Phosphoproteomic analysis reveals the effects of PilF phosphorylation on type IV pilus and biofilm formation in Thermus thermophilus HB27.

Thermus thermophilus HB27 is an extremely thermophilic eubacteria with a high frequency of natural competence. This organism is therefore often used as a thermophilic model to investigate the molecular basis of type IV pili-mediated functions, such as the uptake of free DNA, adhesion, twitching motility, and biofilm formation, in hot environments. In this study, the phosphoproteome of T. thermophilus HB27 was analyzed via a shotgun approach and high-accuracy mass spectrometry. Ninety-three unique phosphopeptides, including 67 in vivo phosphorylated sites on 53 phosphoproteins, were identified. The distribution of Ser/Thr/Tyr phosphorylation sites was 57%/36%/7%. The phosphoproteins were mostly involved in central metabolic pathways and protein/cell envelope biosynthesis. According to this analysis, the ATPase motor PilF, a type IV pili-related component, was first found to be phosphorylated on Thr-368 and Ser-372. Through the point mutation of PilF, mimic phosphorylated mutants T368D and S372E resulted in nonpiliated and nontwitching phenotypes, whereas nonphosphorylated mutants T368V and S372A displayed piliation and twitching motility. In addition, mimic phosphorylated mutants showed elevated biofilm-forming abilities with a higher initial attachment rate, caused by increasing exopolysaccharide production. In summary, the phosphorylation of PilF might regulate the pili and biofilm formation associated with exopolysaccharide production.

Cutting edge: NKp80 uses an atypical hemi-ITAM to trigger NK cytotoxicity.

The human NK cell receptor NKp80 stimulates cytotoxicity upon engagement of its genetically linked ligand AICL. However, the mechanisms underlying NKp80-mediated signaling are unknown. In this study, we dissected NKp80 signaling using the NK cell line NK92MI. We demonstrated that NKp80, but not NKp80 mutated at tyrosine 7 (NKp80/Y7F), is tyrosine phosphorylated. Accordingly, NKp80/Y7F, but not NKp80/Y30F or NKp80/Y37F, failed to induce cytotoxicity. NKp80 phosphopeptides comprising the hemi-ITAM-like sequence surrounding tyrosine 7 bound Lck- and Syk-family kinases; accordingly, cross-linking of NKp80, but not NKp80/Y7F, induced Syk phosphorylation. Moreover, inhibition of Syk kinase, but not ZAP-70 kinase, impaired cytotoxic responses through NKp80. Atypical residues in the hemi-ITAM-like motif of NKp80 cause an altered stoichiometry of phosphorylation but did not substantially affect NK cytotoxicity. Altogether, these results show that NKp80 uses an atypical hemi-ITAM and Syk kinase to trigger cellular cytotoxicity.

Remote changes in the dynamics of the phosphotyrosine-binding domain of insulin receptor substrate-1 induced by phosphopeptide binding.

Protein structures consist of cooperative networks of interactions that can extend substantial distances across the protein structure and have significant consequences for stability and function. To characterize such interaction networks within the phosphotyrosine-binding domain of insulin receptor substrate-1 (IRS-PTB), we have used NMR relaxation to determine the dynamics of backbone amide groups, side chain methyl groups, and tryptophan side chain indole groups in IRS-PTB, both in the absence and in the presence of a bound phosphotyrosine-containing peptide. Although there are minimal differences between the structures of apo and peptide-bound forms, primarily localized close to the peptide binding site, we observe significant changes in dynamics for residues located remotely from the binding site. These residues are clustered together and appear to constitute a network of interactions that is coupled to the peptide binding site through intervening residues.

BRCT domains: phosphopeptide binding and signaling modules.

The BRCA1 C-terminus (BRCT) domains are essential for the tumor suppressor function of BRCA1, and have been found in a variety of proteins from bacteria to men. Recent studies demonstrate that the BRCT domain constitutes a novel phosphopeptide binding region. In this review we seek to discuss the recent biochemical and structural data that have helped elucidate the molecular basis of BRCT domain function and BRCT-mediated interactions, with special emphasis on the role of phospho-specific interactions in key networks that regulate DNA repair. Finally we offer predictions on additional phospho-interacting BRCT domains and potential in vivo binding sites for several BRCT domains.

Profiling of UV-induced ATM/ATR signaling pathways.

To ensure survival in the face of genomic insult, cells have evolved complex mechanisms to respond to DNA damage, termed the DNA damage checkpoint. The serine/threonine kinases ataxia telangiectasia-mutated (ATM) and ATM and Rad3-related (ATR) activate checkpoint signaling by phosphorylating substrate proteins at SQ/TQ motifs. Although some ATM/ATR substrates (Chk1, p53) have been identified, the lack of a more complete list of substrates limits current understanding of checkpoint pathways. Here, we use immunoaffinity phosphopeptide isolation coupled with mass spectrometry to identify 570 sites phosphorylated in UV-damaged cells, 498 of which are previously undescribed. Semiquantitative analysis yielded 24 known and 192 previously uncharacterized sites differentially phosphorylated upon UV damage, some of which were confirmed by SILAC, Western blotting, and immunoprecipitation/Western blotting. ATR-specific phosphorylation was investigated by using a Seckel syndrome (ATR mutant) cell line. Together, these results provide a rich resource for further deciphering ATM/ATR signaling and the pathways mediating the DNA damage response.

Casein phosphopeptide promotion of calcium uptake in HT-29 cells - relationship between biological activity and supramolecular structure.

Casein phosphopeptides (CPPs) form aggregated complexes with calcium phosphate and induce Ca2+ influx into HT-29 cells that have been shown to be differentiated in culture. The relationship between the aggregation of CPPs assessed by laser light scattering and their biological effect was studied using the CPPs beta-CN(1-25)4P and alpha(s1)-CN(59-79)5P, the commercial mixture CPP DMV, the 'cluster sequence' pentapeptide, typical of CPPs, and dephosphorylated beta-CN(1-25)4P, [beta-CN(1-25)0P]. The biological effect was found to be: (a) maximal with beta-CN(1-25)4P and null with the 'cluster sequence'; (b) independent of the presence of inorganic phosphate; and (c) maximal at 4 mmol.L(-1) Ca2+. The aggregation of CPP had the following features: (a) rapid occurrence; (b) maximal aggregation by beta-CN(1-25)4P with aggregates of 60 nm hydrodynamic radius; (c) need for the concomitant presence of Ca2+ and CPP for optimal aggregation; (d) lower aggregation in Ca2+-free Krebs/Ringer/Hepes; (e) formation of bigger aggregates (150 nm radius) with beta-CN(1-25)0P. With both beta-CN(1-25)4P and CPP DMV, the maximum biological activity and degree of aggregation were reached at 4 mmol.L(-1) Ca2+.

Unique structural determinants for Stat3 recruitment and activation by the granulocyte colony-stimulating factor receptor at phosphotyrosine ligands 704 and 744.

G-CSFR cytoplasmic tyrosine (Y) residues (Y704, Y729, Y744, and Y764) become phosphorylated upon ligand binding and recruit specific Src homology 2 domain-containing proteins that link to distinct yet overlapping programs for myeloid cell survival, differentiation, proliferation, and activation. The structural basis for recruitment specificity is poorly understood but could be exploited to selectively target deleterious G-CSFR-mediated signaling events such as aberrant Stat3 activation demonstrated in a subset of acute myeloid leukemia patients with poor prognosis. Recombinant Stat3 bound to G-CSFR phosphotyrosine peptide ligands pY704VLQ and pY744LRC with similar kinetics. Testing of three models for Stat3 Src homology 2-pY ligand binding in vitro and in vivo revealed unique determinants for Stat3 recruitment and activation by the G-CSFR, the side chain of Stat3 R609, which interacts with the pY ligand phosphate group, and the peptide amide hydrogen of E638, which bonds with oxygen/sulfur within the + 3 Q/C side chain of the pY ligand when it assumes a beta turn. Thus, our findings identify for the first time the structural basis for recruitment and activation of Stat3 by the G-CSFR and reveal unique features of this interaction that can be exploited to target Stat3 activation for the treatment of a subset of acute myeloid leukemia patients.

Design and functional activity of phosphopeptides with potential immunomodulating capacity, based on the sequence of Grb2-associated binder 1.

A cell membrane permeable phosphopeptide corresponding to the SHP-2 binding motif of Grb2-associated binder 1 (Gab1) interferes with the Gab1 adaptor-dependent functions and modulates B cell receptor-triggered intracellular signaling in B cell tumors.

The role of salivary peptides in dental caries.

Dental caries is a complex disease, characterized by demineralization of tooth structure. With a protective role, several salivary phosphopeptides appear to be involved in remineralization processes, delaying the loss of tooth structure. In this work we have correlated peptide saliva composition with dental caries susceptibility through the analysis of saliva and hydroxyapatite-adsorbed salivary peptides samples. Saliva samples were obtained from two groups, a caries-free and a cariessusceptible group, and were analysed using HPLC-MS and a sequential extraction with 6 m of guanidine followed by tri fluoroacetate. Data analysis has allowed us to verify a strong correlation between large amounts phosphopeptides (PRP1/3, histatin 1 and statherin), and the absence of dental caries, which reinforces the importance of these peptides in the maintenance of tooth integrity. In addition, in the caries-susceptible group a high number of peptide fragments was observed, suggesting a high proteolytic activity.

Transduction of peptide analogs of the small heat shock-related protein HSP20 inhibits intimal hyperplasia.

BACKGROUND: Human saphenous vein (HSV) is the autologous conduit of choice for peripheral vascular reconstructions. However, vasospasm can lead to early graft failure. The leading cause of delayed graft failure is intimal hyperplasia. OBJECTIVE: To develop a proteomic approach to prevent vein-graft spasm and intimal hyperplasia. METHODS: Biomimetic peptide analogs of the small heat shock-related protein HSP20, containing a protein transduction domain (PTD), a phosphorylated serine, and a sequence of HSP20 surrounding the phosphorylation site (PTD-pHSP20), or a scrambled sequence of the same amino acids surrounding the phosphorylation site (PTD-scHSP20) were synthesized. The peptides were used in muscle bath and organ culture experiments with human saphenous vein (HSV) segments. Cultured smooth muscle cell lines were used to determine the effect of the peptides on proliferation and migration. RESULTS: In HSV rings precontracted with norepinephrine, PTD-pHSP20 but not PTD-scHSP20 led to relaxation. There was no significant difference in smooth muscle cell proliferation in cells treated with PTD-pHSP20 compared with PTD-scHSP20. Treatment with PTD-pHSP20 significantly inhibited cellular migration compared with PTD-scHSP20. Control, untreated, and PTD-scHSP20-treated saphenous veins had significant increases in intimal thickness after culture. This intimal thickening was completely inhibited by treatment with PTD-pHSP20. CONCLUSIONS: Protein transduction of biologically active motifs of HSP20 can affect pathologic and physiologic responses of HSV and represents a novel proteomic-based therapeutic approach. CLINICAL RELEVANCE: We have been a part of the genomics era and are now viewing the emergence of "proteomics." The genome is linear and relatively easy to examine; however the proteome is much more complex and dynamic. In essence, the purpose of gene therapy is to manipulate the genome to produce a particular protein. This manuscript describes a new proteomic approach in which the biologically active part of a protein is directly introduced into vascular cells. Peptides were synthesized which contained a total of 24 amino acids, 11 of which represent a protein transduction domain or "carrier" while the other 13 are the biologically active "cargo." These synthetic peptides prevent spasm (contraction) and intimal hyperplasia in segments of human saphenous vein treated ex vivo. Preclinical development is currently underway to develop these molecules as a proteomic-based vein harvest solution to enhance vein-graft patency.

Binding specificity of multiprotein signaling complexes is determined by both cooperative interactions and affinity preferences.

The generation of multiprotein complexes at receptors and adapter proteins is crucial for the activation of intracellular signaling pathways. In this study, we used multiple biochemical and biophysical methods to examine the binding properties of several SH2 and SH3 domain-containing signaling proteins as they interact with the adapter protein linker for activation of T-cells (LAT) to form multiprotein complexes. We observed that the binding specificity of these proteins for various LAT tyrosines appears to be constrained both by the affinity of binding and by cooperative protein-protein interactions. These studies provide quantitative information on how different binding parameters can determine in vivo binding site specificity observed for multiprotein signaling complexes.

Heat shock protein expression in cerebral vessels after subarachnoid hemorrhage.

OBJECTIVE: The mechanisms of cerebral vasospasm after subarachnoid hemorrhage (SAH) remain controversial. Recent data have implicated two small heat shock proteins (HSPs), namely HSP20 and HSP27, in the regulation of vascular tone. Increases in the phosphorylation of HSP20 are associated with vasorelaxation, and increases in the phosphorylation of HSP27 are associated with impaired vasorelaxation. Therefore, we hypothesized that alterations in the expression and/or phosphorylation of these two small HSPs might play a role in cerebral vasospasm after SAH. METHODS: A rat model of endovascular perforation was used to induce SAH. Middle cerebral arteries were harvested from control animals, sham-treated animals, and animals with SAH, 48 hours after SAH induction. Dose-response curves for endothelium-independent (sodium nitroprusside, 10(-8) to 10(-4) mol/L) and endothelium-dependent (bradykinin, 10(-10) to 10(-5) mol/L) relaxing agents were recorded ex vivo. Physiological responses were correlated with the expression and phosphorylation of HSP20 and HSP27 by using one- and two-dimensional immunoblots. RESULTS: There was impaired endothelium-independent and endothelium-dependent relaxation in cerebral vessels after SAH. These changes were associated with decreased expression of both total and phosphorylated HSP20 and increases in the amount of phosphorylated HSP27. CONCLUSION: In this model, impaired relaxation of cerebral vessels after SAH was associated with increases in the amount of phosphorylated HSP27 and decreases in the expression and phosphorylation of HSP20. These data are consistent with alterations in the expression and phosphorylation of these small HSPs in other models of vasospasm.

The NH(2)-terminal propeptides of fibrillar collagens: highly conserved domains with poorly understood functions.

The impetus for this review comes from the recent finding that the absence of the majority of the non-triple-helical sequence in the NH(2)-terminal propeptide (N-propeptide) of the pro alpha 1(I) collagen chain fails to generate a significant phenotype in the mouse (Bornstein et al., J. Biol. Chem., 277:2605-2613, 2002). This result is in apparent conflict with those of numerous studies in vitro that have implicated the N-propeptide in a number of processes that are involved in the biogenesis, maturation and function of type 1 collagen. To seek an explanation for this discrepancy, the sequences of the highly conserved, 55-57-amino acid, cysteine-rich repeats (CRR), which constitute the majority of the globular domains in the N-propeptides, were compared among 13 vertebrate species. Surprisingly, the CRR in mice and rats differs substantially from those in other mammalian species. Indeed, the CRR in birds, fish and amphibia are more similar to those of other mammals than are the CRR in rodents. This finding raises the possibility that the mutant mouse, which lacks exon 2 that encodes the CRR in the N-propeptide, might not be an appropriate model in which to study the function of the N-propeptide in other mammals. Alternatively, compensation, possibly by procollagens II or III, could account for the mild phenotype of the exon 2-deleted mouse. Yet another possibility is that the CRR plays a developmental role in the mouse, akin to that recently proposed for the N-propeptide in type IIA procollagen, rather than a function in collagen biogenesis. Some support for the latter possibility is provided by the observation that, on one background, the breeding of heterozygous exon 2-deleted mice generated homozygous mutants at less than the expected frequency. Experiments to examine these possibilities are proposed.

Trimer carboxyl propeptide of collagen I produced by mature osteoblasts is chemotactic for endothelial cells.

During the second phase of osteogenesis in vitro, rat osteoblasts secrete inducer(s) of chemotaxis and chemoinvasion of endothelial and tumor cells. We report here the characterization and purification from mature osteoblast conditioned medium of the agent chemotactic for endothelial cells. The chemoactive conditioned medium specifically induces directional migration of endothelial cells, not affecting the expression and activation of gelatinases, cell proliferation, and scattering. Directional migration induced in endothelial cells by conditioned medium from osteoblasts is inhibited by pertussis toxin, by blocking antibodies to integrins alpha(1), beta(1), and beta(3), and by antibodies to metalloproteinase 2 and 9. The biologically active purified protein has two sequences, coincident with the amino-terminal amino acids, respectively, of the alpha(1) and of the alpha(2) carboxyl propeptides of type I collagen, as physiologically produced by procollagen C proteinase. Antibodies to type I collagen and to the carboxyl terminus of alpha(1) or alpha(2) chains inhibit chemotaxis. The chemoattractant is the propeptide trimer carboxyl-terminal to type I collagen, and its activity is lost upon reduction. These data illustrate a previously unknown function for the carboxyl-terminal trimer, possibly relevant in promoting endothelial cell migration and vascularization of tissues producing collagen type I.

Effects of milk-derived bioactives: an overview.

Milk contains various components with physiological functionality. Peptides derived from caseins and whey proteins including opioid peptides, antihypertensive peptides, casein phosphopeptides, alpha- and beta-lactorphins and albutensin have been shown to possess various bioactive properties. This review considers an overview of the bioactive components in milk proteins and whey and their physiological function.

Dual posttranscriptional targets of retinoic acid-induced gene expression.

Retinoic acid-induced differentiation of the pre-osteoblastic cell line, UMR 201, is associated with a marked increase in the proficiency of posttranscriptional nuclear processing of alkaline phosphatase mRNA. In this study we attempted to correlate the posttranscriptional actions of retinoic acid with changes in phosphorylation, or abundance of spliceosome components, or both. Treatment with retinoic acid for periods of < or = 4 h resulted in dephosphorylation of nuclear U1 70K protein without affecting its abundance. Peptide mapping showed that U1 70K dephosphorylation was related to the disappearance of one specific phosphopeptide out of four major U1 70K phosphopeptides. A twofold decrease in mRNA expression of an isoform of alternative splicing factor that inhibits splicing was also observed over the same period. Tumor necrosis factor-alpha, which enhances the posttranscriptional action of retinoic acid, reduced U1 70K mRNA expression, while an inhibition of retinoic acid action by transforming growth factor-beta was associated with a marked increase in U1 70K mRNA levels. Our results draw attention to the complex interactions between short- and long-term alterations in the abundance and functional status of U1 70K, as well as SR proteins by growth and/or differentiation factors in the regulation of spliceosome formation and function.

Isolation and characterization of small phosphorylated peptides controlling transcription "in vitro" from trout testis chromatin DNA.

Low molecular weight peptides are linked to the chromatin DNA of several tissues, from which they can be dissociated by alkaline extraction. They show very high specific activity in the control of transcription "in vitro". In this work the biochemical properties of controlling transcription peptide effectors isolated from trout testis DNA are reported. The purified peptides prevailingly contain glutamic acid, serine, aspartic acid, glycine and alanine. Studies of the peptide structure by N-terminal analysis using the dansyl chloride procedure was unsuccessful, suggesting the presence of a blocked NH2 group. At the same time the active peptides cannot be digested by carboxypeptidases. The gel filtration of the chromatin peptidic fractions on Sephadex G-25, Trisacryl GF05 or Sephadex G-15 shows that the active peptides elute as a single major peak with an elution volume corresponding to a molecular weight of about 1000. The paper electrophoresis performed at different pH and ionic strength shows that the chromatin peptides are separated in two fractions. One of them is strongly acidic and migrates towards the positive pole until pH 1.9, indicating the presence of phosphoric residues which probably exert an important role in the control of transcription "in vitro". The chromatin peptides are further purified by Sephadex G-10 and high performance liquid chromatography. The amino acid analysis of the purified peptides are reported.

Non-competitive inhibition of ornithine decarboxylase by a phosphopeptide and phosphoamino acids.

In Tetrahymena pyriformis the cytosolic ornithine decarboxylase (L-ornithine carboxy-lyase, EC 4.1.1.17) activity is considerably inhibited by the presence of polyamines in the growth medium, while the nuclear ornithine decarboxylase is only slightly affected. Experimental evidence suggests that the presence of putrescine and/or spermidine elicits the appearance of non-competitive inhibitors of ornithine decarboxylase. One of the inhibitors has a molecular weight of 25,000 and properties of antizyme. In addition, two other low molecular weight inhibitors are extracted, one which is a phosphoserine oligopeptide, and the other which is phosphotyrosine. All inhibit non-competitively the homologous and heterologous (Escherichia coli and rat liver) ornithine decarboxylases. Similarly, non-competitive inhibition was obtained when the commercially available phosphoamino acids were tested against the already mentioned ornithine decarboxylases.