Conserved phosphorylation of serines in the Ser-X-Glu/Ser(P) sequences of the vitamin K-dependent matrix Gla protein from shark, lamb, rat, cow, and human.

The present studies demonstrate that matrix Gla protein (MGP), a 10-kDa vitamin K-dependent protein, is phosphorylated at 3 serine residues near its N-terminus. Phosphoserine was identified at residues 3, 6, and 9 of bovine, human, rat, and lamb MGP by N-terminal protein sequencing. All 3 modified serines are in tandemly repeated Ser-X-Glu sequences. Two of the serines phosphorylated in shark MGP, residues 2 and 5, also have glutamate residues in the n + 2 position in tandemly repeated Ser-X-Glu sequences, whereas the third, shark residue 3, would acquire an acidic phosphoserine in the n + 2 position upon phosphorylation of serine 5. The recognition motif found for MGP phosphorylation, Ser-X-Glu/Ser(P), has been seen previously in milk caseins, salivary proteins, and a number of regulatory peptides. A review of the literature has revealed an intriguing dichotomy in the extent of serine phosphorylation among secreted proteins that are phosphorylated at Ser-X-Glu/Ser(P) sequences. Those phosphoproteins secreted into milk or saliva are fully phosphorylated at each target serine, whereas phosphoproteins secreted into the extracellular environment of cells are partially phosphorylated at target serine residues, as we show here for MGP and others have shown for regulatory peptides and the insulin-like growth factor binding protein 1. We propose that the extent of serine phosphorylation regulates the activity of proteins secreted into the extracellular environment of cells, and that partial phosphorylation can therefore be explained by the need to ensure that the phosphoprotein be poised to gain or lose activity with regulated changes in phosphorylation status.(ABSTRACT TRUNCATED AT 250 WORDS)     

Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome

The current progression from genomics to proteomics is fueled by the realization that many properties of proteins (e.g., interactions, post-translational modifications) cannot be predicted from DNA sequence. Although it has become feasible to rapidly identify proteins from crude cell extracts using mass spectrometry after two-dimensional electrophoretic separation, it can be difficult to elucidate low-abundance proteins of interest in the presence of a large excess of relatively abundant proteins. Therefore, for effective proteome analysis it becomes critical to enrich the sample to be analyzed in subfractions of interest. For example, the analysis of protein kinase substrates can be greatly enhanced by enriching the sample of phosphorylated proteins. Although enrichment of phosphotyrosine-containing proteins has been achieved through the use of high-affinity anti-phosphotyrosine antibodies, the enrichment of phosphoserine/threonine-containing proteins has not been routinely possible. Here, we describe a method for enriching phosphoserine/threonine-containing proteins from crude cell extracts, and for subsequently identifying the phosphoproteins and sites of phosphorylation. The method, which involves chemical replacement of the phosphate moieties by affinity tags, should be of widespread utility for defining signaling pathways and control mechanisms that involve phosphorylation or dephosphorylation of serine/threonine residues.     

Characterization of the phosphoserine of pepsinogen using 31P nuclear magnetic resonance: corroboration of X-ray crystallographic results

The endogenous phosphoserine residue in porcine pepsinogen has been titrated with use of phosphorus-31 nuclear magnetic resonance (31P NMR). It has an observed pKa2 of 6.7 and a narrow line width (congruent to 10 Hz). The phosphate can be readily removed by an acid phosphatase from potato; however, it is resistant to hydrolysis by several alkaline phosphatases. The X-ray crystal structure of porcine pepsinogen at 1.8-A resolution [James, M. N. G., & Sielecki, A. (1986) Nature (London) 319, 33-38] shows a rather weak and diffuse region of electron density in the vicinity of the phosphorylated serine residue. This suggests considerable dynamic mobility or conformational disorder of the phosphate. In order to define more fully this behavior, the NMR data have been used to corroborate these crystallographic results. All these physical data are consistent with a highly mobile phosphoserine residue on the surface of the zymogen and freely exposed to solvent. In addition, certain properties of this phosphoserine moiety on pepsinogen are similar to those of one of the phosphorylated residues of ovalbumin. The possible significance of this is discussed.     

Interleukin 1 and tumour necrosis factor increase phosphorylation of the small heat shock protein. Effects in fibroblasts, Hep G2 and U937 cells

Interleukin 1 alpha and tumour necrosis factor-alpha stimulated phosphorylation of three 27 kDa phosphoproteins in MRC-5 fibroblasts which was sustained for up to 2 h after adding the cytokines. All three phosphoproteins were immunoprecipitated by a specific antiserum to the small mammalian heat shock protein, hsp 27. The three phosphoproteins from stimulated or control cells contained phosphoserine but not phosphothreonine or phosphotyrosine. Similar increases in phosphorylation of immunoprecipitable 27 kDa proteins were seen in U937 cells stimulated by TNF alpha and Hep G2 cells stimulated by IL1 alpha.     

Biosynthesis of phosphoserine in the Methanococcales

Methanococcus maripaludis and Methanocaldococcus jannaschii produce cysteine for protein synthesis using a tRNA-dependent pathway. These methanogens charge tRNA(Cys) with l-phosphoserine, which is also an intermediate in the predicted pathways for serine and cystathionine biosynthesis. To establish the mode of phosphoserine production in Methanococcales, cell extracts of M. maripaludis were shown to have phosphoglycerate dehydrogenase and phosphoserine aminotransferase activities. The heterologously expressed and purified phosphoglycerate dehydrogenase from M. maripaludis had enzymological properties similar to those of its bacterial homologs but was poorly inhibited by serine. While bacterial enzymes are inhibited by micromolar concentrations of serine bound to an allosteric site, the low sensitivity of the archaeal protein to serine is consistent with phosphoserine's position as a branch point in several pathways. A broad-specificity class V aspartate aminotransferase from M. jannaschii converted the phosphohydroxypyruvate product to phosphoserine. This enzyme catalyzed the transamination of aspartate, glutamate, phosphoserine, alanine, and cysteate. The M. maripaludis homolog complemented a serC mutation in the Escherichia coli phosphoserine aminotransferase. All methanogenic archaea apparently share this pathway, providing sufficient phosphoserine for the tRNA-dependent cysteine biosynthetic pathway.     

Oligophosphopeptides of varied structural complexity derived from the egg phosphoprotein, phosvitin

Phosvitins are the principal phosphoproteins in the eggs of oviparous vertebrates. They have an exceptionally high serine content and most, or even all, of the serine residues are esterified to phosphate. The phosphorylated residues tend to occur in uninterrupted runs of as many as 28 phosphoserines (as inXenopus phosvitin). This unique structural feature gives phosvitins extraordinary properties and can be expected to play a key role in phosvitin function. For example, the concentration of phosphate groups provides for numerous highly efficient metal-binding sites in clusters. The mode of binding had been shown to be affected by the size of the protein and the degree to which serine residues are phosphorylated. For structure-function studies of phosvitins (and other polyphospho-proteins), phosphopeptides of differentiated structural complexity are desirable. Such model peptides were produced in this work by limited proteolysis of chicken phosvitin, and oligophosphopeptides of widely varying sizes, phosphoserine content, and sequence were purified and characterized. These include phosvitin segments containing one, two, or several oligophosphoserine runs, corresponding to segments of the N-terminal, C-terminal, and core sequence of the protein.     

Phosphoserine phosphatase of human brain: Partial purification,characterization, regional distribution,and effect of certain modulators including psychoactive drugs

Phosphoserine phosphatase (PSPase), a cytosolic enzyme has been purified 106 fold from human brain, by employing conventional protein purification techniques. The use of MgCl₂ (10 mM) and chloroform treatment, during purification enabled the removal of non-specific proteins. The final enzyme preparation exhibited a broad pH optimum of 5.6–6.6 and could dephosphorylate bothl andd enantiomers of the phosphoserine, but with different Km values for O-P-L serine (3.6×10^–5M) and O-P-D serine (1×10^–4M). Enzyme activity was found to be specific for phosphoserine, whereas other phosphoesters including phosphothreonine and phosphoproteins such as casein and phosvitin were found to be poor substrates. The enzyme activity was uncompetitively inhibited byl-serine. Further the PSPase activity was inhibited by vanadate, (41%), trifluoperazine (23%), chlorpromazine (34%) at an equimolar concentration of 1 mM, whereas lithium and ethanol did not influence the enzyme activity. Minor tranquilizers such as diazepam and chlordiazepoxide activated the enzyme activity to an extent of 13% and 59% respectively. In addition, species and regionwise heterogeneity was observed with respect to distribution of enzyme activity in six major areas of human, rabbit and rat brains.     

Phosphoproteins and the phosphoenolpyruvate:sugar phosphotransferase system of Streptococcus salivarius. Detection of two different ATP-dependent phosphorylations of the phosphocarrier protein HPr

Phosphoproteins which arise from incubation of Streptococcus salivarius ATCC25975 crude extracts with [32P]phosphoenolpyruvate and [gamma-32P]ATP, were separated and detected by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and autoradiography. These procedures were carried out using the methodology that has been developed to allow for the detection of phosphoproteins containing 1-P-histidinyl and 3-P-histidinyl residues, and also to distinguish between these and phosphoproteins containing acid-stable phosphoamino acids such as phosphoserine, phosphothreonine, and phosphotyrosine. Extracts of cells which had been grown with various sugars as carbon sources were investigated to determine both constitutive and inducible phosphoproteins. No evidence was found for phosphoproteins specifically induced by a sugar, and in particular no evidence was found for any IIIsugar phosphocarrier protein of the phosphoenolpyruvate:sugar phosphotransferase system (PTS). Incubation with [gamma-32P]ATP showed that histidine-containing phosphocarrier protein (HPr) of the PTS could be phosphorylated to give both acid-stable and acid-labile phosphoamino acid residues. The acid-labile ATP-dependent phosphorylation activity was activated by glucose-6-P and appeared to produce a 3-P-histidinyl residue in HPr.     

Serine synthesis in cyanobacteria by a nonphotorespiratory pathway

The pathway of serine synthesis was investigated in six species of cyanobacteria: Anabaena cylindrica, A. variabilis, A. flos-aquae, Coccochloris peniocystis, Gleo-capsa alpicola and Phormidium molle . Activity of the enzymes phosphoglycerate (PGA) dehydrogenase (EC 1.1.1.95), phosphoserine transaminase (EC 2.6.1.52) and phosphoserine phosphatase (EC 3.1.3.3) was detected in vitro in all species, but no PGA phosphatase (EC 3.1.3.20) or hydroxypyruvate reductase (EC 1.1.1.26) activity could be detected. Metabolism of [1-¹⁴C]PGA by cell-free extracts of C. peniocystis resulted in the labelling of serine, alanine and aspartate, which represented 84, 11 and 4% of the labelled amino acid pool, respectively, Labelled serine isolated from these experiments was 100% carboxyl-labelled indicating that it was formed directly from PGA. The labelling of serine was markedly reduced by 5 mM phosphoserine. These in vitro findings indicate that cyanobacteria are capable of synthesizing serine directly from PGA, independent of ribulose-1.5-bisphosphate oxidation, and that the route of serine synthesis via phosphohydroxypyruvate and phosphoserine is the predominant pathway in these organisms.     

Protein phosphorylation in irradiated human melanoma cells

In the present study, we examined the response of confluent, primary human fibroblasts and cells of a melanoma (YUSAC2) cell line to ionizing radiation mediated through post-translational protein phosphorylation. Since the purpose of our study was to identify novel radiation-induced phosphoproteins in the DNA damage stress response of melanoma cells, we were primarily interested in changes in protein phosphoserine expression at early times after irradiation. Our rationale was that by examining the overall protein phosphorylation profile (the phosphoproteome) in irradiated cells, we might discover novel radiation-induced phosphoproteins that distinguish fibroblasts from melanoma cells. Cell proteins were separated by gel electrophoresis and phosphoproteins were identified by Western blot analysis using nonspecific anti-phosphoamino acid antibodies. This approach was not pursued previously since adequate antibodies for examining global protein phosphoserine expression were unavailable. While some radiation-induced phosphoprotein changes in high-abundance proteins were identified, in general the sensitivity of this approach was not sufficient to detect changes in low-abundance, regulatory proteins. Characterization of these phosphoproteins will require greater enrichment of low-abundance proteins.     

Role of the N-terminal region of the regulatory light chain in the dephosphorylation of myosin by myosin light chain phosphatase.

Myosin regulatory light chain (RLC) is phosphorylated at various sites at its N-terminal region, and heterotrimeric myosin light chain phosphatase (MLCP) has been assigned as a physiological phosphatase that dephosphorylates myosin in vivo. Specificity of MLCP toward the various phosphorylation sites of RLC was studied, as well as the role of the N-terminal region of RLC in the dephosphorylation of myosin by MLCP. MLCP dephosphorylated phosphoserine 19, phosphothreonine 18, and phosphothreonine 9 efficiently with almost identical rates, whereas it failed to dephosphorylate phosphorylated serine 1/serine 2. Deletion of the N-terminal seven amino acid residues of RLC markedly decreased the dephosphorylation rate of phosphoserine 19 of RLC incorporated in the myosin molecule, whereas this deletion did not significantly affect the dephosphorylation rate of isolated RLC. On the other hand, deletion of only four N-terminal amino acid residues showed no effect on dephosphorylation of phosphoserine 19 of incorporated RLC. The inhibition of dephosphorylation by deletion of the seven N-terminal residues was also found with the catalytic subunit of MLCP. Phosphorylation at serine 1/serine 2 and threonine 9 did not influence the dephosphorylation rate of serine 19 and threonine 18 by MLCP. These results suggest that the N-terminal region of RLC plays an important role in substrate recognition of MLCP.     

Multiple forms of rat dentin phosphoproteins

Previous studies have shown that the phosphoprotein from rat dentin is heterogenous and can be partially separated into two fractions by ion-exchange chromatography. These proteins were further characterized by polyacrylamide gel electrophoresis, gel chromatography, and amino acid and phosphate analysis, after chromatographic separations on ion-exchange columns. On 5-15% gradient gels, the phosphoproteins extracted from rat dentin and precipitated by CaCl2 gave three Alcian blue-staining bands with apparent molecular weights in the 90-95,000 range. The two slower-moving bands corresponded to highly phosphorylated proteins (HP) that had phosphoserine contents of greater than 400 residues per thousand and contained little or no valine, leucine, phenylalanine, or arginine. The faster-moving band corresponded to a moderately phosphorylated protein that contained about 250 residues per thousand of phosphoserine and greater quantities of glutamic acid, proline, and several other amino acids than HP. The nature of the phosphoproteins in HP was further studied after total removal of the phosphate with an insoluble form of bovine intestinal alkaline phosphatase. The dephosphorylated product (dP-HP) gave a single major band on gel electrophoresis but showed evidence for two closely related NH2-terminal sequences, Asp-Asp-Asp-Asn and Asp-Asp-Pro-Asn. The dephosphorylated material was separated into two components (dP-HP1 and dP-HP2) by chromatography on QAE-Sephadex A-25. The amino acid compositions of the two components showed that they differed in their primary structures. This conclusion was verified by the finding of the proline-containing sequence in dP-HP2. In addition to these two groups of phosphoproteins, a third class, LP, contains low levels of phosphoserine and high amounts of glutamic acid (W.T. Butler, M. Bhown, M.T. DiMuzio, and A. Linde, (1981) Coll. Res. 1, 187-199).     

Fibroblast growth factor receptor 2 phosphorylation on serine 779 couples to 14-3-3 and regulates cell survival and proliferation

The fibroblast growth factors (FGFs) exert their diverse (or pleiotropic) biological responses through the binding and activation of specific cell surface receptors (FGFRs). While FGFRs are known to initiate intracellular signaling through receptor tyrosine phosphorylation, the precise mechanisms by which the FGFRs regulate pleiotropic biological responses remain unclear. We now identify a new mechanism by which FGFR2 is able to regulate intracellular signaling and cellular responses. We show that FGFR2 is phosphorylated on serine 779 (S779) in response to FGF2. S779, which lies adjacent to the phospholipase Cgamma binding site at Y766, provides a docking site for the 14-3-3 phosphoserine-binding proteins and is essential for the full activation of the phosphatidylinositol 3-kinase and Ras/mitogen-activated protein kinase pathways. Furthermore, S779 signaling is essential for promoting cell survival and proliferation in both Ba/F3 cells and BALB/c 3T3 fibroblasts. This new mode of FGFR2 phosphoserine signaling via the 14-3-3 proteins may provide an increased repertoire of signaling outputs to allow the regulation of pleiotropic biological responses. In this regard, we have identified conserved putative phosphotyrosine/phosphoserine motifs in the cytoplasmic domains of diverse cell surface receptors, suggesting that they may perform important functional roles beyond the FGFRs.     

Occurrence of phosphatidyl-d-serine in the rat cerebrum

Phosphatidylserine (PS), a relatively abundant component of mammalian cell membranes, plays important roles in biological processes including apoptosis and cell signaling. It is believed that phosphatidyl-l-serine is the only naturally occurring PS. Here, we describe for the first time the occurrence of phosphatidyl-d-serine (d-PS) in rat cerebrum. Quantitative HPLC analysis of the derivatives of serine liberated from PS by hydrolysis revealed that the amount of d-PS was approximately 1% of the total PS in the cerebrum. Enzymatic cleavage of cerebrum PS with phospholipase D and phospholipase C resulted in the release of both isomers of serine and phosphoserine, respectively, providing additional evidence for the existence of d-PS. Free d-serine was incorporated into PS in an in vitro system using a cerebrum extract, and this activity was inhibited by EDTA, suggesting the occurrence of a divalent cation-dependent enzyme that synthesizes d-PS by a base-exchange reaction.     

Phosphorylation and dephosphorylation of histidine residues in proteins.

Protein phosphorylation is a key mechanism for intracellular signal transduction in both prokaryotic and eukaryotic cells. Vertebrate proteins are prevalently phosphorylated on side chains that contain a hydroxyl group, such as serine, threonine and tyrosine residues. In the past decade, however, an increasing number of examples of histidine phosphorylation has been described. Because acid treatment of phosphoproteins during purification and detection of phosphoamino acid analysis is routine, O-phosphomonoesters have been studied more often, and the existence of acid-labile phosphates has been largely overlooked. The latter class of N-phosphoamidates may well be more widespread than is generally believed, even though the O-phosphates remain the major class in terms of quantity and extent of distribution in proteins. Phosphohistidine currently is estimated to be 10- to 100-fold more abundant than phosphotyrosine, but less abundant than phosphoserine [Matthews, H.R. (1995) Pharmac. Ther. 67, 323-350.]. This minireview briefly summarizes the extensive knowledge of the key mechanisms and functions of phosphohistidine in bacteria. It also describes the still limited, yet increasing, data from homologs of the bacterial two-component system. Finally, novel mechanisms of phosphorylation and dephosphorylation of histidine residues not related to the two-component system are described.     

Phosphate Acceptor Amino Acid Residues in Structural Proteins of Rhabdoviruses

Partial acid hydrolysates of the [(32)P]phosphate- or [(3)H]serine-labeled proteins of purified vesicular stomatitis, rabies, Lagos bat, Mokola, or spring viremia of carp virions and of purified intracellular nucleocapsids of these viruses have been analyzed by paper electrophoresis for the presence of phosphorylated amino acids. Both phosphoserine and phosphothreonine, with the former predominant, were present in virion and nucleocapsid preparations that contained phosphoproteins. An exception was the fish rhabdovirus, which contained only phosphoserine. When vesicular stomatitis or rabies virus proteins were phosphorylated in a cell-free system by the virion-associated protein kinase and analyzed for the presence of phosphorylated amino acid residues, phosphoserine was again found to be more abundant than phosphothreonine. After in vitro protein phosphorylation, another phospho-compound, possibly a third phosphoamino acid, was detected in the partial acid hydrolysates of these viruses.     

Rudimentary phosvitin domain in a minor chicken vitellogenin gene

We have determined the nucleotide sequence and the derived amino acid sequence of the phosphoprotein-encoding region of the chicken vitellogenin III gene. The sequence of this minor vitellogenin could be aligned with exon 22 up to exon 27 of the previously sequenced major vitellogenin II gene (van het Schip et al., 1987). The exon 23 and 25 sequences are rich in serine codons (26% and 41%, respectively), and this region encodes at least one of the small egg yolk phosphoproteins. The major egg yolk phosphoprotein, phosvitin, is encoded by the analogous region in vitellogenin II. Comparison of the vitellogenin II and vitellogenin III sequences shows a great reduction in the size of the putative exon 23 of the latter (321 base pairs as opposed to 690). The number of serine codons is also drastically reduced from 124 in exon 23 of the vitellogenin II gene to 28 in vitellogenin III. The grouping of synonymous serine codons, as has hitherto been observed in sequenced vitellogenin phosphoproteins, has been maintained in vitellogenin III. A putative asparagine-linked N-glycosylation site which was conserved in the chicken vitellogenin II and the Xenopus laevis vitellogenin A2 gene, at the beginning of exon 23, is also present in vitellogenin III. The two chicken vitellogenins show a low conservation in the phosphoprotein-encoding region (average 33%, at the protein level) compared to that in the peripheral sequences (58% identity), which indicates that it is a rapidly evolving domain of the vertebrate vitellogenin gene.     

Histidyl-tRNA synthetase of Chinese hamster ovary cells contains phosphoserine

The Chinese hamster ovary cell line 2H2-5, which expresses elevated levels of histidyl-tRNA synthetase, was used to demonstrate that histidyl-tRNA synthetase contains phosphoserine. After growth of the cells in medium containing [32P]orthophosphate, histidyl-tRNA synthetase was isolated by partial purification and immunoprecipitation and shown to be a phosphoprotein. Phosphoamino acid analysis showed that histidyl-tRNA synthetase is phosphorylated on serine, as has previously been shown for threonyl-tRNA synthetase of CHO cells.