Mode of insertion of the broad-host-range plasmid RP4 and its derivatives into the chromosome of Myxococcus xanthus

The mode of insertion of the broad-host-range plasmid RP4 into the chromosome of Myxococcus xanthus strain DZ1 has been analyzed. The plasmid integrated in numerous sites of the chromosome and generated insertional mutations. There is a hot spot of integration located between 31.5 and 34.5 kb clockwise from the EcoRI site of the plasmid. In the absence of this segment the insertion can, however, take place, but much less efficiently. The presence of transposable elements on the plasmid decreases severely the insertion frequency. Once integrated, RP4 could be transferred back to Escherichia coli, either by precise excision or with a segment of the Myxococcus chromosome. The role of site-specific recombination in RP4 integration is discussed.     

Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

The organization and mining of malaria genomic and post-genomic data is important to significantly increase the knowledge of the biology of its causative agents, and is motivated, on a longer term, by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should, therefore, be as reliable and versatile as possible. In this context, five aspects of the organization and mining of malaria genomic and post-genomic data were examined: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes, particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Recent progress towards a grid-enabled chemogenomic knowledge space is discussed.     

Photoaffinity labeling of the aglycon binding site of the recombinant human liver UDP-glucuronosyltransferase UGT1A6 with 7-azido-4-methylcoumarin.

7-Azido-4-methylcoumarin (AzMC) is a fluorescent photoactive compound structurally related to 4-methylumbelliferone (4-MU), a marker substrate of the human liver recombinant UDP-glucuronosyltransferase (UGT) 1A6. AzMC was synthesized and utilized to label the substrate binding site of UGT1A6. AzMC exhibits a fluorescence spectrum with maximum excitation and emission wavelengths of 380 and 442 nm, respectively. Upon irradiation, the probe irreversibly inhibited glucuronidation activity measured with para-nitrophenol (pNP) as substrate and interacted with UGT1A6 according to a saturable process indicative of reversible binding before covalent incorporation of the photoaffinity label. This inhibition was both time and concentration dependent and led to the calculation of an inhibition constant, k(2) = 0.113 mM min(-1), and dissociation constant, K(d) = 2.89 mM, for the reaction. Partial photoinactivation of UGT1A6 with AzMC revealed that the probe decreased the apparent V(max) of the pNP glucuronidation reaction, but not the K(m). Moreover, inhibition was partially prevented by 1-naphthol, a surrogate substrate for the enzyme, or by preincubation with an active-site directed inhibitor, 5'-O-[[(2-decanoylamino-3-phenyl-propyloxycarbonyl)amino]-su lfonyl]-2 ',3'-O-isopropylideneuridine. In contrast, UDP-glucuronic acid (UDP-GlcUA) did not have any protective effect against photoinactivation and AzMC did not affect the photoaffinity labeling of UGT1A6 by 5-[beta-(32)P]N(3)UDP-GlcUA, a photoaffinity analog of UDP-GlcUA. Additionally, in the absence of irradiation, AzMC was found to be a competitive inhibitor of 4MU glucuronidation. Collectively, these results strongly indicate that AzMC specifically binds to the UGT1A6 aglycon binding site. Amino acid alignment of phenol-binding proteins revealed a conserved motif, YXXXKXXPXP. It is possible that this motif is involved in phenol binding to UGT1A6 and other phenol-accepting proteins.     

Effect of cell swelling on membrane and cytoplasmic distribution of pICln

pI_Cln is found ubiquitouslyin mammalian cells and is postulated to play a critical role in cellvolume regulation. Mutagenesis studies led to the proposal thatpI_Cln is a swelling-activated anion channel. However, recent studies in Madin-Darby canine kidney cells and endothelial cells have shown that the protein is localized primarily to the cytoplasm. It has therefore been postulated that activation involves reversible translocation ofpI_Cln from the cytoplasm andinsertion into the plasma membrane. We tested this hypothesis usingseveral different approaches. Fractionation of C₆ glioma cells into plasmamembrane- and cytoplasm-containing fractions demonstrated that ~90%of the recovered pI_Cln wasconfined to the cytosol. Swelling had no effect on the relative amount of protein present in the plasma membrane fraction. Immunofluorescence microscopy revealed that pI_Cln islocalized primarily, if not exclusively, to the cytoplasm of swollenand nonswollen cells. Similarly, transfection of cells with a greenfluorescent protein-labeled pI_Clnconstruct failed to reveal any membrane localization of the protein.These findings do not support the hypothesis that pI_Cln is a volume regulatory anionchannel activated by swelling-induced membrane insertion.

     

A new genus and species of Asteriidae (Asteroidea; Echinodermata) from the Upper Cretaceous (Coniacian) of Angola,Africa

Afraster scalariformis n.gen. et sp., from the Upper Cretaceous (Coniacian) of Angola, southwest Africa, is assigned to the Pedicellasterinae, a subfamily of the Asteriidae. An associated foraminiferal fauna is dominated by planktic species; also present are lagenids that are indicative of a shelf setting. The subfamily Pedicellasterinae is peculiar in that only two rows of podia are present, rather than the four typical of the family. Intimate association ofAfraster with oysters suggests the predatory habits typical of modern asteriids; general arm and disk arrangement also suggest such a behavior.Afraster is the first recorded fossil asteroid from Angola.     

Orientation of pigments in the thylakoid membrane and in the isolated chlorophyll-protein complexes of higher plants. I. Determination of optimal conditions for linear dichroism measurement

The nature and possible causes of polarized light-scattering artefacts in linear dichroism measurements are investigated. Using criteria described in this article, the available orientation techniques have been critically assessed in order to obtain the linear dichroism spectra of thylakoids and of pigment-protein complexes isolated from pea. It is demonstrated here that the polyacrylamide gel squeezing technique of Abdourakhmanov et al. (Abdourakhmanov, I.A., Ganago, A.O., Erokhim, Yu.E., Solov'ev, A.A. and Chugunov, V.A. (1979) Biochim. Biophys. Acta 546, 183–186) does not lead to pigment degradation and that the linear dichroism spectra obtained in these conditions are essentially free of scattering artefacts. The linear dichroism spectra of light-harvesting complex isolated in different states of aggregation or incorporated into phospholipid vesicles are compared to the spectra of thylakoids. This comparison indicates: (1) that the isolation procedure of Burke et al. (Burke, J.J., Ditto, C.L. and Arntzen, C.J. (1978) Arch. Biochem. Biophys. 187, 252–263) leads to light-harvesting complex in which the in vivo orientation of pigments is preserved; (2) that the antenna chlorophyll a molecules of this complex have a significant degree of orientation with respect to the plane of the thylakoid.     

On the occurrence of a possible bioconversion of linolenic acid into docosahexaenoic acid by the copepod Eucyclops serrulatus fed on microalgae

Reared in fertilized basins, Eucydops serrulatus appeared tobe able to biosynthesize 22:6     

Experimental evidence for multistability in a photobiochemical system

The kinetic behavior of a typical Hill reaction catalyzed by thylakoids and using the oxidized form of 2,6-dichloroindophenol (DCPIPox) as the artificial electron acceptor, is considered. Here, the light absorption process and the reduction of DCPIPox are autocatalytically coupled, leading to the occurrence of multiple steady states with respect to either the acceptor concentration or the incident light intensity. Experimental evidence is presented for both cases and the emergence of autocatalysis is discussed. The effect of the spatial arrangement on the global behavior of the system described is emphasized.