic DNA amplified by the polymerase chain reaction has been used to define exon-intron boundaries. Both vasotocin genes contain introns in positions corresponding to those found in the gene of their mammalian counterpart vasopressin. The predicted vasotocin precursors show a surprising degree of sequence divergence, amounting to 45% at the amino acid level, of which only approximately half can be accounted for by conservative amino acid changes. The precursors include a hormone moiety followed by a putative neurophysin sequence that is longer at the C-terminus by a tract of some 30 amino acids by comparison to their mammalian counterpart. Each of these sequences contains a leucine-rich core segment resembling that found in copeptin, a glycopeptide moiety present in mammalian vasopressin precursors.

Molecular cloning of two distinct vasotocin precursor cDNAs from chum salmon (Oncorhynchus keta) suggests an ancient gene duplication.

The structures of two different vasotocin precursors from chum salmon brain have been elucidated through the molecular cloning of their corresponding cDNAs. Although the predicted precursors, consisting respectively of 153 and 158 amino acids, have the same structural organisation, they show 35% amino acid sequence divergence, of which only approximately half are isofunctional substitutions. Remarkably, while the C terminal segments of both precursors resemble the glycopeptide moiety of the related mammalian vasopressin precursor, both salmon precursors lack consensus sequences for N-glycosylation.