Structural characterization of the bifunctional glucanase-xylanase CelM2 reveals the metal effect and substrate-binding moiety

The bifunctional glycoside hydrolase enzyme, CelM2, is able to hydrolyze glucan and xylan effectively. The crystal structure of this protein has been determined, providing useful sequential and structural information [K.H. Nam, S.J. Kim, K.Y. Hwang, Crystal structure of CelM2, a bifunctional glucanase-xylanase protein from a metagenome library, Biochem. Biophys. Res. Commun. 383 (2009) 183-186]. In addition, this protein is a good model for understanding bifunctional enzymes, and it will provide information relevant for genetic engineering that will be useful in the design of bifunctional proteins. However, previous structural characterization was not sufficient to develop an understanding of the metal ion and substrate-binding moiety.Herein, we determined the metal-binding site of CelM2 using zinc ions. Our results revealed that the zinc ions participate in the crystallographic packing and enzyme folding of the external region of the TIM-like barrel domain. Based on our structure, zinc ions induce the passive form of the CAP region at the catalytic cleft of the CelM2 protein. Moreover, glucose was bound to the CelM2 structure at the catalytic site. This structure provides the binding moiety that binds to the hydroxyl group of substrates such as cellulose. In addition, a structural comparison of celM2 with Cel44 provides a good model of the binding mode of CelM2. Thus, our study represents a novel structural characterization of the metal-binding site and the structure of the complex formed between CelM2 and its substrate.     

Induced changes in the proteomic profile of the phaeophyte Saccharina japonica upon colonization by the bryozoan Membranipora membranacea

The lacy crust bryozoan Membranipora membranacea frequently colonizes the late harvested blades of aquacultured Saccharina japonica. From proteomic profiles of S. japonica, 145 and 91 protein spots were detected from colonized and healthy tissues, respectively. Among them, 69 and 32 spots were significantly up- and downregulated, respectively, in expression level upon colonization. In M. membranacea colonized tissue, tripartite motif protein 2-like, microcompartments protein, carboxysome peptide shell peptide, trypsin precursor-like, transmembrane protein, two-component response regulator PilR, spermine/spermidine synthase, vanadium-dependent bromoperoxidase, peptide chain release factor 1, interaptin, 50S ribosomal protein L1P, plus agglutinin and leucine-rich repeat protein were upregulated, whereas protoporphyrinogen oxidase, PIH1 domain-containing protein 2, GTPase-activating protein alpha, cytoplasmic threonyl-tRNA synthetase, flavanone 3-hydroxylase, and eukaryotic translation initiation factor 3 proteins were downregulated. Moreover, DEAD/DEAH box helicase, glutamyl-tRNA reductase, and chaperone DnaJ protein were newly expressed in the colonized tissue. Most of the up- and downregulated proteins are known to be related to stress control, defense mechanisms, signal transduction, photosynthesis, protein metabolism, and the cytoskeleton.     

Structural Basis of Lipid Binding for the Membrane-embedded Tetraacyldisaccharide-1-phosphate 4′-Kinase LpxK

The membrane-bound tetraacyldisaccharide-1-phosphate 4′-kinase, LpxK, catalyzes the sixth step of the lipid A (Raetz) biosynthetic pathway and is a viable antibiotic target against emerging Gram-negative pathogens. We report the crystal structure of lipid IV_A, the LpxK product, bound to the enzyme, providing a rare glimpse into interfacial catalysis and the surface scanning strategy by which many poorly understood lipid modification enzymes operate. Unlike the few previously structurally characterized proteins that bind lipid A or its precursors, LpxK binds almost exclusively to the glucosamine/phosphate moieties of the lipid molecule. Steady-state kinetic analysis of multiple point mutants of the lipid-binding pocket pinpoints critical residues involved in substrate binding, and characterization of N-terminal helix truncation mutants uncovers the role of this substructure as a hydrophobic membrane anchor. These studies make critical contributions to the limited knowledge surrounding membrane-bound enzymes that act upon lipid substrates and provide a structural template for designing small molecule inhibitors targeting this essential kinase.     

The Synergistic Immunoregulatory Effects of Culture-Expanded Mesenchymal Stromal Cells and CD4+25+Foxp3+ Regulatory T Cells on Skin Allograft Rejection

Mesenchymal stromal cells (MSCs) are seen as an ideal source of cells to induce graft acceptance; however, some reports have shown that MSCs can be immunogenic rather than immunosuppressive. We speculate that the immunomodulatory effects of regulatory T cells (Tregs) can aid the maintenance of immunoregulatory functions of MSCs, and that a combinatorial approach to cell therapy can have synergistic immunomodulatory effects on allograft rejection. After preconditioning with Fludarabine, followed by total body irradiation and anti-asialo-GM-1(ASGM-1), tail skin grafts from C57BL/6 (H-2k^b) mice were grafted onto the lateral thoracic wall of BALB/c (H-2k^d) mice. Group A mice (control group, n = 9) did not receive any further treatment after preconditioning, whereas groups B and C (n = 9) received cell therapy with MSCs or Tregs, respectively, on days −1, +6 and +13 relative to the skin transplantation. Group D (n = 10) received cell therapy with MSCs and Tregs on days −1, +6 and +13. Cell suspensions were obtained from the spleens of five randomly chosen mice from each group on day +7, and the immunomodulatory effects of the cell therapy were evaluated by flow cytometry and real-time PCR. Our results show that allograft survival was significantly longer in group D compared to the control group (group A). Flow cytometric analysis and real-time PCR for splenocytes revealed that the Th2 subpopulation in group D increased significantly compared to the group B. Also, the expression of Foxp3 and STAT 5 increased significantly in group D compared to the conventional cell therapy groups (B and C). Taken together, these data suggest that a combined cell therapy approach with MSCs and Tregs has a synergistic effect on immunoregulatory function in vivo, and might provide a novel strategy for improving survival in allograft transplantation.     

Molecular evidence for hybridization ofIlex x wandoensis (Aquifoliaceae) by RAPD analysis

Based on the presence of intermediate morphological characters, such as serrated leaf margins and flower structures,Ilex x wandoensis was initially described as a putative natural hybrid betweenI. cornuta andI. Integra, and was formally described as a new hybrid species,I. x wandoensis C. F. Mill., and M. Kim. However, using molecular markers generated via random amplified polymorphic DNA (RAPD), we have now discovered hybridization in populations of theI. x wandoensis complex collected from Wando and Jeju Islands, Korea. Marker bands of the putative parent taxa also were found in some populations ofI. x wandoensis, confirming its hybrid origin. Morphological variability within and among those populations was confirmed by model-based clustering methods, using multilocus genotype data. Phenograms generated from RAPD bands indicated that some accessions ofI. x wandoensis clustered with one of the parental species. This implied the occurrence of hybridization and recurring backcrosses of the hybrid to both parents, resulting in various hybrid derivatives because of the segregation and recombination of traits.Ilex x wandoensis was more closely related toI. cornuta than toI. integra suggesting that it backcrossed more with the former than with the latter.     

Mapping of Dbr1 and Ypk1 Suggests a Major Revision of the Genetic Map of the Left Arm of Saccharomyces Cerevisiae Chromosome Xi

The Saccharomyces cerevisiae dbr1 mutation has been mapped on the left arm of chromosome XI. XIL is a chromosome arm that was until now rather sparsely populated with accurately mapped markers. On the basis of physical data, the overall order of markers is inverted relative to the existing genetic map of XI. We present tetrad analyses using a variety of markers on XI that indicate that the existing genetic map of XIL should be inverted, at least for the strains in which our mapping was carried out, and probably for other S. cerevisiae strains.