Catalyzing the Critical Path Initiative: FDA's progress in drug development activities.

The US Food and Drug Administration (FDA) has directed considerable effort towards modernizing its regulatory processes over the past decade to address the challenges in the drug development sector. Through partnerships and input from stakeholders, multiple initiatives are under way, many projects have been launched, several have resulted in tangible results, and many are ongoing and under discussion. We are learning that collaborative efforts can better inform and leverage existing knowledge, that the challenges of data sharing and intellectual property can be overcome, and that there is wide interest in partnering to address key public health regulatory science issues. It is crucial that we continue to build on these initial efforts to facilitate drug development.

Gal repressosome contains an antiparallel DNA loop.

Gal repressosome assembly and repression of the gal operon in Escherichia coli occurs when two dimeric GalR proteins and the histone-like HU protein bind to cognate sites causing DNA looping. Structure-based genetic analysis defined the GalR surfaces interacting to form a stacked, V-shaped, tetrameric structure. Stereochemical models of the four possible DNA loops compatible with the GalR tetramer configuration were constructed using the sequence-dependent structural parameters of the interoperator DNA and conformation changes caused by GalR and asymmetric HU binding. Evaluation of their DNA elastic energies gave unambiguous preference to a loop structure in which the two gal operators adopt an antiparallel orientation causing undertwisting of DNA.

GalR mutants defective in repressosome formation.

Transcription repression of the galactose operon of Escherichia coli requires (1) the binding of the GalR repressor to tandem operators flanking the promoters, (2) the binding of histone-like protein, HU, to a site between the GalR-binding sites, and (3) negatively supercoiled DNA. Under these conditions, protein-protein interactions mediate the formation of a nucleoprotein complex in the form of a DNA loop, which we have termed a repressosome. To analyze the structure of the repressosome, we have screened and isolated galR mutants in which single amino acid substitutions in GalR lead to defects in loop formation while the protein's operator-binding activity is retained. The mutant proteins were purified and their properties confirmed in vitro. We verified that in the case of the two stronger mutations, the proteins had secondary structures that were identical to that of wild-type GalR as reflected by circular dichroism spectroscopy. Homology-based modeling of GalR by use of the crystal structures of PurR and LacI has enabled us to place the three sites of mutation in a structural context. They occur in the carboxy-terminal subdomain of the GalR core, are surface exposed, and, therefore, may be involved in protein-protein interactions. On the basis of our model of GalR and its structural alignment with LacI and PurR, we have identified additional residues, the substitution of which leads to a specific defect in repression by looping. The effects of the mutations are the same in the presence of HMG-17, a eukaryotic protein unrelated to HU, which can also mediate GalR-dependent repression of the gal promoter. This observation suggests that the mutations define sites of GalR-GalR interaction rather than HU-GalR interaction in the repressosome.

Role of HU and DNA supercoiling in transcription repression: specialized nucleoprotein repression complex at gal promoters in Escherichia coli.

Efficient repression of the two promoters P1 and P2 of the gal operon requires the formation of a DNA loop encompassing the promoters. In vitro, DNA looping-mediated repression involves binding of the Gal repressor (GalR) to two gal operators (OE and OI) and binding of the histone-like protein HU to a specific locus (hbs) about the midpoint between OE and OI, and supercoiled DNA. Without DNA looping, GalR binding to OE partially represses P1 and stimulates P2. We investigated the requirement for DNA supercoiling and HU in repression of the gal promoters in vivo in strains containing a fusion of a reporter gene, gusA or lacZ, to each promoter individually. While the P1 promoter was found to be repressible in the absence of DNA supercoiling and HU, the repression of P2 was entirely dependent upon DNA supercoiling in vivo. The P2 promoter was fully derepressed when supercoiling was inhibited by the addition of coumermycin in cells. P2, but not P1, was also totally derepressed by the absence of HU or the OI operator. From these results, we propose that the repression of the gal promoters in vivo is mediated by the formation of a higher order DNA-multiprotein complex containing GalR, HU and supercoiled DNA. In the absence of this complex, P1 but not P2 is still repressed by GalR binding to OE. The specific nucleoprotein complexes involving histone-like proteins, which repress promoter activity while remaining sensitive to inducing signals, as discussed, may occur more generally in bacterial nucleoids.

Transcription regulation by repressosome and by RNA polymerase contact.

The original model of repression of transcription initiation is steric interference of RNA polymerase binding to a promoter by its repressor protein bound to a DNA site that overlaps the promoter. From the results described here, we propose two other mechanisms of repressor action, both of which involve formation of higher-order DNA-multiprotein complexes. These models also explain the problem of RNA polymerase gaining access to a promoter in the condensed nucleoid in response to an inducing signal to initiate transcription.

Functional characterization of roles of GalR and GalS as regulators of the gal regulon.

An isorepressor of the gal regulon in Escherichia coli, GalS, has been purified to homogeneity. In vitro DNase I protection experiments indicated that among operators of the gal regulon, GalS binds most strongly to the external operator of the mgl operon, which encodes the high-affinity beta-methylgalactoside galactose transport system, and with less affinity to the operators controlling expression of the gal operon, which codes for enzymes of galactose metabolism. GalS has even less affinity for the external operator of galP, which codes for galactose permease, the major low-affinity galactose transporter in the cell. This order of affinities is the reverse of that of GalR, which binds most strongly to the operator of galP and most weakly to that of mgl. Our results also show that GalS, like its homolog, GalR, is a dimeric protein which in binding to the bipartite operators of the gal operon selectively represses its P1 promoter. Consistent with the fact that GalR is the exclusive regulator of the low-affinity galactose transporter, galactose permease, and that the major role of GalS is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, we found that the DNA binding of GalS is 15-fold more sensitive than that of GalR to galactose.

Platelet adhesion to collagen via the alpha 2 beta 1 integrin under arterial flow conditions causes rapid tyrosine phosphorylation of pp125FAK.

Adhesion of human platelets to collagen under arterial flow conditions mediated by the alpha 2 beta 1 integrin increased tyrosine phosphorylation of several proteins, one of which was the focal adhesion tyrosine kinase, pp125FAK. Tyrosine phosphorylation of pp125FAK did not occur in non-adherent flowing platelets or in platelets attached to poly(L-lysine). Neither adhesion nor tyrosine phosphorylation was affected by pretreatment of platelets with GRGDSP peptide or by anti-alpha IIb beta 3 monoclonal antibody P2. Adherent platelets retained their discoid shape, suggesting that induction of pp125FAK precedes platelet spreading. The tyrosine kinase inhibitor erbstatin decreased tyrosine phosphorylation in non-stimulated platelets and blocked platelet adhesion. These results suggest that pp125FAK plays an important role in platelet adhesion to collagen via the alpha 2 beta 1 integrin.

The role of protein kinase C in the initial events of platelet activation by thrombin assessed with a selective inhibitor.

The role of protein kinase C (PKC) in platelet activation by thrombin was assessed using a PKC inhibitor Ro 31-7549/001 (R2) which, in vitro, shows more selectivity for PKC than other kinase inhibitors. During early (1.5 s) thrombin-induced platelet activation, when phosphorylation of 47 kDa protein (pleckstrin) and myosin light chain by PKC and myosin light chain kinase, respectively, are most readily differentiated, R2 suppressed phosphorylation of pleckstrin more effectively than myosin light chain. R2-inhibited dense granule secretion (measured 0-10 s using quenched-flow techniques) with a dose dependency similar to that for inhibition of pleckstrin phosphorylation, supporting a role for PKC in this process. R2, at 0.5 microM inhibited 47 kDa protein phosphorylation by more than 60%, but had only minimal effects on the kinetics (0-3s) of ADP-induced primary aggregation. At this same concentration, R2 potentiated the thrombin-induced rise in cytosolic calcium during early (0-15 s) activation as measured in the presence or absence of external calcium. These data support the hypothesis that activation of PKC during early platelet function helps regulate cytosolic calcium levels by limiting calcium release into the cytosol.

Application of spray-freezing to the study of rapid platelet reactions by a quenched-flow approach.

A spray-freezing approach coupled to quenched-flow techniques has been developed to study rapid (0.3-5.0 s) biochemical and morphological changes during platelet activation. Platelet-rich plasma (PRP) pumped through the quenched-flow system was atomized and quenched within 50 ms in liquid propane at -196 degrees C. Analysis of platelet size and morphology by scanning electron microscopy (SEM) indicated that platelets can be sprayed without morphological damage. The spray-frozen platelets can be subjected to freeze-fracture, freeze-substitution, or freeze-drying procedures for later analysis by electron microscopy. Quenched-flow techniques have permitted investigation of rapid increases in cytosolic calcium protein phosphorylation and morphological changes which occur within 0.5 s after exposure to an activator. The combination of quenched-flow and spray-freezing methodologies should prove useful for studying equally rapid changes in protein distribution in activated platelets by means of electron microscopy coupled with immunocytochemical approaches.