Protein-tyrosine phosphorylation interaction network in Bacillus subtilis reveals new substrates, kinase activators and kinase cross-talk

Signal transduction in eukaryotes is generally transmitted through phosphorylation cascades that involve a complex interplay of transmembrane receptors, protein kinases, phosphatases and their targets. Our previous work indicated that bacterial protein-tyrosine kinases and phosphatases may exhibit similar properties, since they act on many different substrates. To capture the complexity of this phosphorylation-based network, we performed a comprehensive interactome study focused on the protein-tyrosine kinases and phosphatases in the model bacterium Bacillus subtilis. The resulting network identified many potential new substrates of kinases and phosphatases, some of which were experimentally validated. Our study highlighted the role of tyrosine and serine/threonine kinases and phosphatases in DNA metabolism, transcriptional control and cell division. This interaction network reveals significant crosstalk among different classes of kinases. We found that tyrosine kinases can bind to several modulators, transmembrane or cytosolic, consistent with a branching of signaling pathways. Most particularly, we found that the division site regulator MinD can form a complex with the tyrosine kinase PtkA and modulate its activity in vitro. In vivo, it acts as a scaffold protein which anchors the kinase at the cell pole. This network highlighted a role of tyrosine phosphorylation in the spatial regulation of the Z-ring during cytokinesis.

Quantitative phosphoproteome analysis of Bacillus subtilis reveals novel substrates of the kinase PrkC and phosphatase PrpC

Reversible protein phosphorylation on serine, threonine, and tyrosine (Ser/Thr/Tyr) residues plays a critical role in regulation of vital processes in the cell. Despite of considerable progress in our understanding of the role of this modification in bacterial physiology, the dynamics of protein phosphorylation during bacterial growth has rarely been systematically addressed. In addition, little is known about in vivo substrates of bacterial Ser/Thr/Tyr kinases and phosphatases. An excellent candidate to study these questions is the Gram-positive bacterium Bacillus subtilis, one of the most intensively investigated bacterial model organism with both research and industrial applications. Here we employed gel-free phosphoproteomics combined with SILAC labeling and high resolution mass spectrometry to study the proteome and phosphoproteome dynamics during the batch growth of B. subtilis. We measured the dynamics of 1666 proteins and 64 phosphorylation sites in five distinct phases of growth. Enzymes of the central carbon metabolism and components of the translation machinery appear to be highly phosphorylated in the stationary phase, coinciding with stronger expression of Ser/Thr kinases. We further used the SILAC workflow to identify novel putative substrates of the Ser/Thr kinase PrkC and the phosphatase PrpC during stationary phase. The overall number of putative substrates was low, pointing to a high kinase and phosphatase specificity. One of the phosphorylation sites affected by both, PrkC and PrpC, was the Ser281 on the oxidoreductase YkwC. We showed that PrkC phosphorylates and PrpC dephosphorylates YkwC in vitro and that phosphorylation at Ser281 abolishes the oxidoreductase activity of YkwC in vitro and in vivo. Our results present the most detailed phosphoproteomic analysis of B. subtilis growth to date and provide the first global in vivo screen of PrkC and PrpC substrates.

Interaction of bacterial fatty-acid-displaced regulators with DNA is interrupted by tyrosine phosphorylation in the helix-turn-helix domain

Bacteria possess transcription regulators (of the TetR family) specifically dedicated to repressing genes for cytochrome P450, involved in oxidation of polyunsaturated fatty acids. Interaction of these repressors with operator sequences is disrupted in the presence of fatty acids, and they are therefore known as fatty-acid-displaced regulators. Here, we describe a novel mechanism of inactivating the interaction of these proteins with DNA, illustrated by the example of Bacillus subtilis regulator FatR. FatR was found to interact in a two-hybrid assay with TkmA, an activator of the protein-tyrosine kinase PtkA. We show that FatR is phosphorylated specifically at the residue tyrosine 45 in its helix-turn-helix domain by the kinase PtkA. Structural modelling reveals that the hydroxyl group of tyrosine 45 interacts with DNA, and we show that this phosphorylation reduces FatR DNA binding capacity. Point mutants mimicking phosphorylation of FatR in vivo lead to a strong derepression of the fatR operon, indicating that this regulatory mechanism works independently of derepression by polyunsaturated fatty acids. Tyrosine 45 is a highly conserved residue, and PtkA from B. subtilis can phosphorylate FatR homologues from other bacteria. This indicates that phosphorylation of tyrosine 45 may be a general mechanism of switching off bacterial fatty-acid-displaced regulators.

Protein-serine/threonine/tyrosine kinases in bacterial signaling and regulation

In this review, we address some recent developments in the field of bacterial protein phosphorylation, focusing specifically on serine/threonine and tyrosine kinases. We present an overview of recent studies outlining the scope of physiological processes that are regulated by phosphorylation, ranging from cell cycle, growth, cell morphology, to metabolism, developmental phenomena, and virulence. Specific emphasis is placed on Mycobacterium tuberculosis as a showcase organism for serine/threonine kinases, and Bacillus subtilis to illustrate the importance of protein phosphorylation in developmental processes. We argue that bacterial serine/threonine and tyrosine kinases have a distinctive feature of phosphorylating multiple substrates and might thus represent integration nodes in the signaling network. Some open questions regarding the evolutionary benefits of relaxed substrate selectivity of these kinases are treated, as well as the notion of nonfunctional 'background' phosphorylation of cellular proteins. We also argue that phosphorylation events for which an immediate regulatory effect is not clearly established should not be dismissed as unimportant, as they may have a role in cross-talk with other post-translational modifications. Finally, recently developed methods for studying protein phosphorylation networks in bacteria are briefly discussed.

Protein phosphorylation from the perspective of systems biology

Protein phosphorylation pathways emerge as large and interconnected networks, involving mutually activating protein kinases, kinases acting as network nodes by phosphorylating different substrates, and cross-talk of phosphorylation with other post-translational modifications. The complexity of these networks clearly necessitates the use of systems biology approaches. Phosphoproteomics represents the basis for detection of phosphoproteins and phosphorylation sites, but it must be combined with transcriptomics and interactomics in attempts to build in silico phosphorylation networks. This review highlights the implication of phosphorylation in cellular physiology across all domains of life. It focuses particularly on reports of human disease correlated to defects in phosphorylation networks. Brief outline of developments in quantitative mass spectrometry-based proteomics and bioinformatic tools specific for phosphoproteome studies is provided.

[Cardiac metastasis of renal cell carcinoma, a rare location]

The renal carcinoma is situated in the third rank of the urologic cancers. It is metastatic in a third of the cases, when we made the diagnosis of the cancer. Lungs, bone, the liver, the suprarenal gland and the brain stay metastatic sites of preference. Some metastatic locations are anecdotal and made the object of some publications. We report the case of a cardiac metastasis of renal carcinoma at an old patient 81 years old operated for cardiac tumor.

Critical microphase properties of crosslinked polymer blends with quenched random impurities

We extend published works dealing with microphase separation in crosslinked polymer blends to the case where these are surrounded by random impurities. To study their influence on critical microphase properties, from a static and kinetics point of view, we first assume that the (real) disorder caused by impurities is quenched. Second, the replica theory is used to study such critical properties, upon the impurities concentration and their interaction strength. More precisely, we compute the spinodal temperature and structure factor. We find that the spinodal temperature is shifted towards its lower and higher values, for attractive and repulsive impurities, respectively. The obtained expression for the static structure factor suggests that, contrarily to repulsive impurities, the crosslinked mixture scatters better in the presence of attractive ones. Thereafter, the study is extended to kinetics of microphase separation, when the mixture is impregnated by small random impurities. Kinetics is investigated through the growth rate, and in particular, we demonstrate that the latter is increased by the presence of repulsive impurities. This is natural, since these play a stabilizer role. Finally, the discussion is extended to crosslinked polymer blends immersed in a good solvent, which induces drastic changes of the critical microphase properties.

Theory of microphase separation in crosslinked polymer blends immersed in a θ-solvent

The aim of this work is a theoretical study of the effects of the solvent quality on the microphase separation in crosslinked polymer blends, from a static and kinetics point of view. More precisely, we assume that the crosslinked mixture is trapped in a θ-solvent. The static microphase properties are studied through the static structure factor. The latter is computed using an extended blob model, where the crosslinked unlike chains can be viewed as sequences of blobs. We demonstrate that the presence of the θ-solvent simply leads to a multiplicative renormalization of these properties, and the renormalization factors are powers of the overall monomer volume fraction. Second, we investigate the early kinetics of the microphase separation, via the relaxation rate, τ(q), which is a function of the wave number q (at fixed temperature and monomer volume fraction). We first show that the kinetics is entirely controlled by local motions of Rouse type, since the slow motions are frozen out by the presence of crosslinks. Using the blob model, we find an explicit form for the growth rate Ω(q) = τ(q)⁻¹, which depends, in addition to the wave number q , on the overall monomer volume fraction, Φ. Also, we discuss the effect of initial entanglements that are trapped when the system is crosslinked. In fact, these play the role of true reticulation points, and then, they quantitatively contribute to the microseparation phenomenon. Finally, the results are compared to their homologous relatively to the molten state and to the good solvent case. The main conclusion is that the quality of the solvent induces drastic changes of the microphase properties.

Urothelial carcinoma with plasmocytoid component

Plasmocytoid urothelial carcinoma is a rare subtype of tumour of the urinary bladder. Its clinical and histopathological features have not been well characterized. There are few reports of this type of tumour. We report a case of 65-year-old man who was operated in our department for bladder tumour. The pathological diagnosis was high-grade urothelial carcinoma with plasmocytoid component. The patient died shortly thereafter from liver and bone metastasis.

Cystic nephroma in the adult: pathological aspects and therapeutic implications

Cystic nephroma is a benign renal neoplasm. Since its initial description, there has been much debate regarding its origin. Preoperative diagnosis of Cystic nephroma is difficult to achieve. The differential diagnoses of Cystic nephroma are recently described mixed epithelial and stromal tumours of the kidney and cystic renal cell carcinoma. The Authors report three cases of Cystic nephroma and illustrate the clinical, radiological and histological features of this renal neoplasm.

Segmental infarction of the testis: an exceptional complication of diabetes microangiopathy

We report a case of segmental infarction of the testis in a 55-year-old man. Past medical history included 12 years of type II diabetes and hypertension. The patient presented with a 2-month history of testicular pain and was found clinically and sonographically to have a testicular tumour. The pathological examination of the partial orchiectomy specimen revealed segmental infarction of the testicle secondary to diabetes microangiopathy. We propose diabetes microangiopathy as a localization and aetiology of segmental testicular infarction. A possible testicular sparing procedure through an inguinal approach may be considered in cases of testicular masses for which the clinical and imaging findings are suggestive of focal testicular infarction.

Management of penile fractures complicated by urethral rupture

The combination of lesions of the penile urethra and the corpus cavernosum is rare and likely to go unremarked. It worsens the immediate and long-term prognosis and poses a problem of management. Among 312 cases of penile fracture, we performed a retrospective study of a series of 10-case of traumatic corpora cavernosa rupture complicated with urethral rupture, treated in the department of Urology at 'Charles Nicolle' Hospital in Tunis. The median patients' age was 30 years. The most common mechanism was manipulation of an erect penis, found in six cases. Urethral rupture was suspected in all patients given the presence of bloody urethral discharge. No preoperative radiographic investigations were necessary. All patients underwent immediate surgical exploration. The urethral injury was always partial and localized at the level of the corpora tear. Surgical repair of both urethral and corpora tear was done in all patients. The follow up was uneventful. Urethrography at the removal of the transurethral catheter did not visualize contrast extravasation in any patient. No urethral stricture or erectile complaints were noted within a 36-month mean follow-up. Urethral rupture must be suspected in any case of penile fracture presenting with bloody urethral discharge. Standard treatment is immediate surgical repair.

[Paratesticular pleomorphic rhabdomyosarcoma in an adult: diagnosis and management]

A paratesticular pleomorphic rhabdomyosarcoma occurring in a 63-year old man is reported. Clinical signs were like any intrascrotal tumor. CT-scan and histological examination with immunohistochemical study were necessary for the diagnosis and stadification of this cancer. The patient underwent a radical inguinal orchidectomy. The patient developed a local recurrence, which was treated by radiotherapy, and subsequently developed metastases two years later, which were treated by chemotherapy.

False penile fracture: report of 16 cases

We determined the value of diagnostic and therapeutic approaches of false penile fractures and the outcome of treatment. We retrospectively reviewed 16 cases of presumed penile fracture with a negative surgical exploration. Clinical presentation, technique of treatment and outcome were noted. The mean age was 39 years (17-64). Nine patients were injured during sexual intercourse. All the patients presented with the presumptive diagnosis of penile fracture. False penile fracture was evoked in one patient presenting a new erection. Surgical penile exploration was carried out for all the patients without any radiological explorations. It revealed nonspecific dartos bleeding in 10 cases and avulsed superficial dorsal vein in six cases requiring venous ends ligation. All the patients regained penile appearance and potency. We can hardly distinguish false penile fracture from 'true' penile fracture with certainty either clinically or radiologically, thus, surgical exploration is mostly necessary. The prognosis is excellent.

Primitive neuroectodermal tumor of the kidney with vena caval tumor thrombus: diagnosis and management

Primitive neuroectodermal tumors (PNET) of the kidney are rare and highly aggressive malignancies. We report a case of 28-year-old male with PNET of the kidney with inferior vena caval thrombus. Immunohistochemistry revealed strong positivity for CD99 and weak positivity for vimentin. Neuron-specific enolase (NSE), chromogranin and cytokeratin were negative. Patient underwent nephrectomy and six cycles of polychemotherapy the patient was in partial remission. He underwent two further cycles of high dose chemotherapy and died 9 months after diagnosis due to liver metastases. The diagnosis of renal PNET must be considered in young patients with renal neoplasm, particularly those with advanced disease at presentation. Achieving exact diagnosis has important clinical consequences.

Nutritional Intervention Study with Argan Oil in Man: Effects on Lipids and Apolipoproteins

AIM

To evaluate whether the consumption of virgin argan oil (VAO) is associated with a change in serum lipids and reduces the risk of cardiovascular disease in healthy Moroccans.

METHODS

Sixty volunteers consumed butter (25 g/day) during 2 weeks (stabilization period) and were randomly divided into two groups: the treatment group received 25 g/day of VAO during 3 weeks (intervention period), and the control group received 25 g/day of extra virgin olive oil (EVO). Throughout the study, weight, blood pressure, and daily food intake were measured. Serum total cholesterol and low- and high-density lipoprotein cholesterol, triglycerides, and apolipoproteins A-I and B were measured at the end of each diet period.

RESULTS

Analysis of food intake showed that the daily diet is isocaloric for the butter regimen (2,537 +/- 244 kcal/day) as well as for the VAO and EVO regimens (2,561+/- 246 and 2,560 +/- 253 kcal/day, respectively). Analysis of the lipid intake showed a reduction in saturated fatty acids with VAO and EVO regimens (27 +/- 1.4 and 26.4 +/- 3.4%, respectively) as compared with the stabilization period (41.6 +/- 2.4%). The analysis of serum lipids showed a significant increase in high-density lipoprotein cholesterol and apolipoprotein A-I in both VAO group (8.4%, p = 0.012, and 5.2%, p = 0.027, respectively) and EVO group (17.3%, p = 0.001, and 5.9%, p = 0.036, respectively). However, low-density lipoprotein cholesterol and apolipoprotein B (13.8%, p = 0.037, and 7.8%, p = 0.039, respectively) decreased significantly only in EVO group as compared with the stabilization period, while triglycerides decreased significantly by 17.5% (p = 0.039) only in VAO group.

CONCLUSION

These results confirm the cholesterol-lowering effect of EVO and show for the first time the triglyceride-lowering effect of VAO in men.

Colloidal aggregation in polymer blends

We consider here a low-density assembly of colloidal particles immersed in a critical polymer mixture of two chemically incompatible polymers. We assume that, close to the critical point of the free mixture, the colloids prefer to be surrounded by one polymer (critical adsorption). As result, one is assisted to a reversible colloidal aggregation in the nonpreferred phase, due the existence of a long-range attractive Casimir force between particles. This aggregation is a phase transition driving the colloidal system from dilute to dense phases, as the usual gas-liquid transition. We are interested in a quantitative investigation of the phase diagram of the immersed colloids. We suppose that the positions of particles are disordered, and the disorder is quenched and follows a Gaussian distribution. To apprehend the problem, use is made of the standard phi(4) theory, where the field phi represents the composition fluctuation (order parameter), combined with the standard cumulant method. First, we derive the expression of the effective free energy of colloids and show that this is of Flory-Huggins type. Second, we find that the interaction parameter u between colloids is simply a linear combination of the isotherm compressibility and specific heat of the free mixture. Third, with the help of the derived effective free energy, we determine the complete shape of the phase diagram (binodal and spinodal) in the (Psi,u) plane, with Psi as the volume fraction of immersed colloids. The continuous "gas-liquid" transition occurs at some critical point K of coordinates (Psi(c) = 0.5,u(c) = 2). Finally, we emphasize that the present work is a natural extension of that, relative to simple liquid mixtures incorporating colloids.

Kinetics of phase separation in ramified polymer blends of arbitrary topology

We present here a theoretical study of kinetics of phase separation within a mixture made of two chemically incompatible ramified polymers. For simplicity, we assume that they have the same topology. We are interested in the variation of the relaxation rate, tau(q), versus the wave number q, in the vicinity of the spinodal temperature. The kinetics is governed by local (Rouse) and reptation motions (faster and slower modes). For qRG >> 1 (RG being the gyration radius), kinetics is entirely controlled by local motions where each chain moves inside its own tube, and we show that the corresponding characteristic frequency, tau(q)(-1), scales as tau(q)(-1) approximately kappaGq6, where kappaG is a known topological factor. For qR(G) << 1, however, kinetics is rather dominated by long-wavelength (reptation) motions where unlike ramified polymers creep inside a long tube. For this case, we find that tau(q)(-1) approximately delta (0) q2 (chi(c) - chi), where delta (0) is another known topological factor that represents the total mobility of free monomers belonging to connected chains and reticulation points, and chi(c) accounts for the critical value of the segregation parameter. Finally, the derived relaxation rate must be compared to that relative to a linear polymer mixture.

Kinetics of microphase separation in interpenetrated polymer networks in solution

We present here a theoretical study of the early kinetics of the microphase separation in crosslinked polymer blends, made of two incompatible polymers A and B, dissolved in a common good solvent. Use is made of an extended blob model used previously for the investigation of the static properties of such a transition. We are interested in the variation of the relaxation rate, tau(q), versus the wave number q, in the vicinity of the spinodal temperature. We first show that kinetics is entirely dominated by local motions, which are of Rouse type. Slow motions are absent, because of the permanent presence of crosslinks. Second, we find that the characteristic frequency, omega (q) = tau(q)(-1), increases with increasing wave number q according to a sixth power law, that is omega (q) approximately q6 phi(-9/4), where phi is the overall monomer volume fraction. Therefore, the swelling of strands due to the excluded-volume forces leads to a renormalization of the characteristic frequency by a multiplicative factor scaling as phi(-9/4). The main conclusion is that the presence of a good solvent necessitates relaxation rates less important than those relative to crosslinked mixtures in the molten state.

Exact effective force between star-polymers in a Theta-solvent

We re-examine here the computation of the effective force between two star-polymers of respective numbers of branches f(1) and f(2), immersed in a common Theta-solvent. Such a force originates essentially from the repulsive three-body interactions. To achieve this, we take advantage of some established results using renormalization theory for three-dimensional star-polymers, or conformal invariance for two-dimensional ones. We first show that, in dimension d = 3, the force, F(r), decreases with the center-to-center distance r as F(r)/kappa BT congruent with Af1f2 x [r ln (R2/r2]-1 (r<R), with the exact universal amplitude Af1f2 = f1f2(f1 + f2 - 2)/22. Second, in dimension d = 2, we find that the force decays more slowly as F(r)/kappa BT congruent with Bf1f2 x r-1 (r<R), with the exact universal amplitude Bf1f2. For high distances compared to the gyration radius, R approximately a square root of N, of a single polymer chain at the Theta-point, an exponential decay of the force is expected.