Heterogeneity of Mitochondrial Protein Biogenesis during Primary Leaf Development in Barley

The natural developmental gradient of light-grown primary leaves of barley (Hordeum vulgare L.) was used to analyze the biogenesis of mitochondrial proteins in relation to the age and physiological changes within the leaf. The data indicate that the protein composition of mitochondria changes markedly during leaf development. Three distinct patterns of protein development were noted: group A proteins, consisting of the E1 β-subunit of the pyruvate dehydrogenase complex, ORF156, ORF577, alternative oxidase, RPS12, cytochrome oxidase subunits II and III, malic enzyme, and the α- and β-subunits of F₁-ATPase; group B proteins, consisting of the E1 α-subunit of the pyruvate dehydrogenase complex, isocitrate dehydrogenase, HSP70A, cpn60C, and cpn60B; and group C proteins, consisting of the four subunits of the glycine decarboxylase complex (P, H, T, and L proteins), fumarase, and formate dehydrogenase. All of the proteins increased in concentration from the basal meristem to the end of the elongation zone (20.0 mm from the leaf base), whereupon group A proteins decreased, group B proteins increased to a maximum at 50 mm from the leaf base, and group C proteins increased to a maximum at the leaf tip. This study provides evidence of a marked heterogeneity of mitochondrial protein composition, reflecting a changing function as leaf cells develop photosynthetic and photorespiratory capacity.     

Mitotic Phosphorylation of Golgi Reassembly Stacking Protein 55 by Mitogen-activated Protein Kinase ERK2

The role of the mitogen-activated protein kinase kinase (MKK)/extracellular-activated protein kinase (ERK) pathway in mitotic Golgi disassembly is controversial, in part because Golgi-localized targets have not been identified. We observed that Golgi reassembly stacking protein 55 (GRASP55) was phosphorylated in mitotic cells and extracts, generating a mitosis-specific phospho-epitope recognized by the MPM2 mAb. This phosphorylation was prevented by mutation of ERK consensus sites in GRASP55. GRASP55 mitotic phosphorylation was significantly reduced, both in vitro and in vivo, by treatment with U0126, a potent and specific inhibitor of MKK and thus ERK activation. Furthermore, ERK2 directly phosphorylated GRASP55 on the same residues that generated the MPM2 phospho-epitope. These results are the first demonstration of GRASP55 mitotic phosphorylation and indicate that the MKK/ERK pathway directly phosphorylates the Golgi during mitosis.     

Calcium-Dependent Protein Phosphorylation May Mediate the Gibberellic Acid Response in Barley Aleurone

Peptide substrates of well-defined protein kinases were microinjected into aleurone protoplasts of barley (Hordeum vulgare L. cv Himalaya) to inhibit, and therefore identify, protein kinase-regulated events in the transduction of the gibberellin (GA) and abscisic acid signals. Syntide-2, a substrate designed for Ca²⁺- and calmodulin (CaM)-dependent kinases, selectively inhibited the GA response, leaving constitutive and abscisic acid-regulated events unaffected. Microinjection of syntide did not affect the GA-induced increase in cytosolic [Ca²⁺], suggesting that it inhibited GA action downstream of the Ca²⁺ signal. When photoaffinity-labeled syntide-2 was electroporated into protoplasts and cross-linked to interacting proteins in situ, it selectively labeled proteins of approximately 30 and 55 kD. A 54-kD, soluble syntide-2 phosphorylating protein kinase was detected in aleurone cells. This kinase was activated by Ca²⁺ and was CaM independent, but was inhibited by the CaM antagonist N-(6-aminohexyl)-5-chloro-1-naphthalene-sulfonamide (250 μm), suggesting that it was a CaM-domain protein kinase-like activity. These results suggest that syntide-2 inhibits the GA response of the aleurone via an interaction with this kinase, implicating the 54-kD kinase as a Ca²⁺-dependent regulator of the GA response in these cells.     

Protein Kinase C-mediated Phosphorylation and Activation of PDE3A Regulate cAMP Levels in Human Platelets

The elevation of [cAMP]_i is an important mechanism of platelet inhibition and is regulated by the opposing activity of adenylyl cyclase and phosphodiesterase (PDE). In this study, we demonstrate that a variety of platelet agonists, including thrombin, significantly enhance the activity of PDE3A in a phosphorylation-dependent manner. Stimulation of platelets with the PAR-1 agonist SFLLRN resulted in rapid and transient phosphorylation of PDE3A on Ser³¹², Ser⁴²⁸, Ser⁴³⁸, Ser⁴⁶⁵, and Ser⁴⁹², in parallel with the PKC (protein kinase C) substrate, pleckstrin. Furthermore, phosphorylation and activation of PDE3A required the activation of PKC, but not of PI3K/PKB, mTOR/p70S6K, or ERK/RSK. Activation of PKC by phorbol esters also resulted in phosphorylation of the same PDE3A sites in a PKC-dependent, PKB-independent manner. This was further supported by the finding that IGF-1, which strongly activates PI3K/PKB, but not PKC, did not regulate PDE3A. Platelet activation also led to a PKC-dependent association between PDE3A and 14-3-3 proteins. In contrast, cAMP-elevating agents such as PGE₁ and forskolin-induced phosphorylation of Ser³¹² and increased PDE3A activity, but did not stimulate 14-3-3 binding. Finally, complete antagonism of PGE₁-evoked cAMP accumulation by thrombin required both G_i and PKC activation. Together, these results demonstrate that platelet activation stimulates PKC-dependent phosphorylation of PDE3A on Ser³¹², Ser⁴²⁸, Ser⁴³⁸, Ser⁴⁶⁵, and Ser⁴⁹² leading to a subsequent increase in cAMP hydrolysis and 14-3-3 binding.Upon vascular injury, platelets adhere to the newly exposed subintimal collagen and undergo activation leading to platelet spreading to cover the damaged region and release of thrombogenic factors such as ADP and thromboxane A₂. In addition, platelets are activated by thrombin, which is generated as a result of activation of the coagulation pathway, and stimulates platelets by cleaving the protease-activated receptors (PAR),² PAR-1 and PAR-4. The final common pathway is the exposure of fibrinogen binding sites on integrin α_IIbβ₃ resulting in platelet aggregation and thrombus formation.Thrombin-mediated cleavage of PARs leads to activation of phospholipase C β (PLC), hydrolysis of phosphatidylinositol (PI) 4,5-bisphosphate and a subsequent increase in [Ca²⁺]_i and activation of protein kinase C (PKC). Protein kinase C contributes to platelet activation both directly, through affinity regulation of the fibrinogen receptor, integrin α_IIbβ₃ (1), and indirectly by enhancing degranulation (2). Thrombin also stimulates activation of PI 3-kinases and subsequent generation of PI (3, 4, 5) trisphosphate and PI (3, 4) bisphosphate (3), which recruit protein kinase B (PKB) to the plasma membrane where it becomes phosphorylated and activated.Platelet activation is opposed by agents that raise intracellular 3′-5′-cyclic adenosine monophosphate ([cAMP]_i). cAMP is a powerful inhibitory second messenger that down-regulates platelet function by interfering with Ca²⁺ homeostasis, degranulation and integrin activation (4). Synthesis of cAMP is stimulated by mediators such as prostaglandin I₂ (PGI₂), which bind to G_s-coupled receptors leading to activation of adenylate cyclase (AC). This inhibitory pathway is opposed by thrombin, which inhibits the elevation of cAMP indirectly via autocrine activation of the G_i-coupled ADP receptor P2Y₁₂. cAMP signaling is terminated by hydrolysis to biologically inert 5′-AMP by 3′-phosphodiesterases. Platelets express two cAMP phosphodiesterase isoforms, cGMP-stimulated PDE2 and cGMP-inhibited PDE3A. PDE3A is the most abundant isoform in platelets and has a ∼250-fold lower K_m for cAMP than PDE2 (4). As a consequence of these properties, PDE3A exerts a greater influence on cAMP homeostasis, particularly at resting levels. The importance of PDE3A in platelet function is further emphasized by the finding that the PDE3A inhibitors cilostamide and milrinone raise basal cAMP levels and strongly inhibit thrombin-induced platelet activation (5). Furthermore, PDE3A^-/- mice demonstrate increased resting levels of platelet cAMP and are protected against a model of pulmonary thrombosis (6). In contrast, the PDE2 inhibitor EHNA has no significant effect on cAMP levels and platelet aggregation (7, 8). The activity of PDE3A is therefore essential to maintain low equilibrium levels of cAMP and determine the threshold for platelet activation (7).Like its paralogue PDE3B, it has recently become clear that PDE3A activity can be positively regulated by phosphorylation in platelets and human oocytes (9, 10). There is some evidence that PKB may be involved in this regulation, although the phosphorylation sites are poorly characterized. In contrast, phosphorylation of PDE3A in HeLa cells was stimulated by phorbol esters and blocked by inhibitors of PKC (11). In this study, we aimed to identify the signaling pathways and phosphorylation sites that are involved in regulation of platelet PDE3A. Here, we show strong evidence that PKC, and not PKB, is involved in agonist-stimulated PDE3A phosphorylation on Ser³¹², Ser⁴²⁸, Ser⁴³⁸, Ser⁴⁶⁵, and Ser⁴⁹², leading to an increase in PDE3A activity, 14-3-3 binding and modulation of intracellular cAMP levels.     

A Role for Protein Phosphorylation in Cytochrome P450 3A4 Ubiquitin-dependent Proteasomal Degradation

Cytochromes P450 (P450s) incur phosphorylation. Although the precise role of this post-translational modification is unclear, marking P450s for degradation is plausible. Indeed, we have found that after structural inactivation, CYP3A4, the major human liver P450, and its rat orthologs are phosphorylated during their ubiquitin-dependent proteasomal degradation. Peptide mapping coupled with mass spectrometric analyses of CYP3A4 phosphorylated in vitro by protein kinase C (PKC) previously identified two target sites, Thr²⁶⁴ and Ser⁴²⁰. We now document that liver cytosolic kinases additionally target Ser⁴⁷⁸ as a major site. To determine whether such phosphorylation is relevant to in vivo CYP3A4 degradation, wild type and CYP3A4 with single, double, or triple Ala mutations of these residues were heterologously expressed in Saccharomyces cerevisiae pep4Δ strains. We found that relative to CYP3A4wt, its S478A mutant was significantly stabilized in these yeast, and this was greatly to markedly enhanced for its S478A/T264A, S478A/S420A, and S478A/T264A/S420A double and triple mutants. Similar relative S478A/T264A/S420A mutant stabilization was also observed in HEK293T cells. To determine whether phosphorylation enhances CYP3A4 degradation by enhancing its ubiquitination, CYP3A4 ubiquitination was examined in an in vitro UBC7/gp78-reconstituted system with and without cAMP-dependent protein kinase A and PKC, two liver cytosolic kinases involved in CYP3A4 phosphorylation. cAMP-dependent protein kinase A/PKC-mediated phosphorylation of CYP3A4wt but not its S478A/T264A/S420A mutant enhanced its ubiquitination in this system. Together, these findings indicate that phosphorylation of CYP3A4 Ser⁴⁷⁸, Thr²⁶⁴, and Ser⁴²⁰ residues by cytosolic kinases is important both for its ubiquitination and proteasomal degradation and suggest a direct link between P450 phosphorylation, ubiquitination, and degradation.Hepatic cytochromes P450 (P450s)³ are integral endoplasmic reticulum (ER)-anchored hemoproteins engaged in the oxidative biotransformation of various endo- and xenobiotics. Of these, human CYP3A4 is the most dominant liver enzyme, accounting for >30% of the hepatic microsomal P450 complement, and responsible for the oxidative metabolism of over 50% of clinically relevant drugs (1). In common with all the other ER-bound P450s, CYP3A4 is a monotopic protein with its N-terminal ≈33-residue domain embedded in the ER membrane with the bulk of its structure in the cytosol. Our in vivo studies of the heterologously expressed CYP3A4 in the yeast Saccharomyces cerevisiae as well as of its rat liver CYP3A2/3A23 orthologs in primary hepatocytes have revealed that human and rat liver CYPs 3A are turned over via ubiquitin (Ub)-dependent proteasomal degradation (UPD) (2–8). Thus, CYPs 3A represent excellent prototypic substrates of ER-associated degradation (ERAD), specifically of the ERAD-C pathway (6–11). Consistent with this CYP3A ERAD process, our studies of in vivo and/or in vitro reconstituted systems have led us to conclude that CYPs 3A are ubiquitinated by the UBC7/gp78 Ub-ligase complex and recruited by the p97-Npl4-Ufd1 complex before their degradation by the 26 S proteasome (4–8, 12). Because all these processes are energy-dependent, it is not surprising that in vitro reconstitution of CYP3A4 UPD requires ATP. However, inclusion of γ-S-[³²P]ATP in an in vitro reconstituted CYP3A4 ubiquitination system catalyzed by rat liver cytosolic fraction II (FII) resulted in CYP3A4 protein phosphorylation, i.e. γ-[³²P]phosphoryl transfer onto CYP3A4 target residues (13, 14). This phosphorylation was enhanced after cumene hydroperoxide (CuOOH)-mediated CYP3A4 inactivation. The physiological role, if any, of this CYP3A4 post-translational modification is unclear.CYP3A4 is not the only P450 that is phosphorylated. Since the in vitro phosphorylation of a hepatic P450 (CYP2B4) by cAMP-dependent protein kinase A (PKA) was first described (15), various P450s, particularly those belonging to the subfamily 2, were documented to be phosphorylated in cell-free systems, hepatocyte incubations, and intact animals (16–32). Common features of such P450 phosphorylation were the presence of a cytosolically exposed PKA recognition sequence (RRXS) with the Ser residue as the exclusive kinase target, and the ensuing loss of prosthetic heme, conversion to the inactive P420 species, and consequent dramatic functional inactivation (15–20). Studies in intact rats also identified CYPs 3A and 2C6 as kinase targets (21). Although both these P450s lack the hallmark PKA recognition sequence, apparently they possess secondary PKA targeting sequences or are phosphorylated by other protein kinases such as PKC. Indeed, in vitro studies revealed that P450s were phosphorylated in an isoform-dependent manner by either PKA or PKC, except for CYP2B1, which was heavily phosphorylated by both (20). Over the years since this particular post-translational P450 modification was recognized, it has been assigned various functional roles (17, 29–33). Among these, as first proposed by Taniguchi et al. (16) and later explored both by Eliasson et al. (23–26) and us (13, 14), P450 phosphorylation served as a marker for its degradation. Accordingly, the phosphorylation of CYP2E1Ser¹²⁹ and CYP3A1Ser³⁹³ by a microsomal cAMP-dependent protein kinase has been proposed to predispose these P450s but not the similarly phosphorylated CYP2B1 to proteolytic degradation by an integral ER Mg²⁺-ATP-activated serine protease (23–27). However, heterologous expression of CYP2E1S129A/S129G site-directed mutants in COS7 cells apparently had no effect on its relative stability thereby revealing that if CYP2E1 phosphorylation is important for its degradation (34, 35), then alternate Ser/Thr residues (i.e. in plausible secondary PKA recognition sites, Lys-Lys-Ser²⁰⁹-Lys and Lys-Lys-Ser⁴⁴⁹-Ala) may be recruited.On the other hand, on the basis of rapid phosphorylation of CuOOH-inactivated CYP3A4 that precedes its ubiquitination and 26 S proteasomal degradation in an in vitro liver cytosolic FII-catalyzed system, we have proposed that CYP3A4 phosphorylation was essential for targeting it to proteins participating in its UPD/ERAD (13). Indeed, several examples of similar phosphorylation for targeting proteins to UPD exist, of which IκBα phosphorylation is the most notable and perhaps the best documented (36–47; see “Discussion”).Our in vitro studies with specific kinase inhibitors as probes identified both PKC and PKA as the major FII kinases responsible for CYP3A4 phosphorylation (14). Indeed, in vitro model studies of CYP3A4 with PKC as the kinase, coupled with lysylendopeptidase C (Lys-C) digestion of the phosphorylated protein and liquid chromatography-tandem mass spectrometric (LC-MS/MS) analyses of the Lys-C digests, identified two PKC-phosphorylated CYP3A4 peptides ²⁵⁸ESRLEDpTQK²⁶⁶ and ⁴¹⁴FLPERFpSK⁴²¹ unambiguously phosphorylated at Thr²⁶⁴ and Ser⁴²⁰ (14). These same residues were also phosphorylated in corresponding studies with PKA.⁴ Furthermore, although both native and CuOOH-inactivated CYP3A4 were phosphorylated at Thr²⁶⁴, Ser⁴²⁰ phosphorylation was particularly enhanced after CuOOH-mediated CYP3A4 inactivation (14). Corresponding studies of CuOOH-inactivated CYP3A4 using rat liver cytosolic FII as the source of the kinase(s), revealed ³²P phosphorylation of both these peptides as well as that of an additional CYP3A4 peptide ⁴⁷⁷LS(p)LGGLLQPEKPVVLK⁴⁹². Unlike the unambiguous mass spectrometric identification of Thr²⁶⁴ and Ser⁴²⁰ as the phosphorylated CYP3A4 residues, the phosphorylation of Ser⁴⁷⁸, the only plausible phosphorylatable residue in this ³²P-labeled peptide, was not similarly established. Nevertheless, the predominant phosphorylation of Thr²⁶⁴ in native CYP3A4 (14), but of two additional residues in the CuOOH-inactivated enzyme, is consistent with the inactivation-induced structural unraveling of this enzyme with exposure of otherwise concealed and/or kinase-inaccessible domains (48). Such unraveling of CYP3A4 protein stems from the irreversible modification of its active site by fragments generated from CuOOH-mediated oxidative destruction of its prosthetic heme (49). In this study, using mass spectrometric analyses of Lys-C digests of FII-phosphorylated CYP3A4, we have provided unambiguous evidence that in addition to Thr²⁶⁴ and Ser⁴²⁰, Ser⁴⁷⁸ is indeed phosphorylated. More importantly, through alanine-scanning mutagenesis of these three residues, we now document that although neither the structural conformation nor the catalytic function of this triple CYP3A4T264A/S420A/S478A mutant is altered, its degradation after heterologous expression in S. cerevisiae is significantly impaired. This is also true of CYP3A4T264A/S420A/S478A mutant degradation in human embryonic kidney (HEK293T) cells. Furthermore, using an in vitro reconstituted CYP3A4 ubiquitination system, catalyzed by human Ub-conjugating E2 enzyme UBC7 and integral ER protein gp78 as the E3 Ub ligase (12), we document that PKA/PKC-mediated phosphorylation of the wild type CYP3A4 (CYP3A4wt) considerably enhanced its UBC7/gp78-mediated ubiquitination. Together these findings reveal the critical importance of CYP3A4 phosphorylation at these residues for its UPD and suggest a direct link between phosphorylation and its ubiquitination and degradation.     

Protein Kinase D Mediates Mitogenic Signaling by Gq-coupled Receptors through Protein Kinase C-independent Regulation of Activation Loop Ser744 and Ser748 Phosphorylation

Rapid protein kinase D (PKD) activation and phosphorylation via protein kinase C (PKC) have been extensively documented in many cell types cells stimulated by multiple stimuli. In contrast, little is known about the role and mechanism(s) of a recently identified sustained phase of PKD activation in response to G protein-coupled receptor agonists. To elucidate the role of biphasic PKD activation, we used Swiss 3T3 cells because PKD expression in these cells potently enhanced duration of ERK activation and DNA synthesis in response to G_q-coupled receptor agonists. Cell treatment with the preferential PKC inhibitors GF109203X or Gö6983 profoundly inhibited PKD activation induced by bombesin stimulation for <15 min but did not prevent PKD catalytic activation induced by bombesin stimulation for longer times (>60 min). The existence of sequential PKC-dependent and PKC-independent PKD activation was demonstrated in 3T3 cells stimulated with various concentrations of bombesin (0.3–10 nm) or with vasopressin, a different G_q-coupled receptor agonist. To gain insight into the mechanisms involved, we determined the phosphorylation state of the activation loop residues Ser⁷⁴⁴ and Ser⁷⁴⁸. Transphosphorylation targeted Ser⁷⁴⁴, whereas autophosphorylation was the predominant mechanism for Ser⁷⁴⁸ in cells stimulated with G_q-coupled receptor agonists. We next determined which phase of PKD activation is responsible for promoting enhanced ERK activation and DNA synthesis in response to G_q-coupled receptor agonists. We show, for the first time, that the PKC-independent phase of PKD activation mediates prolonged ERK signaling and progression to DNA synthesis in response to bombesin or vasopressin through a pathway that requires epidermal growth factor receptor-tyrosine kinase activity. Thus, our results identify a novel mechanism of G_q-coupled receptor-induced mitogenesis mediated by sustained PKD activation through a PKC-independent pathway.The understanding of the mechanisms that control cell proliferation requires the identification of the molecular pathways that govern the transition of quiescent cells into the S phase of the cell cycle. In this context the activation and phosphorylation of protein kinase D (PKD),⁴ the founding member of a new protein kinase family within the Ca²⁺/calmodulin-dependent protein kinase (CAMK) group and separate from the previously identified PKCs (for review, see Ref. 1), are attracting intense attention. In unstimulated cells, PKD is in a state of low catalytic (kinase) activity maintained by autoinhibition mediated by the N-terminal domain, a region containing a repeat of cysteinerich zinc finger-like motifs and a pleckstrin homology (PH) domain (1–4). Physiological activation of PKD within cells occurs via a phosphorylation-dependent mechanism first identified in our laboratory (5–7). In response to cellular stimuli (1), including phorbol esters, growth factors (e.g. PDGF), and G protein-coupled receptor (GPCR) agonists (6, 8–16) that signal through G_q, G₁₂, G_i, and Rho (11, 15–19), PKD is converted into a form with high catalytic activity, as shown by in vitro kinase assays performed in the absence of lipid co-activators (5, 20).During these studies multiple lines of evidence indicated that PKC activity is necessary for rapid PKD activation within intact cells. For example, rapid PKD activation was selectively and potently blocked by cell treatment with preferential PKC inhibitors (e.g. GF109203X or Gö6983) that do not directly inhibit PKD catalytic activity (5, 20), implying that PKD activation in intact cells is mediated directly or indirectly through PKCs. Many reports demonstrated the operation of a rapid PKC/PKD signaling cascade induced by multiple GPCR agonists and other receptor ligands in a range of cell types (for review, see Ref. 1). Our previous studies identified Ser⁷⁴⁴ and Ser⁷⁴⁸ in the PKD activation loop (also referred as activation segment or T-loop) as phosphorylation sites critical for PKC-mediated PKD activation (1, 4, 7, 17, 21). Collectively, these findings demonstrated the existence of a rapidly activated PKC-PKD protein kinase cascade(s). In a recent study we found that the rapid PKC-dependent PKD activation was followed by a late, PKC-independent phase of catalytic activation and phosphorylation induced by stimulation of the bombesin G_q-coupled receptor ectopically expressed in COS-7 cells (22). This study raised the possibility that PKD mediates rapid biological responses downstream of PKCs, whereas, in striking contrast, PKD could mediate long term responses through PKC-independent pathways. Despite its potential importance for defining the role of PKC and PKD in signal transduction, this hypothesis has not been tested in any cell type.Accumulating evidence demonstrates that PKD plays an important role in several cellular processes and activities, including signal transduction (14, 23–25), chromatin organization (26), Golgi function (27, 28), gene expression (29–31), immune regulation (26), and cell survival, adhesion, motility, differentiation, DNA synthesis, and proliferation (for review, see Ref. 1). In Swiss 3T3 fibroblasts, a cell line used extensively as a model system to elucidate mechanisms of mitogenic signaling (32–34), PKD expression potently enhances ERK activation, DNA synthesis, and cell proliferation induced by G_q-coupled receptor agonists (8, 14). Here, we used this model system to elucidate the role and mechanism(s) of biphasic PKD activation. First, we show that the G_q-coupled receptor agonists bombesin and vasopressin, in contrast to phorbol esters, specifically induce PKD activation through early PKC-dependent and late PKC-independent mechanisms in Swiss 3T3 cells. Subsequently, we demonstrate for the first time that the PKC-independent phase of PKD activation is responsible for promoting ERK signaling and progression to DNA synthesis through an epidermal growth factor receptor (EGFR)-dependent pathway. Thus, our results identify a novel mechanism of G_q-coupled receptor-induced mitogenesis mediated by sustained PKD activation through a PKC-independent pathway.     

Streptococcus mutans Protein Synthesis during Mixed-Species Biofilm Development by High-Throughput Quantitative Proteomics

Biofilms formed on tooth surfaces are comprised of mixed microbiota enmeshed in an extracellular matrix. Oral biofilms are constantly exposed to environmental changes, which influence the microbial composition, matrix formation and expression of virulence. Streptococcus mutans and sucrose are key modulators associated with the evolution of virulent-cariogenic biofilms. In this study, we used a high-throughput quantitative proteomics approach to examine how S. mutans produces relevant proteins that facilitate its establishment and optimal survival during mixed-species biofilms development induced by sucrose. Biofilms of S. mutans, alone or mixed with Actinomyces naeslundii and Streptococcus oralis, were initially formed onto saliva-coated hydroxyapatite surface under carbohydrate-limiting condition. Sucrose (1%, w/v) was then introduced to cause environmental changes, and to induce biofilm accumulation. Multidimensional protein identification technology (MudPIT) approach detected up to 60% of proteins encoded by S. mutans within biofilms. Specific proteins associated with exopolysaccharide matrix assembly, metabolic and stress adaptation processes were highly abundant as the biofilm transit from earlier to later developmental stages following sucrose introduction. Our results indicate that S. mutans within a mixed-species biofilm community increases the expression of specific genes associated with glucan synthesis and remodeling (gtfBC, dexA) and glucan-binding (gbpB) during this transition (P<0.05). Furthermore, S. mutans up-regulates specific adaptation mechanisms to cope with acidic environments (F1F0-ATPase system, fatty acid biosynthesis, branched chain amino acids metabolism), and molecular chaperones (GroEL). Interestingly, the protein levels and gene expression are in general augmented when S. mutans form mixed-species biofilms (vs. single-species biofilms) demonstrating fundamental differences in the matrix assembly, survival and biofilm maintenance in the presence of other organisms. Our data provide insights about how S. mutans optimizes its metabolism and adapts/survives within the mixed-species community in response to a dynamically changing environment. This reflects the intricate physiological processes linked to expression of virulence by this bacterium within complex biofilms.     

Spy1 Protein Mediates Phosphorylation and Degradation of SCG10 Protein in Axonal Degeneration

Axon loss is a destructive consequence of a wide range of neurological diseases without a clearly defined mechanism. Recent data demonstrate that SCG10 is a novel axonal maintenance factor and that rapid SCG10 loss after injury requires JNK activity; how JNK induces degradation of SCG10 is not well known. Here we showed that SCG10 was a binding partner of Spy1, a Speedy/RINGO family protein, which participated in cellular response to sciatic nerve injury. During the early stage of axonal injury, Spy1 expression was inversely correlated with SCG10. Spy1 mediated SCG10 phosphorylation and degradation partly in a JNK-dependent manner. Inhibition of Spy1 attenuated SCG10 phosphorylation and delayed injury-induced axonal degeneration. Taken together, these data suggest that Spy1 is an important regulator of SCG10 and can be targeted in future axo-protective therapeutics.     

The Protein Phosphorylation Landscape of Mouse Spermatids during Spermiogenesis

The characteristic tadpole shape of sperm is formed from round spermatids via spermiogenesis, a process which results in dramatic morphological changes in the final stage of spermatogenesis in the testis. Protein phosphorylation, as one of the most important post‐translational modifications, can regulate spermiogenesis; however, the phosphorylation events taking place during this process have not been systematically analyzed. In order to better understand the role of phosphorylation in spermiogenesis, large‐scale phosphoproteome profiling is performed using IMAC and TiO₂ enrichment. In total, 13 835 phosphorylation sites, in 4196 phosphoproteins, are identified in purified mouse spermatids undergoing spermiogenesis in two biological replicates. Overall, 735 testis‐specific proteins are identified to be phosphorylated, and are expressed at high levels during spermiogenesis. Gene ontology analysis shows enrichment of the identified phosphoproteins in terms of histone modification, cilium organization, centrosome and the adherens junction. Further characterization of the kinase‐substrate phosphorylation network demonstrates enrichment of phosphorylation substrates related to the regulation of spermiogenesis. This global protein phosphorylation landscape of spermiogenesis shows wide phosphoregulation across a diverse range of processes during spermiogenesis and can help to further characterize the process of sperm generation. All MS data are available via ProteomeXchange with the identifier PXD011890.     

Phosphorylation of Collapsin Response Mediator Protein 2 on Tyr-479 Regulates CXCL12-induced T Lymphocyte Migration

In the central nervous system, collapsin response mediator protein 2 (CRMP2) is a transducer protein that supports the semaphorin-induced guidance of axons toward their cognate target. However, we previously showed that CRMP2 is also expressed in immune cells and plays a crucial role in T lymphocyte migration. Here we further investigated the molecular mechanisms underlying CRMP2 function in chemokine-directed T-cell motility. Examining Jurkat T-cells treated with the chemokine CXCL12, we found that 1) CXCL12 induces a dynamic re-localization of CRMP2 to uropod, the flexible structure of migrating lymphocyte, and increases its binding to the cytoskeletal protein vimentin; 2) CXCL12 decreases phosphorylation of the glycogen synthase kinase-3β-targeted residues CRMP2-Thr-509/514; and 3) tyrosine Tyr-479 is a new phosphorylation CRMP2 residue and a target for the Src-family kinase Yes. Moreover, phospho-Tyr-479 increased under CXCL12 signaling while phospho-Thr-509/514 decreased. The functional importance of this tyrosine phosphorylation was demonstrated by Y479F mutation that strongly reduced CXCL12-mediated T-cell polarization and motility as tested in a transmigration model and on neural tissue. We propose that differential phosphorylation by glycogen synthase kinase-3β and Yes modulates the contribution of CRMP2 to cytoskeletal reorganization during chemokine-directed T-cell migration. In addition to providing a novel mechanism for T lymphocyte motility, our findings reveal CRMP2 as a transducer of chemokine signaling.T lymphocyte migration is the basis of major immune functions such as responses to infection and inflammation, as well as normal recirculation through the lymphoid organs. Indeed, the role of T-cells depends strongly on their ability to travel between organs via the blood and lymph and to move rapidly within these tissues, by extravasation (1). This latter function is dependent on extracellular signals, among which chemokines play a major role.Chemokines form a superfamily of small proteins that orchestrate lymphocyte polarization and migration (2). These proteins exert their functions by binding specific seven-transmembrane-domain G-protein-coupled receptors on the T-cell surface (3). T-lymphocytes exposed to chemokines, in a soluble or surface-bound gradient, develop a polarized shape, extending at the front, an F-actin-rich lamellipodium, which constitutes the leading edge, and a trailing edge or uropod in which both the microtubule and vimentin networks are retracted during migration. Although F-actin has the well known function of producing the mechanical forces required to generate movement (4), the role of microtubules and vimentin in T-cell migration requires further investigation.Cytoskeletal remodeling is of key importance in migrating cells (5) and is one of the functions carried out by the chemokine stromal cell-derived factor-1α, also named CXCL12. In association with its cognate receptor CXCR4, CXCL12 is a potent chemoattractant for mature T-cells and monocytes (6). Following ligand recognition and binding, CXCR4 signaling starts with the activation of G proteins, followed by various signaling cascade effectors, including MAP² kinases, phosphoinositide 3-kinase, and phospholipase Cγ (7). Although this intracellular signaling cascade has not been completely elucidated, the Src family non-receptor tyrosine kinase Lck and the Syk kinase ZAP-70 have emerged as the main candidates for delivering the input signal following CXCR4 activation (8). Thus, tyrosine kinase activity appears as a central step in CXCR4-dependent chemotaxis.While searching for molecules involved in T-cell motility, we recently identified collapsin response mediator protein 2 (CRMP2) (9), a protein first described in the context of neuronal growth cone advance (10, 11). We demonstrated that CRMP2 regulated both T-cell polarization and spontaneous/chemokine-induced migration of T-lymphocytes. Moreover, CRMP2 was found at the uropod of motile T-cells and has the ability to bind cytoskeletal elements, including vimentin. A correlation between CRMP2 expression levels and cell migratory rates toward a chemokine gradient, including CXCL12, was demonstrated by overexpression and knockdown experiments in T-cells (9). In addition, we recently reported that, in mouse model of neuroinflammation, elevated CRMP2 expression in T lymphocytes correlated with their elevated migratory rates and their ability to target the central nervous system (12). The importance of CXCL12 in the central nervous system and its implication in the pathogenesis of central nervous system disorders, including neuroinflammatory diseases, are well documented (review in Ref. 13). Thus, the aim of the present study was to determine whether and how CRMP2 participates in the transduction pathway induced by CXCL12 on T lymphocytes.     

Protein Distribution during Human Erythroblast Enucleation In Vitro

Enucleation is the step in erythroid terminal differentiation when the nucleus is expelled from developing erythroblasts creating reticulocytes and free nuclei surrounded by plasma membrane. We have studied protein sorting during human erythroblast enucleation using fluorescence activated cell sorting (FACS) to obtain pure populations of reticulocytes and nuclei produced by in vitro culture. Nano LC mass spectrometry was first used to determine the protein distribution profile obtained from the purified reticulocyte and extruded nuclei populations. In general cytoskeletal proteins and erythroid membrane proteins were preferentially restricted to the reticulocyte alongside key endocytic machinery and cytosolic proteins. The bulk of nuclear and ER proteins were lost with the nucleus. In contrast to the localization reported in mice, several key erythroid membrane proteins were detected in the membrane surrounding extruded nuclei, including band 3 and GPC. This distribution of key erythroid membrane and cytoskeletal proteins was confirmed using western blotting. Protein partitioning during enucleation was investigated by confocal microscopy with partitioning of cytoskeletal and membrane proteins to the reticulocyte observed to occur at a late stage of this process when the nucleus is under greatest constriction and almost completely extruded. Importantly, band 3 and CD44 were shown not to restrict specifically to the reticulocyte plasma membrane. This highlights enucleation as a stage at which excess erythroid membrane proteins are discarded in human erythroblast differentiation. Given the striking restriction of cytoskeleton proteins and the fact that membrane proteins located in macromolecular membrane complexes (e.g. GPA, Rh and RhAG) are segregated to the reticulocyte, we propose that the membrane proteins lost with the nucleus represent an excess mobile population of either individual proteins or protein complexes.     

Spatial Distribution of Protein Kinase A Activity during Cell Migration Is Mediated by A-kinase Anchoring Protein AKAP Lbc

Protein kinase A (PKA) has been suggested to be spatially regulated in migrating cells due to its ability to control signaling events that are critical for polarized actin cytoskeletal dynamics. Here, using the fluorescence resonance energy transfer-based A-kinase activity reporter (AKAR1), we find that PKA activity gradients form with the strongest activity at the leading edge and are restricted to the basal surface in migrating cells. The existence of these gradients was confirmed using immunocytochemistry using phospho-PKA substrate antibodies. This observation holds true for carcinoma cells migrating randomly on laminin-1 or stimulated to migrate on collagen I with lysophosphatidic acid. Phosphodiesterase inhibition allows the formation of PKA activity gradients; however, these gradients are no longer polarized. PKA activity gradients are not detected when a non-phosphorylatable mutant of AKAR1 is used, if PKA activity is inhibited with H-89 or protein kinase inhibitor, or when PKA anchoring is perturbed. We further find that a specific A-kinase anchoring protein, AKAP-Lbc, is a major contributor to the formation of these gradients. In summary, our data show that PKA activity gradients are generated at the leading edge of migrating cells and provide additional insight into the mechanisms of PKA regulation of cell motility.Cell motility is controlled by a complex network of signals that are initiated by binding to the extracellular matrix. Understanding the biochemical mechanisms that control cell migration is necessary for better comprehension of processes like wound healing, embryonic development, and angiogenesis as well as cancer metastasis (1). PKA³ is an important regulator of cell signaling and various biological functions (2-4). Previous studies have shown that cell motility is delicately controlled by synthesis and breakdown of cAMP through its effects on PKA. PKA regulates key signaling events that are critical for actin cytoskeletal remodeling and cell polarization during migration, including control of the activation states of RhoA, Rac, cdc42, Pak, and c-Abl. For example, PKA is known to inhibit the activation of RhoA, whereas it is required for the activation of Rac1, two proteins that are spatially regulated during cell migration. Therefore, it has been suggested that PKA activity in migrating cells is spatially regulated (5-9). The mounting evidence for the formation of cAMP/PKA gradients and their influence over directed cell motility is compelling. To conclusively determine that PKA activity gradients exist, the visualization of these gradients in single cells is needed to determine the nature of gradients and the mechanisms governing how they are formed.The compartmental action of cAMP was suggested over three decades ago (10, 11) and has hence been shown to mediate the precise spatiotemporal control of its effectors (12-15). Tight control of cAMP levels is governed by the coordinated actions of cyclic nucleotide phosphodiesterases (PDEs) and adenylyl cyclases. Gradients of cAMP and, thus, PKA activity are expected to exist in a cell. This idea is based, most simplistically, on the fact that cAMP is generated by membrane-bound adenylyl cyclases and broken down by cytosolic PDEs; that is, the two arms of cAMP metabolism are spatially separated. Further compartmentalization of PKA activity also occurs as a result of the anchoring of PKA and cAMP-specific PDEs to A-kinase anchoring proteins (AKAPs), which has been demonstrated in a variety of cell types (16, 17). The anchoring of PKA occurs typically through the binding of the type II regulatory (RII) subunits to AKAPs where the relative levels of PDE activity and cAMP generated regulate the regional activity of PKA. PKA anchoring, in addition to cAMP synthesis and degradation, is believed to control spatial signaling of PKA (14, 15). Until recently, we have lacked both the model systems and technology to adequately study the possibility that cAMP/PKA activity gradients exist. We and others (5-8) have established that polarization and migration of cells are dependent on cAMP synthesis and breakdown. Here, we sought to demonstrate the existence of cAMP/PKA gradients in single migrating cells using the fluorescence resonance energy transfer (FRET)-based PKA biosensor A-kinase activity reporter (AKAR1) and determine how signaling components that regulate PKA activity, including cAMP synthesis, PDEs, and PKA anchoring, affect the formation of these gradients.     

Blood–Brain Barrier Protein and Phosphorylation and Dephosphorylation

Capillaries in vertebrate brain have unique permeability properties that make up the blood-brain barrier (BBB). Although it is known that capillaries are innervated by nerve endings of intracerebral origin and that brain capillary function is likely acutely regulated by neuronal inputs, the possible mechanisms of neuronal regulation of capillary function are at present unknown. One possible mode of regulation is via the phosphorylation of brain capillary proteins. The present studies characterize, for the first time, the major phosphoproteins in the bovine brain capillary using both intact bovine brain capillaries and plasma membrane fractions from bovine brain capillaries. The patterns of endogenous phosphorylation of capillary proteins are compared to similar patterns obtained with synaptosomal (P2) fractions from bovine brain. The major findings of this study are: (a) The activity of protein phosphorylation in brain capillaries is localized almost exclusively to the capillary plasma membrane, and is nearly comparable to the activity of protein phosphorylation in synaptosomal membranes. (b) A major phosphoprotein doublet in the capillary fraction comigrates on a sodium dodecyl sulfate gel with a major phosphoprotein doublet of approximate molecular weight of 80K in the synaptosomal fraction, and the latter is presumed to be synapsin I; in dephosphorylation assays the synaptosomal 80K phosphoprotein doublet is not subject to measurable dephosphorylation, whereas the capillary 80K doublet is subject to rapid dephosphorylation, and is essentially completely dephosphorylated within 5 s at 0 degrees C. (c) A prominent triplet of phosphoproteins with molecular weight of 50-55K is present in the capillary fraction, and is not present in the synaptosomal fraction; thus, this 50-55K triplet of phosphoproteins appears specific for brain capillaries.(ABSTRACT TRUNCATED AT 250 WORDS)     

Ablation of Ventricular Myosin Regulatory Light Chain Phosphorylation in Mice Causes Cardiac Dysfunction in Situ and Affects Neighboring Myofilament Protein Phosphorylation

There is little direct evidence on the role of myosin regulatory light chain phosphorylation in ejecting hearts. In studies reported here we determined the effects of regulatory light chain (RLC) phosphorylation on in situ cardiac systolic mechanics and in vitro myofibrillar mechanics. We compared data obtained from control nontransgenic mice (NTG) with a transgenic mouse model expressing a cardiac specific nonphosphorylatable RLC (TG-RLC(P-). We also determined whether the depression in RLC phosphorylation affected phosphorylation of other sarcomeric proteins. TG-RLC(P-) demonstrated decreases in base-line load-independent measures of contractility and power and an increase in ejection duration together with a depression in phosphorylation of myosin-binding protein-C (MyBP-C) and troponin I (TnI). Although TG-RLC(P-) displayed a significantly reduced response to β₁-adrenergic stimulation, MyBP-C and TnI were phosphorylated to a similar level in TG-RLC(P-) and NTG, suggesting cAMP-dependent protein kinase signaling to these proteins was not disrupted. A major finding was that NTG controls were significantly phosphorylated at RLC serine 15 following β₁-adrenergic stimulation, a mechanism prevented in TG-RLC(P-), thus providing a biochemical difference in β₁-adrenergic responsiveness at the level of the sarcomere. Our measurements of Ca²⁺ tension and Ca²⁺-ATPase rate relations in detergent-extracted fiber bundles from LV trabeculae demonstrated a relative decrease in maximum Ca²⁺-activated tension and tension cost in TG-RLC(P-) fibers, with no change in Ca²⁺ sensitivity. Our data indicate that RLC phosphorylation is critical for normal ejection and response to β₁-adrenergic stimulation. Our data also indicate that the lack of RLC phosphorylation promotes compensatory changes in MyBP-C and TnI phosphorylation, which when normalized do not restore function.Phosphorylation of sarcomeric proteins tunes the intensity and dynamics of cardiac contraction and relaxation independent of membrane Ca²⁺ fluxes to meet physiologic demands (1, 2). We focus here on ventricular myosin regulatory light chain, which is phosphorylated in vivo (3–5) but whose functional role in control of cardiac dynamics has remained unclear. The identification of RLC² mutations linked to familial hypertrophic cardiomyopathy (6) underscores the importance of understanding its action as a regulator of contraction. Functionally, in vitro cardiac RLC phosphorylation by MLCK produces a sensitizing shift in the force-Ca²⁺ relation in skinned fibers (7–11). Moreover, studies show that RLC phosphorylation manifests as a gradient across the wall of the heart, which may be important for both normalizing wall stress and for generation of torsion about the long axis of the ejecting heart (12–14). Yet there remains a lack of understanding of the in situ functional effects of RLC phosphorylation and whether phosphorylation of RLC influences other sarcomeric sites as substrates for kinases and phosphatases.Understanding the precise mechanisms by which phosphorylation of RLC affects function of ejecting ventricles is particularly important, because mechanisms downstream of Ca²⁺ fluxes at the level of the sarcomere appear to dominate ejection and to sustain ventricular elastance (15). Myosin motors are important in this, and RLC is well positioned at the S1-S2 junction to modulate myosin heavy chain directly by fine-tuning lever arm motion and indirectly by interacting with the essential light chain, the thick filament backbone, and MyBP-C (16, 17). Accordingly, the hypothesis underlying this study was that ablation of N-terminal RLC phosphorylation would elicit a depression in ventricular ejection and compensatory changes in phosphorylation of sarcomeric proteins neighboring RLC.To understand the role of RLC phosphorylation in the ejection phase of the cardiac cycle, we determined in situ pressure-volume functions in ejecting, auxotonically loaded ventricles expressing either wild type RLC (NTG) or a nonphosphorylatable RLC (TG-RLC(P-)) (10). Our experiments provide novel data demonstrating the importance of RLC phosphorylation in systolic pump function and provide new insights into how a lack of phosphorylation of RLC induces a redistribution of charge among myofilament proteins. Furthermore, our data demonstrate an enigmatic blunting of TG-RLC(P-) functional response to β₁-adrenergic simulation despite a normal TnI and MyBP-C phosphorylation profile. RLC serine 15 phosphorylation increased significantly in NTG controls but was not permitted in TG-RLC(P-) (RLC S14/15/19/A), suggesting that a change in RLC phosphorylation following β₁-adrenergic simulation may be critical for eliciting a normal response.     

In Vitro Phosphorylation and Acetylation of the Murine Pocket Protein Rb2/p130

The retinoblastoma protein (pRb) and the related proteins Rb2/p130 and 107 represent the “pocket protein” family of cell cycle regulators. A key function of these proteins is the cell cycle dependent modulation of E2F-regulated genes. The biological activity of these proteins is controlled by acetylation and phosphorylation in a cell cycle dependent manner. In this study we attempted to investigate the interdependence of acetylation and phosphorylation of Rb2/p130 in vitro. After having identified the acetyltransferase p300 among several acetyltransferases to be associated with Rb2/p130 during S-phase in NIH3T3 cells in vivo, we used this enzyme and the CDK4 protein kinase for in vitro modification of a variety of full length Rb2/p130 and truncated versions with mutations in the acetylatable lysine residues 1079, 128 and 130. Mutation of these residues results in the complete loss of Rb2/p130 acetylation. Replacement of lysines by arginines strongly inhibits phosphorylation of Rb2/p130 by CDK4; the inhibitory effect of replacement by glutamines is less pronounced. Preacetylation of Rb2/p130 strongly enhances CDK4-catalyzed phosphorylation, whereas deacetylation completely abolishes in vitro phosphorylation. In contrast, phosphorylation completely inhibits acetylation of Rb2/p130 by p300. These results suggest a mutual interdependence of modifications in a way that acetylation primes Rb2/p130 for phosphorylation and only dephosphorylated Rb2/p130 can be subject to acetylation. Human papillomavirus 16-E7 protein, which increases acetylation of Rb2/p130 by p300 strongly reduces phosphorylation of this protein by CDK4. This suggests that the balance between phosphorylation and acetylation of Rb2/p130 is essential for its biological function in cell cycle control.