PhosphoSitePlus (http://www.phosphosite.org) is an open, comprehensive, manually curated and interactive resource for studying experimentally observed post-translational modifications, primarily of human and mouse proteins. It encompasses 1 30 000 non-redundant modification sites, primarily phosphorylation, ubiquitinylation and acetylation. The interface is designed for clarity and ease of navigation. From the home page, users can launch simple or complex searches and browse high-throughput data sets by disease, tissue or cell line. Searches can be restricted by specific treatments, protein types, domains, cellular components, disease, cell types, cell lines, tissue and sequences or motifs. A few clicks of the mouse will take users to substrate pages or protein pages with sites, sequences, domain diagrams and molecular visualization of side-chains known to be modified; to site pages with information about how the modified site relates to the functions of specific proteins and cellular processes and to curated information pages summarizing the details from one record. PyMOL and Chimera scripts that colorize reactive groups on residues that are modified can be downloaded. Features designed to facilitate proteomic analyses include downloads of modification sites, kinase–substrate data sets, sequence logo generators, a Cytoscape plugin and BioPAX download to enable pathway visualization of the kinase–substrate interactions in PhosphoSitePlus®.

We show that brome mosaic virus (BMV) RNA replication protein 1a, 2a polymerase, and a cis-acting replication signal recapitulate the functions of Gag, Pol, and RNA packaging signals in conventional retrovirus and foamy virus cores. Prior to RNA replication, 1a forms spherules budding into the endoplasmic reticulum membrane, sequestering viral positive-strand RNA templates in a nuclease-resistant, detergent-susceptible state. When expressed, 2a polymerase colocalizes in these spherules, which become the sites of viral RNA synthesis and retain negative-strand templates for positive-strand RNA synthesis. These results explain many features of replication by numerous positive strand RNA viruses and reveal that these viruses, reverse transcribing viruses, and dsRNA viruses share fundamental similarities in replication and may have common evolutionary origins.

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Current immunosuppressive therapies act on T lymphocytes by modulation of cytokine production, modulation of signaling pathways or by inhibition of the enzymes of nucleotide biosynthesis. We have identified a previously unknown series of immunomodulatory compounds that potently inhibit human and rat T lymphocyte proliferation in vitro and in vivo in immune-mediated animal models of disease, acting by a novel mechanism. Here we identify the target of these compounds, the monocarboxylate transporter MCT1 (SLC16A1), using a strategy of photoaffinity labeling and proteomic characterization. We show that inhibition of MCT1 during T lymphocyte activation results in selective and profound inhibition of the extremely rapid phase of T cell division essential for an effective immune response. MCT1 activity, however, is not required for many stages of lymphocyte activation, such as cytokine production, or for most normal physiological functions. By pursuing a chemistry-led target identification strategy, we have discovered that MCT1 is a previously unknown target for immunosuppressive therapy and have uncovered an unsuspected role for MCT1 in immune biology.

Many forages experience significant proteolytic losses when preserved by ensiling. Such losses in alfalfa (Medicago sativa L.) are especially high, with degradation of 44 to 87% of the forage protein to nonprotein N (NPN). In contrast, red clover (Trifolium pratense L.) has up to 90% less proteolysis during ensiling. Here we demonstrate that the combination of polyphenol oxidase (PPO) and o‐diphenol PPO substrates, both abundantly present in red clover, is responsible for postharvest proteolytic inhibition in this forage crop. Proteolysis in red clover leaf extracts increased nearly fivefold when endogenous o‐diphenols were removed by gel filtration but returned to starting levels by adding back an exogenous o‐diphenol. Proteolysis in leaf extracts of red clover plants silenced for PPO expression was dramatically increased compared to control plants. Leaf extracts of transgenic alfalfa expressing a red clover PPO gene showed a nearly fivefold o‐diphenol–dependent decrease in proteolysis compared to those of control alfalfa. We also demonstrate that PPO levels 10‐ to 20‐fold lower than those typically found in red clover are sufficient for proteolytic inhibition, that as little as 0.25 μmol o‐diphenol mg−1 protein has a substantial impact on proteolysis, that a wide variety of o‐diphenols are functional substrates in proteolytic inhibition, and that proteolysis is reduced for PPO‐expressing alfalfa in small‐scale ensiling experiments. Together, these results indicate that PPO and o‐diphenols can be an effective treatment to prevent protein loss in ensiled forage crops.

Red clover (Trifolium pratense) leaves contain high levels of polyphenol oxidase (PPO) activity and o-diphenol substrates. Wounding of leaves during harvest and ensiling results in browning of leaf tissues from activity of PPO on the o-diphenols. In association with browning, leaf proteins remain undegraded during ensiling, presumably due to PPO-generated o-quinone inhibition of leaf proteases. We cloned three red clover PPO cDNAs, PPO1, PPO2, and PPO3, from a leaf cDNA library. Sequence comparisons among the three red clover PPO clones indicated they are 87% to 90% identical at the nucleotide level (80%-83% amino acid identity). All three encode proteins predicted to localize to the chloroplast thylakoid lumen. RNAblotting and immunoblotting experiments indicated PPO1 is expressed primarily in young leaves, PPO2 in flowers and petioles, and PPO3 in leaves and possibly flowers. We expressed mature PPO1 in Escherichia coli. A portion of the expressed protein was soluble and functional in an assay for PPO activity. We also expressed the red clover PPO cDNAs under the control of a constitutive promoter in alfalfa (Medicago sativa). The expressed red clover PPO proteins were active in alfalfa extracts as evidenced by o-diphenol-dependant extract browning and quantitative assays of PPO activity. Proteolysis in leaf extracts of alfalfa expressing red clover PPO1 was dramatically reduced in the presence of an o-diphenol compared to controls. Transgenic alfalfa expressing red clover PPO should prove an excellent model system to further characterize the red clover PPO enzymes and PPO-mediated inhibition of postharvest proteolysis in forage plants.Ensiling crops is a popular method of preserving forage for animal feed, especially in the humid northern regions of the United States. During harvesting and early stages of ensiling, plant membranes are ruptured, releasing proteolytic enzymes that rapidly degrade available substrates. Once fermentation by lactobacteria has progressed sufficiently to lower silage pH to less than about 5, proteolytic activity slows significantly. The wider the window between harvest and reaching a low pH, the more extensive is the proteolytic degradation. Unfortunately, excessive proteolysis in ensiled forages results in economic losses to farmers (Rotz et al., 1993) amounting to approximately $100 million annually. This economic loss is due to purchasing additional protein to supplement diets because of poor utilization of the nonprotein nitrogen products of proteolysis (ammonia, amino acids, and small peptides) by ruminant animals. Ruminants excrete much of this nonprotein nitrogen as urea, resulting in increasing nitrogen burdens upon the environment.For some ensiled forages, such as alfalfa (Medicago sativa), proteolytic losses are especially high with degradation of 44% to 87% of the forage protein (Papadopoulos and McKersie, 1983;Muck, 1987). By contrast, red clover (Trifolium pratense), a forage with protein content similar to alfalfa, has up to 90% less proteolysis than alfalfa during ens...

Transfection of COS7 cells with a plasmid encoding the human cyclic AMP-specific PDE4A phosphodiesterase PDE-46 (HSPDE4A4B) led to the expression of a rolipram-inhibited PDE4 activity, which contributed ϳ96% of the total COS cell PDE activity. A fusion protein was generated which encompassed residues (788 -886) at the extreme C terminus of PDE-46 and was used to generate an antiserum that detected PDE-46 in transfected COS7 cells. Immunoblotting studies identified PDE-46 as a ϳ125-kDa species that was associated with both the soluble and particulate fractions. The relative V max of particulate PDE-46 was ϳ56% that of cytosolic PDE-46. Particulate PDE-46 was not solubilized using Triton X-100 or high NaCl concentrations. Immunofluorescence analysis by laser scanning confocal microscopy showed that PDE-46 was located at discrete margins of the cell, indicative of association with membrane cortical regions. The human PDE4A species, h6.1 (HSPDE4A4C), which lacks the N-terminal extension of PDE-46, was found as an entirely soluble species when expressed in COS7 cells. h6.1 was shown to have an ϳ11-fold higher V max relative to that of PDE-46. In doseresponse studies rolipram inhibited particulate PDE-46 at much lower concentrations (IC 50 ‫؍‬ 0.195 M) than those needed to inhibit the cytosolic enzyme (IC 50 ‫؍‬ 1.6 M). The basis of this difference lay in the fact that rolipram served as a simple competitive inhibitor of the cytosol enzyme (K i ‫؍‬ 1.6 M) but as a partial competitive inhibitor of the particulate enzyme (K i ‫؍‬ 0.037 M; K i ‫؍‬ 2.3 M). Particulate PDE-46 thus showed a ϳ60-fold higher affinity for rolipram than cytosolic PDE-46.

The main finding of this work is that providing a relatively low cell concentration is used in IonWorks HT, the potency information generated correlates well with that determined using conventional electrophysiology. The effect on potency of increasing cell concentration may relate to a reduced free concentration of test compound owing to partitioning into cell membranes. In summary, the IonWorks HT hERG assay can generate pIC50 values based on a direct assessment of channel function in a timeframe short enough to influence chemical design.