Effects of Chloride Ion Binding on the Photochemical Properties of Salinibacter Sensory Rhodopsin I

Microbial organisms utilize light not only as energy sources but also as signals by which rhodopsins (containing retinal as a chromophore) work as photoreceptors. Sensory rhodopsin I (SRI) is a dual photoreceptor that regulates both negative and positive phototaxis in microbial organisms, such as the archaeon Halobacterium salinarum and the eubacterium Salinibacter ruber. These organisms live in highly halophilic environments, suggesting the possibility of the effects of salts on the function of SRI. However, such effects remain unclear because SRI proteins from H. salinarum (HsSRI) are unstable in dilute salt solutions. Recently, we characterized a new SRI protein (SrSRI) that is stable even in the absence of salts, thus allowing us to investigate the effects of salts on the photochemical properties of SRI. In this study, we report that the absorption maximum of SrSRI is shifted from 542 to 556 nm in a Cl⁻-dependent manner with a K_m of 307 ± 56 mM, showing that Cl⁻-binding sites exist in SRI. The bathochromic shift was caused not only by NaCl but also by other salts (NaI, NaBr, and NaNO₃), implying that I⁻, Br⁻, and NO₃⁻ can also bind to SrSRI. In addition, the photochemical properties during the photocycle are also affected by chloride ion binding. Mutagenesis studies strongly suggested that a conserved residue, His131, is involved in the Cl⁻-binding site. In light of these results, we discuss the effects of the Cl⁻ binding to SRI and the roles of Cl⁻ binding in its function.     

Pancreatic cancer cells activate CCL5 expression in mesenchymal stromal cells through the insulin-like growth factor-I pathway

Mesenchymal stromal cells (MSCs) have a critical role in cancer progression and metastasis. Despite extensive studies of the physiological responses in cancer cells, the molecular mechanisms regulating gene expression in MSCs by cancer cells remain undefined. Here we demonstrate that CC chemokine ligand 5 (CCL5) expression was increased in MSCs co-cultured with pancreatic cancer cells (PCCs), and this activation was dependent on extracellular insulin-like growth factor (IGF-I). Moreover, CCL5 induction in MSCs was required for the activation of IGF-I pathway in PCCs. These results reveal a link between the IGF-I pathway in PCCs and CCL5 pathway in MSCs through the interaction of those cells.     

Drosophila big brain does not act as a water channel, but mediates cell adhesion

The neurogenic gene Drosophilabig brain (bib) has a high sequence homology to aquaporin-4. However, its cellular functions in Drosophila neurogenesis have remained elusive. Here we investigated cell adhesion, and the ion and water permeability of Bib. The adhesive function was examined by a cell aggregation assay using L cells. Bib-transfected L cells formed aggregated clusters, while control-L cells remained as a single cell suspension. Ion permeation was not confirmed in L cells stably expressing Bib. When expressed in COS7 cells, Bib exhibited limited water permeability. This newly found cell adhesive function of Bib may be important for Drosophila neurogenesis.     

Optimizing pH Response of Affinity between Protein G and IgG Fc: HOW ELECTROSTATIC MODULATIONS AFFECT PROTEIN-PROTEIN INTERACTIONS*S?

Protein-protein interaction in response to environmental conditions enables sophisticated biological and biotechnological processes. Aiming toward the rational design of a pH-sensitive protein-protein interaction, we engineered pH-sensitive mutants of streptococcal protein G B1, a binder to the IgG constant region. We systematically introduced histidine residues into the binding interface to cause electrostatic repulsion on the basis of a rigid body model. Exquisite pH sensitivity of this interaction was confirmed by surface plasmon resonance and affinity chromatography employing a clinically used human IgG. The pH-sensitive mechanism of the interaction was analyzed and evaluated from kinetic, thermodynamic, and structural viewpoints. Histidine-mediated electrostatic repulsion resulted in significant loss of exothermic heat of the binding that decreased the affinity only at acidic conditions, thereby improving the pH sensitivity. The reduced binding energy was partly recovered by “enthalpy-entropy compensation.” Crystal structures of the designed mutants confirmed the validity of the rigid body model on which the effective electrostatic repulsion was based. Moreover, our data suggested that the entropy gain involved exclusion of water molecules solvated in a space formed by the introduced histidine and adjacent tryptophan residue. Our findings concerning the mechanism of histidine-introduced interactions will provide a guideline for the rational design of pH-sensitive protein-protein recognition.Molecular interactions govern a number of biological processes, including metabolism, signal transduction, and immunoreaction. A better understanding of the molecular basis for these interactions is crucial for a complete elucidation of biological phenomena and redesign of interactions for drug discovery and industrial biotechnology applications. Interactions between biomolecules are generally characterized by their affinity, specificity, and environmental responsiveness, such as sensitivity to pH. Such pH-dependent ligand binding enables biological processes to function in an “on and off” manner in response to environmental conditions, resulting in sophisticated systems of regulation (e.g. pheromone production (1, 2), immune systems (3-5), and mechanisms of virus survival (6)).From an industrial perspective, pH sensitivity is advantageous to various fields, such as drug delivery systems for medications (7), biosensing techniques (8, 9), and affinity chromatography (10, 11). Although structure-based protein design is a promising technique for improving molecular function (12-15), it is yet difficult to specifically modulate pH sensitivity of a protein-protein interaction without an associated loss of inherent function and/or structural stability. Some naturally occurring proteins undergo substantial conformational change by pH shift, thereby achieving pH-dependent binding for small molecules (2, 4, 16, 17). However, artificial design of an equivalent mechanism involving conformational change is highly problematic. Indeed, proteins have multiple degrees of freedom and consist of a large number of atoms. Therefore, given that the resulting protein must maintain both its innate binding ability and structural stability, the system appears too complicated for rational design. By contrast to the method based on conformational change, a rigid body-based model (i.e. introduction of electrostatic repulsion or attraction into a binding interface between rigid protein domains) could be a more promising approach for pH switching. Naturally occurring proteins with pH sensitivity generally conserve histidine residues (18-21), which function as a pH switch at slightly acidic conditions (pH ∼6.5) near the pK_a of the histidine side chain. In the presence of a histidine residue at a binding interface, dissociation under acidic conditions would be driven by electrostatic repulsion between rigid domains without conformational change (Fig. 1). This mechanism is rather simple and applicable to protein engineering (22, 23). However, to our knowledge, it still remains unclear how systematic design should be carried out and, in particular, how histidine-mediated electrostatic repulsion influences protein-protein interactions. Indeed, very little experimental data are available for the molecular basis of histidine-introduced protein binders.Open in a separate windowFIGURE 1.A schematic model for introduction of histidine-mediated electrostatic repulsion into the binding interface between protein G (GB) and Fc. Protein G residues positioned closely to basic side chains (depicted as B) on Fc were systematically identified by distance calculations and mutated into histidine to cause electrostatic repulsion under acidic conditions. The inset shows an example of candidate positions for the mutation.To better understand the design methodology for a pH-sensitive protein-protein interaction, we generated a number of pH-sensitive streptococcal protein G B1 (24) mutants by rationally introducing histidine residues onto the binding surface. Protein G, a bacterial Fc (fragment of crystallizable region) receptor to the constant region of IgG, has been used as an affinity chromatography binder for antibody immobilization and purification. Protein G has an acidic pH optimum for binding relative to another bacterial Fc receptor, Staphylococcus aureus protein A. The harsh elution conditions are likely to induce acidic conformational changes in antibodies (25, 26) during the purification procedure, causing aggregation that is problematic for pharmaceutical applications. The usefulness of the histidine-mediated electrostatic repulsion for antibody purification was examined by constructing affinity chromatography columns. Using the designed mutants, we analyzed the molecular basis of the histidine-mediated interaction from a kinetic, thermodynamic, and structural perspective. The observed data revealed functional and structural consequences for the introduction of histidine residues. Analysis of our results provides a guideline for the design of pH-dependent protein-protein interactions.     

Differences in human macrophage receptor usage, lysosomal fusion kinetics and survival between logarithmic and metacyclic Leishmania infantum chagasi promastigotes

The obligate intracellular protozoan, Leishmania infantum chagasi (Lic) undergoes receptor-mediated phagocytosis by macrophages followed by a transient delay in phagolysosome maturation. We found differences in the pathway through which virulent Lic metacyclic promastigotes or avirulent logarithmic promastigotes are phagocytosed by human monocyte-derived macrophages (MDMs). Both logarithmic and metacyclic promastigotes entered MDMs through a compartment lined by the third complement receptor (CR3). In contrast, many logarithmic promastigotes entered through vacuoles lined by mannose receptors (MR) whereas most metacyclic promastigotes did not ( P  < 0.005). CR3-positive vacuoles containing metacyclic promastigotes stained for caveolin-1 protein, suggesting CR3 localizes in caveolae during phagocytosis. Following entry, the kinetics of phagolysosomal maturation and intracellular survival also differed. Vacuoles containing metacyclic parasites did not accumulate lysosome-associated membrane protein-1 (LAMP-1) at early times after phagocytosis, whereas vacuoles with logarithmic promastigotes did. MDMs phagocytosed greater numbers of logarithmic than metacyclic promastigotes, yet metacyclics ultimately replicated intracellularly with greater efficiency. These data suggest that virulent metacyclic Leishmania promastigotes fail to ligate macrophage MR, and enter through a path that ultimately enhances intracellular survival. The relatively quiescent entry of virulent Leishmania spp. into macrophages may be accounted for by the ability of metacyclic promastigotes to selectively bypass deleterious entry pathways.     

Genetic Evidence That the Non-Homologous End-Joining Repair Pathway Is Involved in LINE Retrotransposition

Long interspersed elements (LINEs) are transposable elements that proliferate within eukaryotic genomes, having a large impact on eukaryotic genome evolution. LINEs mobilize via a process called retrotransposition. Although the role of the LINE-encoded protein(s) in retrotransposition has been extensively investigated, the participation of host-encoded factors in retrotransposition remains unclear. To address this issue, we examined retrotransposition frequencies of two structurally different LINEs—zebrafish ZfL2-2 and human L1—in knockout chicken DT40 cell lines deficient in genes involved in the non-homologous end-joining (NHEJ) repair of DNA and in human HeLa cells treated with a drug that inhibits NHEJ. Deficiencies of NHEJ proteins decreased retrotransposition frequencies of both LINEs in these cells, suggesting that NHEJ is involved in LINE retrotransposition. More precise characterization of ZfL2-2 insertions in DT40 cells permitted us to consider the possibility of dual roles for NHEJ in LINE retrotransposition, namely to ensure efficient integration of LINEs and to restrict their full-length formation.     

Development of EST-SSR markers from an inner bark cDNA library of Fagus crenata (Fagaceae)

Fagus crenata Blume is widely distributed throughout Japanese cool-temperate deciduous broad-leaved forests, but there are two divergent groups of populations in areas with contrasting winter climates separated by Japan’s Central Mountain Range. To facilitate investigations of adaptive genetic differentiation of the species using potentially functional genes, we have collected Expressed Sequence Tags and developed Simple Sequence Repeat markers using a cDNA library constructed from cambium and surrounding tissues. In total, 270 primer pairs were designed, and 87 of the corresponding loci showed polymorphism in 16 individuals, with 2–21 alleles per locus and expected heterozygosities ranging from 0.06 to 0.97. EST-SSR markers developed in the present study will be useful for genomic analyses of F. crenata populations.     

High-Sensitivity Real-Time Imaging of Dual Protein-Protein Interactions in Living Subjects Using Multicolor Luciferases

Networks of protein-protein interactions play key roles in numerous important biological processes in living subjects. An effective methodology to assess protein-protein interactions in living cells of interest is protein-fragment complement assay (PCA). Particularly the assays using fluorescent proteins are powerful techniques, but they do not directly track interactions because of its irreversibility or the time for chromophore formation. By contrast, PCAs using bioluminescent proteins can overcome these drawbacks. We herein describe an imaging method for real-time analysis of protein-protein interactions using multicolor luciferases with different spectral characteristics. The sensitivity and signal-to-background ratio were improved considerably by developing a carboxy-terminal fragment engineered from a click beetle luciferase. We demonstrate its utility in spatiotemporal characterization of Smad1–Smad4 and Smad2–Smad4 interactions in early developing stages of a single living Xenopus laevis embryo. We also describe the value of this method by application of specific protein-protein interactions in cell cultures and living mice. This technique supports quantitative analyses and imaging of versatile protein-protein interactions with a selective luminescence wavelength in opaque or strongly auto-fluorescent living subjects.     

Identification of potent 5-pyrimidinyl-2-aminothiazole CDK4, 6 inhibitors with significant selectivity over CDK1, 2, 5, 7, and 9

5-Pyrimidinyl-2-aminothiazole 1 was identified as an inhibitor of cyclin-dependent kinases (CDKs) by a screening of the Merck sample repository. The introduction of a methyl group at the C-5 or C-6 position on the pyrimidine ring, directed toward the gate keeper residue of CDK4 (Phe93), led to significant enhancement of selectivity for CDK4 over other CDKs. Compound 3 exhibited more than 300-fold selectivity for CDK4 over CDK1, 2, 5, 7, and 9. Subsequent improvements in aqueous solubility afforded compound 4, which is available for further in vivo studies and this compound inhibited pRb phosphorylation and BrdU incorporation in tumor models.