Protein kinases associated with the yeast phosphoproteome

BACKGROUND: Protein phosphorylation is an extremely important mechanism of cellular regulation. A large-scale study of phosphoproteins in a whole-cell lysate of Saccharomyces cerevisiae has previously identified 383 phosphorylation sites in 216 peptide sequences. However, the protein kinases responsible for the phosphorylation of the identified proteins have not previously been assigned. RESULTS: We used Predikin in combination with other bioinformatic tools, to predict which of 116 unique protein kinases in yeast phosphorylates each experimentally determined site in the phosphoproteome. The prediction was based on the match between the phosphorylated 7-residue sequence and the predicted substrate specificity of each kinase, with the highest weight applied to the residues or positions that contribute most to the substrate specificity. We estimated the reliability of the predictions by performing a parallel prediction on phosphopeptides for which the kinase has been experimentally determined. CONCLUSION: The results reveal that the functions of the protein kinases and their predicted phosphoprotein substrates are often correlated, for example in endocytosis, cytokinesis, transcription, replication, carbohydrate metabolism and stress response. The predictions link phosphoproteins of unknown function with protein kinases with known functions and vice versa, suggesting functions for the uncharacterized proteins. The study indicates that the phosphoproteins and the associated protein kinases represented in our dataset have housekeeping cellular roles; certain kinases are not represented because they may only be activated during specific cellular responses. Our results demonstrate the utility of our previously reported protein kinase substrate prediction approach (Predikin) as a tool for establishing links between kinases and phosphoproteins that can subsequently be tested experimentally

Las17p–Vrp1p but not Las17p–Arp2/3 interaction is important for actin patch polarization in yeast

AbstractThe actin cytoskeleton plays a central role in many important cellular processes such as cell polarization, cell division and endocytosis. The dynamic changes to the actin cytoskeleton that accompany these processes are regulated by actin-associated proteins Wiskott–Aldrich Syndrome Protein (WASP) (known as Las17p in yeast) and WASP-Interacting Protein (WIP) (known as Vrp1p in yeast). Both yeast and human WASP bind to and stimulate the Arp2/3 complex which in turn nucleates assembly of actin monomers into filaments at polarized sites at the cortex. WASP–WIP interaction in yeast and humans are important for Arp2/3 complex stimulation in vitro. It has been proposed that these interactions are also important for polarized actin assembly in vivo. However, the redundancy of actin-associated proteins has made it difficult to test this hypothesis. We have identified two point mutations (L80T and H94L) in yeast WASP that in combination abolish WASP–WIP interaction in yeast. We also identify an N-terminal fragment of Las17p (N-Las17p1–368) able to interact with Vrp1p but not Arp2/3. Using these mutant and truncated forms of yeast WASP we provide novel evidence that WASP interaction with WIP is more important than interaction with Arp2/3 for polarized actin assembly and endocytosis in yeast

EGFR and Prion protein promote signaling via FOXO3a-KLF5 resulting in clinical resistance to platinum agents in colorectal cancer

Epidermal growth factor receptor (EGFR) supports colorectal cancer progression via oncogenic signaling. Anti-EGFR therapy is being investigated as a clinical option for colorectal cancer, and an observed interaction between EGFR and Prion protein has been detected in neuronal cells. We hypothesized that PrPC expression levels may regulate EGFR signaling and that detailed understanding of this signaling pathway may enable identification of resistance mechanisms and new actionable targets in colorectal cancer. We performed molecular pathway analysis following knockdown of PrPC or inhibition of EGFR signaling via gefitinib to identify changes in expression of key signaling proteins that determine cellular sensitivity or resistance to cisplatin. Expression of these proteins was examined in matched primary and metastatic patient samples and was correlated for resistance to therapy and progression of disease. Utilizing three colorectal cancer cell lines, we observed a correlation between high expression of PrPC and resistance to cisplatin. Investigation of molecular signaling in a resistant cell line revealed that PrPC contributed to signaling via colocalization with EGFR, which could be overcome by targeting p38 mitogen-activated protein kinases (p38 MAPK). We revealed that the level of Krüppel-like factor 5 (KLF5), a target downstream of p38 MAPK, was predictive for cell line and patient response to platinum agents. Further, high KLF5 expression was observed in BRAF-mutant colorectal cancer. Our study indicates that the EGFR to KLF5 pathway is predictive of patient progression on platinum-based therapy

Study Protocol. ECSSIT – Elective Caesarean Section Syntocinon® Infusion Trial. A multi-centre randomised controlled trial of oxytocin (Syntocinon®) 5 IU bolus and placebo infusion versus oxytocin 5 IU bolus and 40 IU infusion for the control of blood loss at elective caesarean section

<p>Abstract</p> <p>Background</p> <p>Caesarean section is one of the most commonly performed major operations in women throughout the world. Rates are escalating, with studies from the United States of America, the United Kingdom, China and the Republic of Ireland reporting rates between 20% and 25%. Operative morbidity includes haemorrhage, anaemia, blood transfusion and in severe cases, maternal death.</p> <p>The value of routine oxytocics in the third stage of vaginal birth has been well established and it has been assumed that these benefits apply to caesarean delivery as well. A slow bolus dose of oxytocin is recommended following delivery of the baby at caesarean section. Some clinicians use an additional infusion of oxytocin for a further period following the procedure. Intravenous oxytocin has a very short half-life (4–10 minutes) therefore the potential advantage of an oxytocin infusion is that it maintains uterine contractility throughout the surgical procedure and immediate postpartum period, when most primary haemorrhages occur. The few trials to date addressing the optimal approach to preventing haemorrhage at caesarean section have been under-powered to evaluate clinically important outcomes. There has been no trial to date comparing the use of an intravenous slow bolus of oxytocin versus an oxytocin bolus and infusion.</p> <p>Methods and design</p> <p>A multi-centre randomised controlled trial is proposed. The study will take place in five large maternity units in Ireland with collaboration between academics and clinicians in the disciplines of obstetrics and anaesthetics. It will involve 2000 women undergoing elective caesarean section after 36 weeks gestation. The main outcome measure will be major haemorrhage (blood loss >1000 ml). A study involving 2000 women will have 80% power to detect a 36% relative change in the risk of major haemorrhage with two-sided 5% alpha.</p> <p>Discussion</p> <p>It is both important and timely that we evaluate the optimal approach to the management of the third stage at elective caesarean section. Safe operative delivery is now a priority and a reality for many pregnant women. Obstetricians, obstetric anaesthetists, midwives and pregnant women need high quality evidence on which to base management approaches. The overall aim is to reduce maternal haemorrhagic morbidity and its attendant risks at elective caesarean section.</p> <p>Trial registration</p> <p>number: ISRCTN17813715</p

The USNO-B Catalog

USNO-B is an all-sky catalog that presents positions, proper motions, magnitudes in various optical passbands, and star/galaxy estimators for 1,042,618,261 objects derived from 3,643,201,733 separate observations. The data were obtained from scans of 7,435 Schmidt plates taken for the various sky surveys during the last 50 years. USNO-B1.0 is believed to provide all-sky coverage, completeness down to V = 21, 0.2 arcsecond astrometric accuracy at J2000, 0.3 magnitude photometric accuracy in up to five colors, and 85% accuracy for distinguishing stars from non-stellar objects. A brief discussion of various issues is given here, but the actual data are available from http://www.nofs.navy.mil and other sites.Comment: Accepted by Astronomical Journa

Inactivation of the phosphoinositide phosphatases Sac1p and Inp54p leads to accumulation of phosphatidylinositol 4,5-bisphosphate on vacuole membranes and vacuolar fusion defects

Phosphoinositides direct membrane trafficking, facilitating the recruitment of effectors to specific membranes. In yeast phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P-2) is proposed to regulate vacuolar fusion; however, in intact cells this phosphoinositide can only be detected at the plasma membrane. In Saccharomyces cerevisiae the 5-phosphatase, Inp54p, dephosphorylates PtdIns(4,5)P-2 forming PtdIns(4)P, a substrate for the phosphatase Sac1p, which hydrolyzes (PtdIns(4) P). We investigated the role these phosphatases in regulating PtdIns(4,5) P-2 subcellular distribution. PtdIns(4,5)P-2 bioprobes exhibited loss of plasma membrane localization and instead labeled a subset of fragmented vacuoles in Delta sac1 Delta inp54 and sac1(ts) Delta inp54 mutants. Furthermore, sac1(ts) Delta inp54 mutants exhibited vacuolar fusion defects, which were rescued by latrunculin A treatment, or by inactivation of Mss4p, a PtdIns(4)P 5-kinase that synthesizes plasma membrane PtdIns(4,5)P-2. Under these conditions PtdIns(4,5)P-2 was not detected on vacuole membranes, and vacuole morphology was normal, indicating vacuolar PtdIns(4,5)P-2 derives from Mss4p-generated plasma membrane PtdIns(4,5)P-2. Delta sac1 Delta inp54 mutants exhibited delayed carboxypeptidase Y sorting, cargo-selective secretion defects, and defects in vacuole function. These studies reveal PtdIns(4,5)P-2 hydrolysis by lipid phosphatases governs its spatial distribution, and loss of phosphatase activity may result in PtdIns(4,5)P-2 accumulation on vacuole membranes leading to vacuolar fragmentation/fusion defects

The Luminosity and Mass Functions of Low-Mass Stars in the Galactic Disk: I. The Calibration Region

We present measurements of the luminosity and mass functions of low-mass stars constructed from a catalog of matched Sloan Digital Sky Survey (SDSS) and 2 Micron All Sky Survey (2MASS) detections. This photometric catalog contains more than 25,000 matched SDSS and 2MASS point sources spanning ~30 square degrees on the sky. We have obtained follow-up spectroscopy, complete to J=16, of more than 500 low mass dwarf candidates within a 1 square degree sub-sample, and thousands of additional dwarf candidates in the remaining 29 square degrees. This spectroscopic sample verifies that the photometric sample is complete, uncontaminated, and unbiased at the 99% level globally, and at the 95% level in each color range. We use this sample to derive the luminosity and mass functions of low-mass stars over nearly a decade in mass (0.7 M_sun > M_* > 0.1 M_sun). We find that the logarithmically binned mass function is best fit with an M_c=0.29 log-normal distribution, with a 90% confidence interval of M_c=0.20--0.50. These 90% confidence intervals correspond to linearly binned mass functions peaking between 0.27 M_sun and 0.12 M_sun, where the best fit MF turns over at 0.17 M_sun. A power law fit to the entire mass range sampled here, however, returns a best fit of alpha=1.1 (where the Salpeter slope is alpha = 2.35). These results agree well with most previous investigations, though differences in the analytic formalisms adopted to describe those mass functions can give the false impression of disagreement. Given the richness of modern-day astronomical datasets, we are entering the regime whereby stronger conclusions can be drawn by comparing the actual datapoints measured in different mass functions, rather than the results of analytic analyses that impose structure on the data a priori. (abridged)Comment: Accepted for publication in the Astronomical Journal. 21 pages, emulateapj format, 12 figures. Figures 1, 4, 11 and 12 degraded for astroph; full resolution version available for download at http://www.cfa.harvard.edu/~kcovey

The Milky Way Tomography with SDSS: III. Stellar Kinematics

We study Milky Way kinematics using a sample of 18.8 million main-sequence stars with r<20 and proper-motion measurements derived from SDSS and POSS astrometry, including ~170,000 stars with radial-velocity measurements from the SDSS spectroscopic survey. Distances to stars are determined using a photometric parallax relation, covering a distance range from ~100 pc to 10 kpc over a quarter of the sky at high Galactic latitudes (|b|>20 degrees). We find that in the region defined by 1 kpc <Z< 5 kpc and 3 kpc <R< 13 kpc, the rotational velocity for disk stars smoothly decreases, and all three components of the velocity dispersion increase, with distance from the Galactic plane. In contrast, the velocity ellipsoid for halo stars is aligned with a spherical coordinate system and appears to be spatially invariant within the probed volume. The velocity distribution of nearby ($Z<1$ kpc) K/M stars is complex, and cannot be described by a standard Schwarzschild ellipsoid. For stars in a distance-limited subsample of stars (<100 pc), we detect a multimodal velocity distribution consistent with that seen by HIPPARCOS. This strong non-Gaussianity significantly affects the measurements of the velocity ellipsoid tilt and vertex deviation when using the Schwarzschild approximation. We develop and test a simple descriptive model for the overall kinematic behavior that captures these features over most of the probed volume, and can be used to search for substructure in kinematic and metallicity space. We use this model to predict further improvements in kinematic mapping of the Galaxy expected from Gaia and LSST.Comment: 90 pages, 26 figures, submitted to Ap

Vps20p and Vta1p interact with Vps4p and function in multivesicular body sorting and endosomal transport in Saccharomyces cerevisiae

Vps4p (End13p) is an AAA-family ATPase that functions in membrane transport through endosomes, sorting of soluble vacuolar proteins to the vacuole, and multivesicular body (MVB) sorting of membrane proteins to the vacuole lumen. In a yeast two-hybrid screen with Vps4p as bait we isolated VPS20 (YMR077c) and the novel open reading frame YLA181c, for which the name VTA1 has recently been assigned (Saccharomyces Genome Database). Vps4p directly binds Vps20p and Vta1p in vitro and binding is not dependent on ATP-conversely, Vps4p binding to Vps20p is partially sensitive to ATP hydrolysis. Both ATP binding [Vps4p-(K179A)] and ATP hydrolysis [Vps4p-(E233Q)] mutant proteins exhibit enhanced binding to Vps20p and Vta1p in vitro. The Vps4p-Vps20p interaction involves the coiled-coil domain of each protein, whereas the Vps4p-Vta1p interaction involves the (non-coiled-coil) C-terminus of each protein. Deletion of either VPS20 (vps20Delta) or VTA1 (vta1Delta) leads to similar class E Vps(-) phenotypes resembling those of vps4Delta, including carboxypeptidase Y (CPY) secretion, a block in ubiquitin-dependent MVB sorting, and a delay in both post-internalisation endocytic transport and biosynthetic transport to the vacuole. The vacuole resident membrane protein Sna3p (whose MVB sorting is ubiquitin-independent) does not appear to exit the class E compartment or reach the vacuole in cells lacking Vps20p, Vta1p or Vps4p, in contrast to other proteins whose delivery to the vacuole is only delayed. We propose that Vps20p and Vta1p regulate Vps4p function in vivo

The Milky Way Tomography With SDSS. III. Stellar Kinematics

We study Milky Way kinematics using a sample of 18.8 million main-sequence stars with r 20 degrees). We find that in the region defined by 1 kpc < Z < 5 kpc and 3 kpc < R < 13 kpc, the rotational velocity for disk stars smoothly decreases, and all three components of the velocity dispersion increase, with distance from the Galactic plane. In contrast, the velocity ellipsoid for halo stars is aligned with a spherical coordinate system and appears to be spatially invariant within the probed volume. The velocity distribution of nearby (Z < 1 kpc) K/M stars is complex, and cannot be described by a standard Schwarzschild ellipsoid. For stars in a distance-limited subsample of stars (< 100 pc), we detect a multi-modal velocity distribution consistent with that seen by HIPPARCOS. This strong non-Gaussianity significantly affects the measurements of the velocity-ellipsoid tilt and vertex deviation when using the Schwarzschild approximation. We develop and test a simple descriptive model for the overall kinematic behavior that captures these features over most of the probed volume, and can be used to search for substructure in kinematic and metallicity space. We use this model to predict further improvements in kinematic mapping of the Galaxy expected from Gaia and the Large Synoptic Survey Telescope.NSF AST-615991, AST-0707901, AST-0551161, AST-02-38683, AST-06-07634, AST-0807444, PHY05-51164NASA NAG5-13057, NAG5-13147, NNXO-8AH83GPhysics Frontier Center/Joint Institute for Nuclear Astrophysics (JINA) PHY 08-22648U.S. National Science FoundationMarie Curie Research Training Network ELSA (European Leadership in Space Astrometry) MRTN-CT-2006-033481Fermi Research Alliance, LLC, United States Department of Energy DE-AC02-07CH11359Alfred P. Sloan FoundationParticipating InstitutionsJapanese MonbukagakushoMax Planck SocietyHigher Education Funding Council for EnglandMcDonald Observator