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)     

Deciliation Induces Phosphorylation of a 90-kDa Cortical Protein in Tetrahymena thermophila

ABSTRACT. We have used the anti-phosphoprotein antibody MPM-2 to examine changes in phosphorytation of cortical proteins during cilia regeneration in Tetrahymena thermophila . Although numerous cortical proteins are phosphorylated in both nondeciliated and deciliated cells, deciliation induces a dramatic increase in the phosphorylation of a 90-kDa cortical protein. The 90-kDa protein remained phosphorylated during cilia regeneration and then gradually became dephosphorylated. The 90-kDa protein was phosphorylated and dephosphorylated normally in Tetrahymena mutants that assemble short cilia, suggesting that achievement of full length is not the signal that triggers dephosphorylation of the 90-kDa protein. When initiation of cilia assembly is blocked, the 90-kDa protein becomes phosphorylated and remains phosphorylated for an extended period of time, suggesting that initiation of cilia elongation triggers eventual dephosphorylation of the 90-kDa protein, regardless of how long the cilia actually become.     

Functional proteomics analysis of signal transduction pathways of the platelet-derived growth factor beta receptor

We report efficient methods for using functional proteomics to study signal transduction pathways in mouse fibroblasts following stimulation with PDGF. After stimulation, complete cellular proteins were separated using two-dimensional electrophoresis and phosphorylated proteins were detected with anti-phosphotyrosine and anti-phosphoserine antibodies. About 260 and 300 phosphorylated proteins were detected with the anti-phosphotyrosine and anti-phosphoserine antibodies, respectively, at least 100 of which showed prominent changes in phosphorylation as a function of time after stimulation. Proteins showing major time-dependent changes in phosphorylation were subjected to in-gel digestion with trypsin and identified by mass spectroscopy using MALDI-TOF mass fingerprinting and ESI peptide sequencing. We have observed phosphorylated proteins known to be part of the PDGF signal transduction pathway such as ERK 1, serine/threonine protein kinase akt and protein tyrosine phosphatase syp, proteins such as proto-oncogene tyrosine kinase fgr previously known to participate in other signal transduction pathways, and some proteins such as plexin-like protein with no previously known function in signal transduction. Information about the phosphorylation site was obtained for proto-oncogene tyrosine kinase fgr and for cardiac alpha-actin. The methods used here have proven to be suitable for the identification of time-dependent changes in large numbers of proteins involved in signal transduction pathways.     

Highly phosphorylated bacterial proteins

We show in Gram-negative and Gram-positive bacteria the appearance of highly acidic proteins, which are highly phosphorylated. This group of proteins includes many cellular proteins, such as chaperones, biosynthetic, and metabolic enzymes. These proteins accumulate under stress conditions or under conditions, which overload the proteolytic system. Pulse chase experiments using radioactive phosphate indicate that the phosphorylated proteins have a short half-life, suggesting that they could be degradation intermediates. Moreover, results from in vitro experiments in Escherichia coli indicated that ribosomal proteins become susceptible to proteolysis after polyphosphorylation. Therefore, it is possible that the highly phosphorylated proteins represent a group of proteins tagged for degradation by phosphorylation. Such a tagging process may be involved in a general bacterial degradation pathway.     

Protein kinases phosphorylate long disordered regions in intrinsically disordered proteins

Phosphorylation is a major post‐translational modification that plays a central role in signaling pathways. Protein kinases phosphorylate substrates (phosphoproteins) by adding phosphate at Ser/Thr or Tyr residues (phosphosites). A large amount of data identifying and describing phosphosites in phosphoproteins has been reported but the specificity of phosphorylation is not fully resolved. In this report, data of kinase‐substrate pairs identified by the Kinase‐Interacting Substrate Screening (KISS) method were used to analyze phosphosites in intrinsically disordered regions (IDRs) of intrinsically disordered proteins. We compared phosphorylated and nonphosphorylated IDRs and found that the phosphorylated IDRs were significantly longer than nonphosphorylated IDRs. The phosphorylated IDR is often the longest IDR (71%) in a phosphoprotein when only a single phosphosite exists in the IDR, and when the phosphoprotein has multiple phosphosites in an IDR(s), the phosphosites are primarily localized in a single IDR (78%) and this IDR is usually the longest one (81%). We constructed a stochastic model of phosphorylation to estimate the effect of IDR length. The model that accounted for IDR length produced more realistic results when compared with a model that excluded the IDR length. We propose that the IDR length is a significant determinant for locating kinase phosphorylation sites in phosphoproteins.     

The role of vasodilator‐stimulated phosphoprotein in podocyte functioning

Vasodilator‐stimulated phosphoprotein (VASP) is a 39‐kDa protein belonging to the Ena/VASP protein family, which is involved in adhesion, migration, cell–cell interaction, and regulation of pathways connected with actin cytoskeleton remodeling. VASP is phosphorylated at Tyr39, Ser157, Ser239, Thr278, and Ser322 mainly by tyrosine kinase Abl, cAMP‐dependent protein kinase, protein kinase G, AMP‐activated protein kinase, and protein kinase D1, respectively. VASP phosphorylation, as a regulator of actin dynamics, may lead to impaired reorganization of the podocyte actin cytoskeleton not only by indirect interaction of VASP with actin but also by regulation of other signaling pathways. A few studies have shown that VASP participates in the development of renal diseases and mediates podocyte movement through its interaction with proteins of the slit diaphragm. VASP phosphorylation may cause reduced actin filament assembly in podocytes and mediate disturbances in regulation of filtration barrier permeability as a consequence of podocyte foot process effacement. In this paper, we describe the role of VASP in podocyte function, mainly in the context of actin dynamics and glomerular filtration barrier permeability. In addition, we discuss the involvement of VASP and its phosphorylated forms in the development of kidney diseases.     

Phosphoproteome analysis of the human Chang liver cells using SCX and a complementary mass spectrometric strategy

The liver is the largest organ in the body, with many complex, essential functions, such as metabolism, deintoxication, and secretion, often regulated via post-translational modifications, especially phosphorylation. Thus, the detection of phosphoproteins and phosphorylation sites is important to comprehensively explore human liver biological function. The human Chang liver cell line is among the first derived from non-malignant tissue, and its phosphoproteome profile has never been globally analyzed. To develop the complete phosphoproteome and probe the roles of protein phosphorylation in normal human liver, we adopted a shotgun strategy based on strong cation exchange chromatograph, titanium dioxide and LC-MS/MS to isolate and identify phosphorylated proteins. Two types of MS approach, Q-TOF and IT, were used and compared to identify phosphosites from complex protein mixtures of these cells. A total of 1035 phosphorylation sites and 686 phosphorylated peptides were identified from 607 phosphoproteins. A search using the public database of PhosphoSite showed that approximately 344 phosphoproteins and 760 phosphorylation sites appeared to be novel. In addition, N-terminal phosphorylated peptides were a greater fraction of all identified phosphopeptides. With GOfact analysis, we found that most of the identified phosphoproteins are involved in regulating metabolism, consistent with the liver's role as a key metabolic organ.     

Proteomic analysis of in vivo phosphorylated synaptic proteins

In the nervous system, protein phosphorylation is an essential feature of synaptic function. Although protein phosphorylation is known to be important for many synaptic processes and in disease, little is known about global phosphorylation of synaptic proteins. Heterogeneity and low abundance make protein phosphorylation analysis difficult, particularly for mammalian tissue samples. Using a new approach, combining both protein and peptide immobilized metal affinity chromatography and mass spectrometry data acquisition strategies, we have produced the first large scale map of the mouse synapse phosphoproteome. We report over 650 phosphorylation events corresponding to 331 sites (289 have been unambiguously assigned), 92% of which are novel. These represent 79 proteins, half of which are novel phosphoproteins, and include several highly phosphorylated proteins such as MAP1B (33 sites) and Bassoon (30 sites). An additional 149 candidate phosphoproteins were identified by profiling the composition of the protein immobilized metal affinity chromatography enrichment. All major synaptic protein classes were observed, including components of important pre- and postsynaptic complexes as well as low abundance signaling proteins. Bioinformatic and in vitro phosphorylation assays of peptide arrays suggest that a small number of kinases phosphorylate many proteins and that each substrate is phosphorylated by many kinases. These data substantially increase existing knowledge of synapse protein phosphorylation and support a model where the synapse phosphoproteome is functionally organized into a highly interconnected signaling network.     

Mitochondrial tyrosine phosphoproteome: new insights from an up-to-date analysis

Tyrosine phosphorylation is a newcomer in the mitochondrial signaling and is currently emerging as an important mechanism for regulating mitochondrial processes. But to what extent? By analyzing an updated draft of the mitochondrial tyrosine phosphoproteome, the following observations can be drawn: more than a hundred mitochondrial proteins undergo tyrosine phosphorylation, phosphotyrosine proteins are distributed in each of the submitochondrial compartments, and mitochondrial tyrosine phosphorylated proteins are involved in a variety of functions as metabolism (electron transport chain, Krebs cycle, fatty acid and amino acid metabolism), solute and protein transport, mitochondrial translation machinery, quality protein assessment, oxidative stress, apoptosis, fission, and other. This large and varied collection suggests that tyrosine phosphorylation could be a widespread mechanism in modulating mitochondrial functions. Moreover the in silico model is here used to explore potential effects of tyrosine phosphorylation on selected mitochondrial proteins pointing out some future perspectives in this field.     

Phosphorylation Time‐Course Study of the Response during Adenovirus Type 2 Infection

PTMs such as phosphorylations are usually involved in signal transduction pathways. To investigate the temporal dynamics of phosphoproteome changes upon viral infection, a model system of IMR‐90 cells infected with human adenovirus type 2 (Ad2) is used in a time‐course quantitative analysis combining titanium dioxide (TiO₂) particle enrichment and SILAC‐MS. Quantitative data from 1552 phosphorylated sites clustered the highly altered phosphorylated sites to the signaling by rho family GTPases, the actin cytoskeleton signaling, and the cAMP‐dependent protein kinase A signaling pathways. Their activation is especially pronounced at early time post‐infection. Changes of several phosphorylated sites involved in the glycolysis pathway, related to the activation of the Warburg effect, point at virus‐induced energy production. For Ad2 proteins, 32 novel phosphorylation sites are identified and as many as 52 phosphorylated sites on 17 different Ad2 proteins are quantified, most of them at late time post‐infection. Kinase predictions highlighted activation of PKA, CDK1/2, MAPK, and CKII. Overlaps of kinase motif sequences for viral and human proteins are observed, stressing the importance of phosphorylation during Ad2 infection.     

Further studies on the hyperphosphorylated form (p40) of the rabies virus nominal phosphoprotein (P)

We investigated possible mechanisms involved in production of a hyperphosphorylated form (p40) of rabies virus P protein, to which two dimensional (2-D) gel electrophoresis was applied. The P gene products produced in Escherichia coli cells could be detected as a single spot of unphosphorylated 37-kDa form (termed as p37-0) in a 2-D gel. The 37-kDa proteins in the virus-infected cells are composed of some phosphorylated forms, including a major p37-1 and more phosphorylated minor forms (e.g., p37-2, p37-3, etc.), but little p37-0 is detected (Eriguchi et al., 2002). When the E. coli -produced P protein analogues were incubated with BHK-21 cell lysates, heparin-sensitive phosphorylation occurred as described previously (Takamatsu et al., 1998), giving an additional 40-kDa spot. However, such a p40-like derivative displayed a little more basic pI value than that of the authentic p40 produced in the infected cells; hence, the former was termed p40-0 (pI=4.78), while the latter, p40-1 (pI=4.73). In contrast, p40 produced in the P cDNAtransfected animal cell was detected at the p40-1 position. In addition, staurosporine did not affect the p40-1 production in virus-infected nor the P cDNA-transfected animal cells, while the agent reduced production of hyperphosphorylated forms of p37, resulting in accumulation of p37-1, but not of p37-0. These results suggest that, although p37-0 may become a substrate for the heparin-sensitive protein kinase (PK) in vitro, only p37-1 is a substrate for p40 production catalyzed by heparin-sensitive PK in animal cells, and staurosporine-sensitive PK is involved in the production of more phosphorylated forms of p37, but not in p37-1 production from p37-0.     

14-3-3 Protein mediates phosphorylation of microtubule-associated protein tau by serum- and glucocorticoid-induced protein kinase 1

The microtubule-associated protein, tau, is involved in numerous neuronal processes such as vesicle transport, microtubule-plasma membrane interaction and the intracellular localization of proteins. Tau is known to be phosphorylated by several kinases such as mitogen activated protein kinase, microtubule affinity regulating kinase, and protein kinase A. We found a putative serum- and glucocorticoid-induced protein kinase 1 (SGK1) phosphorylation site within the 207GSRSRTPSLP216 tau amino acid sequence. We report here that SGK1 phosphorylates Ser214 of Tau. Using a pull-down assay, we found that 14-3-3q interacts with SGK1 and tau to form a ternary protein complex that leads to phosphorylation of tau. 14-3-3 and phosphorylated tau were mainly co-localized in the nucleus of COS-1 cells. These results demonstrate that 14-3-3 scaffolds tau with SGK1 to facilitate the phosphorylation of tau at Ser214 and to regulate its subcellular localization.     

Kinetic analysis of multisite phosphorylation using analytic solutions to Michaelis-Menten equations

Phosphorylation-induced expression or modulation of a functional protein is a common signal in living cells. Many functional proteins are phosphorylated at multiple sites and it is frequently observed that phosphorylation at one site enhances or suppresses phosphorylation at another site. Therefore, characterizing such cooperative phosphorylation is important. In this study, we determine a temporal progress curve of multisite phosphorylation by analytically integrating the Michaelis-Menten equations in time. Using this theoretical progress curve, we derive the useful criterion that an intersection of two progress curves implies the presence of cooperativity. Experiments generally yield noisy progress curves. We fit the theoretical progress curves to noisy progress curves containing 4% Gaussian noise in order to determine the kinetics of the phosphorylation. This fitting correctly identifies the sites involved in cooperative phosphorylation.     

Separation of novel phosphoproteins of Porphyromonas gingivalis using phosphate‐affinity chromatography

Phosphorylation of serine, threonine and tyrosine is a central mechanism for regulating the structure and function of proteins in both eukaryotes and prokaryotes. However, the action of phosphorylated proteins present in Porphyromonas gingivalis, a major periodontopathogen, is not fully understood. Here, six novel phosphoproteins that possess metabolic activities were identified, namely PGN_0004, PGN_0375, PGN_0500, PGN_0724, PGN_0733 and PGN_0880, having been separated by phosphate‐affinity chromatography. The identified proteins were detectable by immunoblotting specific to phosphorylated Ser (P‐Ser), P‐Thr, and/or P‐Tyr. These results imply that novel phosphorylated proteins might play an important role for regulation of metabolism in P. gingivalis.     

植物响应非生物胁迫的磷酸化修饰组学研究进展

植物具有固着生活的特点,高温、低温、干旱和盐等生境中常见的非生物胁迫会严重影响植物的生长发育。蛋白质磷酸化是植物应对非生物胁迫的重要机制,主要通过蛋白质的磷酸化和去磷酸化修饰来调控植物细胞对外界胁迫的应激反应,在植物细胞快速传递胁迫信号并激活对胁迫环境的形态、生理和分子水平适应机制的过程中起重要作用。该文主要介绍了植物磷酸化蛋白质的富集、检测和鉴定技术,并对近年来国内外有关植物响应高温、低温、干旱、淹水、盐、养分亏缺和元素毒害等非生物胁迫的磷酸化修饰蛋白组学研究进展进行综述。     

Beta-elimination coupled with tandem mass spectrometry for the identification of in vivo and in vitro phosphorylation sites in maize dehydrin DHN1 protein

Dehydrins are a group of proteins that are accumulated during environmental stress such as drought and low temperature or during late embryogenesis. In the present study, we isolated dehydrin DHN1, also known as Rab17 protein, from maize kernel by an acid extraction method, removed the phosphoric acid groups from phosphorylated residues by beta-elimination via treating the protein with barium hydroxide, and identified the sites of phosphorylation by tandem mass spectrometry. Our results showed that each of the seven contiguous serine residues (Ser78-Ser84) in the serine tract could be phosphorylated. The beta-elimination procedure was shown to be essential for the detection and subsequent site mapping of the heavily phosphorylated peptide by mass spectrometry. We also found that protein kinase CK2 could catalyze the phosphorylation of the DHN1 protein in vitro and the level of phosphorylation was comparable to that of the DHN1 isolated from maize seeds. Moreover, the in vitro phosphorylation also occurred on the serine residues in the serine tract region, suggesting that CK2 might be involved in the phosphorylation of the serine track region in maize kernel in vivo.