Involvement of the Galbeta1 - 3GalNAcbeta structure in the recognition of apoptotic bodies by THP-1 cells

A specific apoptotic glycosylation pattern may play an assistant or even a causative role in phagocytosis of apoptotic bodies. To elucidate the role of macrophages in lectin-mediated phagocytosis, an experimental system was used, where monocyte-derived THP-1 cells engulf the apoptotic bodies from the melanoma cell line MELJUSO. A flow cytometry assay was performed to reveal lectin expression and quantify the phagocytosis of apoptotic bodies. Taking into account that siglecs, a mannose receptor and galectins expressed on macrophages could be involved in engulfment of apoptotic bodies we studied their potential expression on THP-1 cells by means of polyacrylamide glycoconjugates. A strong binding of the cells to siglec ligands (3'SiaLac, 6'SiaLac, [Neu5Acalpha2-8]2) and galectin ligands (LacNAc, GalNAcbeta1 - 4GlcNAc, Galbeta1 - 3GalNAcbeta and asialoGM1) was observed. To reveal the corresponding targets on apoptotic bodies, the carbohydrate pattern of MELJUSO cells was analyzed. The apoptotic membrane was characterized by a high level of glycans terminated by galactose or sialic acid. To study lectin-mediated phagocytosis of apoptotic bodies by THP-1 cells, an inhibitory phagocytosis assay was performed. Binding of Galbeta1 - 3GalNAc- or LacNAc-specific reagents (lectins and antibodies) to apoptotic bodies abolished their engulfment by the THP-1 cells whereas blocking of Neu5Acalpha2 - 6 or Neu5Acalpha2 - 3 sites by the corresponding lectins was not effective. Furthermore, Galbeta1 - 3GalNAcbeta-PAA or asialoGM1-PAA binding to the THP-1 cells decreased phagocytosis, whereas two other potent THP-1-binding probes, LacNAc-PAA and GalNAcbeta1 - 4GlcNAc-PAA did not inhibit phagocytosis. Thus, Galbeta1 - 3GalNAcbeta-terminated chains represented on the apoptotic bodies but not the other tested galectin ligands appear to be a target for THP-1 cells.     

Schizosaccharomyces pombe Ddb1 is functionally linked to the replication checkpoint pathway

Schizosaccharomyces pombe Ddb1 is homologous to the mammalian DDB1 protein, which has been implicated in damaged-DNA recognition and global genomic repair. However, a recent study suggested that the S. pombe Ddb1 is involved in cell division and chromosomal segregation. Here, we provide evidence that the S. pombe Ddb1 is functionally linked to the replication checkpoint control gene cds1. We show that the S. pombe strain lacking ddb1 has slow growth due to delayed replication progression. Flow cytometric analysis shows an extensive heterogeneity in DNA content. Furthermore, the Deltaddb1 strain is hypersensitive to UV irradiation in S phase and is unable to tolerate a prolonged replication block imposed by hydroxyurea. Interestingly, the Deltaddb1 strain exhibits a high level of the Cds1 kinase activity during passage through S phase. Moreover, mutation of the cds1 gene relieves the defects observed in Deltaddb1 strain. The results suggest that many of the defects observed in Deltaddb1 cells are linked to an aberrant activation of Cds1, and that Ddb1 is functionally linked to Cds1.     

Quantification of the spatial aspect of chaotic dynamics in biological and chemical systems

The need to study spatio-temporal chaos in a spatially extended dynamical system which exhibits not only irregular, initial-value sensitive temporal behavior but also the formation of irregular spatial patterns, has increasingly been recognized in biological science. While the temporal aspect of chaotic dynamics is usually characterized by the dominant Lyapunov exponent, the spatial aspect can be quantified by the correlation length. In this paper, using the diffusion-reaction model of population dynamics and considering the conditions of the system stability with respect to small heterogeneous perturbations, we derive an analytical formula for an ‘intrinsic length’ which appears to be in a very good agreement with the value of the correlation length of the system. Using this formula and numerical simulations, we analyze the dependence of the correlation length on the system parameters. We show that our findings may lead to a new understanding of some well-known experimental and field data as well as affect the choice of an adequate model of chaotic dynamics in biological and chemical systems.     

Biophysical characterization of cyclic nucleotide phosphodiesterases

We have compared selected biophysical properties of three phosphodiesterases, from Arabidopsis thaliana, Saccharomyces cerevisiae, and Escherichia coli. All of them belong to a recently identified family of cyclic nucleotide phosphodiesterases. Experiments elucidating folding stability, protein fluorescence, oligomerization behavior, and the effects of substrates were conducted, revealing differences between the plant and the yeast protein. According to CD spectroscopy, the latter protein exhibits an (alpha + beta) fold rather than an (alpha/beta) fold as found with CPDase (A. thaliana). The redox-dependent structural reorganization recently found for the plant protein by X-ray crystallography could not be detected by CD spectroscopy due to its only marginal effect on the total percentage of helical content. However, in the present study a redox-dependent effect was also observed for the yeast CPDase. The enzymatic activity of wild type CPDase (A. thaliana) as well as of four mutants were characterized by isothermal titration calorimetry and the results prove the requirement of all four residues of the previously identified tandem signature motif for the catalytic function. Within the comparison of the three proteins in this study, the PDase Homolog/RNA ligase (E. coli) shares more similarities with the plant than with the yeast protein.     

Nucleation and propagation of the collagen triple helix in single-chain and trimerized peptides: transition from third to first order kinetics

The kinetics of triple helix formation from single non-crosslinked peptide chains were studied for the collagen models (ProProGly)10 and (ProHypGly)10 in a broad concentration range and compared with those in nucleated trimers. At very low peptide concentrations the reaction order is 3 but decreases at higher concentrations. For (ProProGly)10 the third order rate constant is 800 M(-2) x s(-1) at 7 degrees C, which corresponds to a very long half time of 15 hours at 60 microM chain concentration. For (ProHypGly)10 the rate constant is about 1000-fold higher, which is consistent with the stabilizing effect of 4-hydroxyproline in collagens. The concentration dependence of the reaction order is explained by a nucleation mechanism in which a very unstable dimer is in fast equilibrium with the monomeric chains and addition of the third chain occurs in a rate-limiting step. At high concentrations nucleation is faster than propagation of helix formation and propagation becomes rate-limiting. To test this hypothesis an artificial nucleus was introduced by fusion of (ProProGly)10 with the trimeric foldon domain of T4 phage or the crosslinking domain of collagen III GlyProProGlyProCysCysGlyGlyGly. These domains were recombinantly attached to the C terminus of (GlyProPro)10 and link the three chains in a similar way to the C-terminal propeptide domain in collagen III. This results in a local intrinsic chain concentration of about 1 M. A first order reaction is observed for the folding of the triple helix in (GlyProPro)10foldon with a half time of 8.3 minutes, which approximately matches the rate of folding from single chains at 1 M peptide concentration. A high activation energy of 54 kJ/mol is found for this reaction, whereas the temperature dependence of the nucleation step is close to zero, confirming earlier findings on natural collagens that cis-trans isomerization of peptide bonds is the rate-limiting step in propagation.     

Structure of dengue virus: implications for flavivirus organization, maturation, and fusion

The first structure of a flavivirus has been determined by using a combination of cryoelectron microscopy and fitting of the known structure of glycoprotein E into the electron density map. The virus core, within a lipid bilayer, has a less-ordered structure than the external, icosahedral scaffold of 90 glycoprotein E dimers. The three E monomers per icosahedral asymmetric unit do not have quasiequivalent symmetric environments. Difference maps indicate the location of the small membrane protein M relative to the overlaying scaffold of E dimers. The structure suggests that flaviviruses, and by analogy also alphaviruses, employ a fusion mechanism in which the distal beta barrels of domain II of the glycoprotein E are inserted into the cellular membrane.     

Tightly bound binary toxin in the cell wall of Bacillus sphaericus

We have shown that urea-extracted cell wall of entomopathogenic Bacillus sphaericus 2297 and some other strains is a potent larvicide against Culex pipiens mosquitoes, with 50% lethal concentrations comparable to that of the well-known B. sphaericus binary toxin, with which it acts synergistically. The wall toxicity develops in B. sphaericus 2297 cultures during the late logarithmic stage, earlier than the appearance of the binary toxin crystal. It disappears with sporulation when the binary toxin activity reaches its peak. Disruption of the gene for the 42-kDa protein (P42) of the binary toxin abolishes both cell wall toxicity and crystal formation. However, the cell wall of B. sphaericus 2297, lacking P42, kills C. pipiens larvae when mixed with Escherichia coli cells expressing P42. Thus, the cell wall toxicity in strongly toxic B. sphaericus strains must be attributed to the presence in the cell wall of tightly bound 51-kDa (P51) and P42 binary toxin proteins. The synergism between binary toxin crystals and urea-treated cell wall preparations reflects suboptimal distribution of binary toxin subunits in both compartments. Binary toxin crystal is slightly deficient in P51, while cell wall is lacking in P42.     

Regulation of Wnt/LRP signaling by distinct domains of Dickkopf proteins

Dickkopfs (Dkks) are secreted developmental regulators composed of two cysteine-rich domains. We report that the effects of Dkks depend on molecular context. Although Wnt8 signaling is inhibited by both Dkk1 and Dkk2 in Xenopus embryos, the same pathway is activated upon interaction of Dkk2 with the Wnt coreceptor LRP6. Analysis of individual Dkk domains and chimeric Dkks shows that the carboxy-terminal domains of both Dkks associate with LRP6 and are necessary and sufficient for Wnt8 inhibition, whereas the amino-terminal domain of Dkk1 plays an inhibitory role in Dkk-LRP interactions. Our study illustrates how an inhibitor of a pathway may be converted into an activator and is the first study to suggest a molecular mechanism for how a ligand other than Wnt can positively regulate beta-catenin signaling.