Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis

Catalytic antibodies 6D9 and 9C10, which were induced by immunization with a haptenic transition-state analog (TSA), catalyze the hydrolysis of a nonbioactive chloramphenicol monoester derivative to generate a bioactive chloramphenicol. These antibodies stabilize the transition state to catalyze the hydrolysis reaction, strictly according to the theoretical relationship: for 6D9, k(cat)/k(uncat)=895 and K(S)/K(TSA)=900, and for 9C10, k(cat)/k(uncat)=56 and K(S)/K(TSA)=60. To elucidate the molecular basis of the antibody-catalyzed reaction, the crystal structure of 6D9 was determined, and the binding thermodynamics of 6D9 and 9C10 with both the substrate and the TSA were analyzed using isothermal titration calorimetry. The crystal structure of the unliganded 6D9 Fab was determined at 2.25 A resolution and compared with that of the TSA-liganded 6D9 Fab reported previously, showing that the TSA is bound into the hydrophobic pocket of the antigen-combining site in an "induced fit" manner, especially at the L1 and H3 CDR loops. Thermodynamic analyses showed that 6D9 binds the substrate of the TSA with a positive DeltaS, differing from general thermodynamic characteristics of antigen-antibody interactions. This positive DeltaS could be due to the hydrophobic interactions between 6D9 and the substrate or the TSA mediated by Trp H100i. The difference in DeltaG between substrate and TSA-binding to 6D9 was larger than that to 9C10, which is in good correlation with the larger k(cat) value of 6D9. Interestingly, the DeltaDeltaG was mainly because of the DeltaDeltaH. The correlation between k(cat) and DeltaDeltaH is suggestive of "enthalpic strain" leading to destabilization of antibody-substrate complexes. Together with X-ray structural analyses, the thermodynamic analyses suggest that upon binding the substrate, the antibody alters the conformation of the ester moiety in the substrate from the planar Z form to a thermodynamically unstable twisted conformation, followed by conversion into the transition state. Enthalpic strain also contributes to the transition-state stabilization by destabilizing the ground state, and its degree is much larger for the more efficient catalytic antibody, 6D9.     

Crosslinking of the CD69 molecule enhances S100A9 production in activated neutrophils

Expression of CD69 on neutrophils and generation of anti-CD69 autoantibodies in patients with rheumatoid arthritis (RA) have been reported. Thus natural ligands for CD69 not yet identified and/or the anti-CD69 autoantibodies possibly affect neutrophils by evoking CD69 signaling, which may further affect joint-composing cells in RA. However, the effect of the CD69 signaling in neutrophils remains largely unclear. To elucidate the issue, we tried to identify proteins affected by the crosslinking of CD69 on neutrophils using a proteomic approach. Specifically, CD69 on granulocyte-macrophage colony stimulating factor (GM-CSF)-activated neutrophils was crosslinked by anti-CD69 monoclonal antibodies, and then intracellular proteins were detected using 2-dimensional electrophoresis and further identified by mass spectrometry and subsequent protein database searching. As a result, we successfully identified multiple proteins that increased their production by the CD69 signaling. Among the proteins, we focused on one of the up-regulated proteins, S100A9 calcium binding protein (S100A9), and investigated proteome changes brought by a recombinant S100A9 in a human synovial sarcoma cell line (SW982), a human chondrosarcoma cell line (OUMS-27), and a human T leukemia cell line (Jurkat). This revealed that the recombinant S100A9 altered proteomes of SW982 and OUMS-27, and to a lesser extent, that of the Jurkat cells. Further, S100A9 induced IL-1beta production from neutrophils and the SW982 cells. These data suggest that unidentified natural ligands for CD69 and/or the anti-CD69 autoantibodies possibly affect joint-composing cell types through the increased production of S100A9 in neutrophils, providing a new insight into functions of CD69 on neutrophils in RA.     

Formation of cytoplasmic P-bodies in sake yeast during Japanese sake brewing and wine making

Recent studies have revealed that cytoplasmic processing bodies (P-bodies) play important roles in the control of eukaryotic gene expression in response to stress. Since the formation of P-bodies is in dynamic competition with translation, the status of translation is reflected in the assembly and disassembly of P-bodies in eukaryotic cells. During the brewing of Japanese sake and the making of wine, yeast cells are exposed to stress caused by increases in the concentration of ethanol. Here we found that ethanol stress enhances the formation of P-bodies in yeast cells in SD medium. In the wine-making process, P-body formation was also enhanced as alcoholic fermentation proceeded, but the formation of P-bodies was not simply affected by the ethanol concentration in the sake mash. These findings suggest differences in the rate of translation and the cytoplasmic mRNA flux during the sake brewing and wine making processes.     

MAMO, a maternal BTB/POZ-Zn-finger protein enriched in germline progenitors is required for the production of functional eggs in Drosophila

A hallmark of germline cells throughout the animal kingdom is their ability to execute meiosis. However, despite its prime importance, little is known about how germline progenitors acquire this ability. In Drosophila, the primordial germ cells (PGCs) are characterized by the inheritance of germ plasm, which contains maternal factors that have sufficient ability to direct germline development. Here, we show that a novel maternal factor, MAMO, is autonomously required in PGCs to produce functional gametes. MAMO protein which contains both a BTB/POZ (Broad Complex, Tramtrack, Bric-a-brac/Pox virus and Zinc finger) domain and C(2)H(2) zinc finger motifs is enriched in PGCs during embryogenesis. The PGCs with reduced maternal MAMO activity are able to undergo oogenesis, but fail to execute meiosis properly. In the resulting oocytes, meiosis-specific chromosomal configurations are impaired. We additionally show that the decondensation of fertilized sperm nuclei is also affected in the eggs. We propose that maternal MAMO activates downstream genes to promote specialized morphological changes of both female meiotic chromosomes and the sperm nucleus, which are critical in zygote formation.     

Deorphanization of Dresden G protein-coupled receptor for an odorant receptor

Dresden G protein-coupled receptor (D-GPCR) is one of orphan G protein-coupled receptors (GPCR). Here we report the identification of the ligands and the characterization of D-GPCR. We investigated over 5000 compounds to evoke the response mediated by D-GPCR and identified 3-methyl-valeric acid and 4-methyl-valeric acid as agonists using a cAMP assay. It is of interest that they dramatically enhanced the intracellular cAMP accumulation and the CRE-luciferase activity in CHO-K1 cells and HEK293 cells expressing the chimeric protein of D-GPCR with a rhodopsin-tag at its N-terminus. Our results established new characteristics of D-GPCR as an olfactory receptor. First, agonists of D-GPCR belong to odorants. Second, D-GPCR mRNA is expressed in the olfactory bulb. In addition, D-GPCR was reported to have similar sequences and its genome locus nearby other olfactory receptors. These results suggest D-GPCR is an olfactory receptor.     

Pars intercerebralis promotes oviposition in the bean bug,Riptortus pedestris (Heteroptera: Alydidae)

Effects of the pars intercerebralis (PI) on the rate of oviposition were examined in adult females of Riptortus pedestris (F.) under long-day conditions that promote reproduction. When the neurosecretory cells in the PI were surgically removed from the females, they laid significantly fewer eggs than control females. When the PI from reproductive females was transplanted to PI-removed females, the number of eggs was significantly greater than that in PI-removed females without transplantation. Therefore, we suggest that the PI neurons promote fecundity or oviposition in R. pedestris.     

α-ENaC in bullfrog embryo: expression in cement gland, gills and skin

The epithelial sodium channel (ENaC) is involved in Na⁺ responses such as Na⁺ absorption and salt taste. The alpha ENaC subunit (α-ENaC) is expressed in the skin of both the adult and larval (tadpole) bullfrog. α-ENaC expression in the developing bullfrog embryo has not been previously investigated. In this study, the expression of α-ENaC at various stages (Sts.) of bullfrog embryonic development is assessed by western blot and immunofluorescence analysis. Bullfrog α-ENaC (α-fENaC) protein was detected by western blot in embryos at Sts. (Gosner/Shumway) 19, 21 and 25. Immunofluorescence studies indicate that α-fENaC was localized to the embryonic cement glands at St. 18 (muscular response), St. 19 (heart beat) and St. 21 (mouth open and/or cornea transparent), to the external gills at St. 21 and to the outermost cell-layer of the skin at St. 25 (operculum complete). The function(s) of ENaC in these embryonic structures remain to be elucidated.     

Structural and Quantitative Evidence for Dynamic Glycome Shift on Production of Induced Pluripotent Stem Cells

We recently reported that induced pluripotent stem cells (iPSCs) prepared from different human origins acquired similar glycan profiles to one another as well as to human embryonic stem cells. Although the results strongly suggested attainment of specific glycan expressions associated with the acquisition of pluripotency, the detailed glycan structures remained to be elucidated. Here, we perform a quantitative glycome analysis targeting both N- and O-linked glycans derived from 201B7 human iPSCs and human dermal fibroblasts as undifferentiated and differentiated cells, respectively. Overall, the fractions of high mannose-type N-linked glycans were significantly increased upon induction of pluripotency. Moreover, it became evident that the type of linkage of Sia on N-linked glycans was dramatically changed from α-2–3 to α-2–6, and the expression of α-1–2 fucose and type 1 LacNAc structures became clearly apparent, while no such glycan epitopes were detected in fibroblasts. The expression profiles of relevant glycosyltransferase genes were fully consistent with these results. These observations indicate unambiguously the manifestation of a “glycome shift” upon conversion to iPSCs, which may not merely be the result of the initialization of gene expression, but could be involved in a more aggressive manner either in the acquisition or maintenance of the undifferentiated state of iPSCs.Induced pluripotent stem cells (iPSCs)¹ are genetically manufactured pluripotent cells obtained by the transfection of reprogramming factors. Such iPSCs were first reported in 2006 for the mouse (1) and in 2007 for humans (2, 3). Although iPSCs have already been used in the fields of drug development and disease models (4–7), basic aspects of iPSCs largely remain to be elucidated to provide us with a fuller understanding of their properties and for therapeutic applications to be developed in the field of regenerative medicine. These aspects include the need for a definitive system to be established to evaluate their properties; e.g. pluripotency, differentiation propensity, risk of possible contamination of xenoantigens, and even the potential for tumorigenesis. Cell surface glycans are often referred to as the “cell signature,” which changes dramatically depending on the cell properties and conditions (8) as a result of changes in gene expression, including epigenetic modifications of glycan-related molecules. Glycans, because of their outermost cell-surface locations and structural complexity, are considered to be most advantageous communication molecules, playing roles in various biological phenomena. Indeed, SSEA3/4 and Tra-1–60/81, which have been used to discriminate pluripotency, are cell surface glycan epitopes that respond to some specific antibodies (9–12).Glycan-mediated cell-to-cell interactions have been shown to play important roles in various biological phenomena including embryogenesis and carcinogenesis (13–16). This might also be the case for the acquisition and maintenance of iPSC and ESC pluripotency, although there remains much to clarify concerning the roles of cell surface glycans in these events. Thus, the development of novel cell surface markers to evaluate the properties of iPSCs and ESCs is keenly required. Toward this goal, a glycomic approach has been made by several groups (17–20). In our previous study using an advanced lectin microarray technique (21), thirty-eight lectins capable of discriminating between iPSCs and SCs were statistically selected, and the characteristic features of the pluripotent state were obtained. The glycan profiles of the parent SCs, derived from four different tissues, were totally different from one another and from those of the iPSCs. Despite this observation, the technique used lacks the ability to determine detailed glycan structures or allow their quantification. For this purpose, a conventional approach based on high performance liquid chromatography (HPLC) combined with matrix-assisted laser desorption-ionization (MALDI) - time of flight (TOF) mass spectrometry (MS) was undertaken for both the definitive identification of glycan structures and their quantitative comparison, which remained unclear in the previous analysis (21).We report here structural data on N-linked and O-linked glycans derived from the human iPSC 201B7 cell line (2) and human dermal fibroblasts (SC) representing undifferentiated and differentiated cells, respectively. For quantitative comparison, the glycans were liberated by gas-phase hydrazinolysis from similar numbers of cells (22–25) fluorescently tagged with 2-aminopyridine (2-AP) at their reducing terminus (26, 27), following which the derived pyridylaminated (PA-) glycans were purified by multiple-mode (i.e. anion-exchange, size-fractionation and reverse-phase) HPLC. Their structures were determined and quantified by HPLC mapping assisted with MALDI-TOF-MS and exoglycosidase digestion analyses. This report thus provides the first structural evidence showing the occurrence of a dynamic “glycome shift” upon induction of pluripotency.