Observation by Real-Time NMR and Interpretation of Length- and Location-Dependent Deamination Activity of APOBEC3B

Human APOBEC3B (A3B) deaminates a cytosine into a uracil in single-stranded (ss) DNA, resulting in human cancers. A3B’s deamination activity is conferred by its C-terminal domain (CTD). However, little is known about the mechanism by which target sequences are searched and deaminated. Here, we applied a real-time NMR method to elucidate the deamination properties. We found that A3B CTD shows higher activity toward its target sequence in short ssDNA and efficiently deaminates a target sequence located near the center of ssDNA. These properties are quite different from those of well-studied APOBEC3G, which shows higher activity toward its target sequence in long ssDNA and one located close to the 5′-end. The unique properties of the A3B CTD can be rationally interpreted by considering that after nonspecific binding to ssDNA, A3B slides only for a relatively short distance and tends to dissociate from the ssDNA before reaching the target sequence

H-ferritin uptake by K562 cells.

<p>(A) Confocal micrographs of AF488-labeled H-ferritin (HFt) and holo-transferrin (Tf). Cells were incubated with 50 μg/ml (110 nM) AF488-labeled human recombinant HFt or 50 μg/ml (625 nM) holo-Tf for 1 h at 37°C. Images are representative results of three independent experiments. (B) Analysis of HFt binding to K562 cells. Cells were incubated with indicated concentrations of AF488-labeled HFt for 60 min on ice, and HFt binding was analyzed by flow cytometry. (C) Competitive inhibition of HFt uptake by K562 cells. Cells were incubated with 11 nM AF488-labeled ferritin in the presence or absence of a 100-fold excess of unlabeled HFt for 60 min on ice, followed by flow cytometric analysis. (D, E) Dose-dependency of HFt and holo-Tf uptake. Cells were incubated with indicated concentrations of AF488-labeled HFt or holo-Tf for 60 min at 37°C, and incorporation of these ligands was analyzed by flow cytometry. (F, G) Time-course of HFt and holo-Tf uptake by K562 cells. Cells were incubated with 11 nM AF488-labeled HFt or 62 nM holo-Tf for indicated times, and incorporation of these ligands was analyzed by flow cytometry. (H) Competition of AF488-labeled HFt uptake with unlabeled ligand. Cells were incubated with 11 nM AF488-labeled HFt and indicated concentrations of unlabeled HFt. (B–H) Data represent the means ± standard errors of three independent experiments.</p

TFR1 expression levels required for H-ferritin uptake.

<p>(A) AF488-labeled H-ferritin (HFt) and holo-transferrin (Tf) uptake was evaluated in CHO-TRVb cells lacking endogenous TFR1 (control) and CHO-TRVb cells expressing either wild-type or mutant human TFR1 (R646H and R646H/647A) or wild-type human TFR2. Shaded areas represent isotype control experiments (CD71 expression) and untreated control experiments (Tf and HFt uptake). (B) AF488-labeled holo-Tf and HFt uptake by CHO-TRVb cells expressing moderate or high levels of human TFR1. Representative histograms are shown (left panels). Uptake of AF488-labeled ligand (solid lines), competition experiments using a 20-fold excess of unlabeled ligand (broken lines), and controls (shaded areas) are shown. Data shown in the right panel represent the mean ± standard error. (C) Relationship between CD71 expression and HFt uptake by CHO-TRVb cells expressing wild-type or mutant forms of human TFR1. Data from two cell lines expressing wild-type TFR1 and two expressing a mutated form of TFR1 (R646H/647A) are shown. Right panels show a schematic representation of two different patterns of ligand uptake.</p

Analysis of H-ferritin and holo-transferrin uptake by hematopoietic cell lines.

<p>(A) Uptake of AF488-labeled human holo-transferrin (Tf), H-ferritin (HFt), and L-ferritin (LFt). Cells were incubated with AF488-labeled ferritins (11 nM) or Tf (62 nM) for 60 min and analyzed by flow cytometry. The MFI ratio was defined as the MFI of cells treated with fluorescence-labeled ligand divided by the MFI of untreated cells. Filled columns denote the results of competition experiments using a 20-fold excess of unlabeled cognate ligand. Graphs for NB4, Reh, and THP–1 cell lines are shown on a larger scale in the in the enclosed areas. Data represent the mean ± standard error of three independent experiments. (B) Relationship between HFt and holo-Tf uptake. Cell lines shown in (A) are shown as blue dots by their MFI ratios for HFt and holo-Tf uptake in a scatter plot (Spearman’s coefficient, ρ = 0.95; P < 0.0001). A red dot in this plot represents the position of human bone marrow erythroblasts shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139915#pone.0139915.g003" target="_blank">Fig 3B</a>.</p

H-ferritin uptake by primary human hematopoietic cells.

<p>(A) Uptake of AF488-labeled human holo-transferrin (Tf), H-ferritin (HFt), and L-ferritin (LFt) by peripheral blood leukocytes. (B) Uptake of AF488-labeled Tf, HFt, and LFt by normal nucleated human BM cells. In (A) and (B), cells were incubated with AF488-labeled ferritins (11 nM) or Tf (62 nM) for 60 min and analyzed by flow cytometry. The MFI ratio was defined as the MFI of cells treated with fluorescence-labeled ligand divided by the MFI of untreated cells. Filled columns denote the results of competition experiments using a 20-fold excess of unlabeled cognate ligand. Data represent the mean ± standard error of three independent experiments. (C) Representative results of HFt uptake by erythroid cells from MDS patients. CD235+ erythroid cells from Patient 1 expressed close to normal levels of CD71 (TFR1) and efficiently incorporated HFt, whereas cells from Patient 2 expressed relatively low levels of TFR1 and incorporated less HFt as compared to cells from normal subjects. Solid lines represent AF488-labeled ligand uptake and shaded areas represent controls.</p

HFt uptake by erythroid cells in various iron statuses.

<p>(A, B) UT7/EPO and HEL cells were incubated with indicated concentrations of FAC or DFO for 24 h before flow cytometry analysis of CD71 (TFR1) expression (upper panels) and HFt (HFt) uptake (lower panels). MFI values relative to those of controls were calculated for each experiment; the results represent the mean ± standard error of at least three independent experiments. *P <0.05, **P <0.01; n.s., not significant.</p

CKIP-1 Is an Intrinsic Negative Regulator of T-Cell Activation through an Interaction with CARMA1

<div><p>The transcription factor NF-κB plays a key regulatory role in lymphocyte activation and generation of immune response. Stimulation of T cell receptor (TCR) induces phosphorylation of CARMA1 by PKCθ, resulting in formation of CARMA1-Bcl10-MALT1 (CBM) complex at lipid rafts and subsequently leading to NF-κB activation. While many molecular events leading to NF-κB activation have been reported, it is less understood how this activation is negatively regulated. We performed a cell-based screening for negative regulators of TCR-mediated NF-κB activation, using mutagenesis and complementation cloning strategies. Here we show that casein kinase-2 interacting protein-1 (CKIP-1) suppresses PKCθ-CBM-NF-κB signaling. We found that CKIP-1 interacts with CARMA1 and competes with PKCθ for association. We further confirmed that a PH domain of CKIP-1 is required for association with CARMA1 and its inhibitory effect. CKIP-1 represses NF-κB activity in unstimulated cells, and inhibits NF-κB activation induced by stimulation with PMA or constitutively active PKCθ, but not by stimulation with TNFα. Interestingly, CKIP-1 does not inhibit NF-κB activation induced by CD3/CD28 costimulation, which caused dissociation of CKIP-1 from lipid rafts. These data suggest that CKIP-1 contributes maintenance of a resting state on NF-κB activity or prevents T cells from being activated by inadequate signaling. In conclusion, we demonstrate that CKIP-1 interacts with CARMA1 and has an inhibitory effect on PKCθ-CBM-NF-κB signaling.</p></div

Lipid rafts accumulated by CD3/CD28 costimulation do not contain CKIP-1.

<p>Jurkat T cells were stimulated for 15-CD3 (10 µg/ml) and anti-CD28 (5 µg/ml), together with 15 µg of mouse IgG. The cells were then lysed and subjected to OptiPrep density gradient centrifugation to isolate lipid rafts. Lysates were subjected to SDS-PAGE and analyzed by Western blotting.</p

PH domain of CKIP-1 is essential not only for the interaction with CARMA1 but also for the inhibitory effect on NF-κB activation.

<p>(A) Jurkat T cells were electroporated with 5 µg of each CKIP-1 truncated form together with 5 µg of κB-Luc and 0.1 µg of <i>Renilla</i>-Luc. Nineteen hours later, cells were stimulated for 5 hr upon PMA (10 ng/ml) or CD3/CD28 (2 µg/ml each). The expressed protein levels were analyzed by Western blotting. (B) Jurkat T cells were electroporated with 5 µg of each CKIP-1 truncated form together with 5 µg of PKCθ AE or Myc-CARMA1, 5 µg of κB-Luc and 0.1 µg of <i>Renilla</i>-Luc. After 24 hr, cells were lysed and luciferase activity was assessed. The expressed protein levels were analyzed by Western blotting. Values represent the average of three independent experiments and error bars represent the SD from the average.</p

CKIP-1 inhibits the interaction between PKCθ and CARMA1.

<p>(A) HEK293T cells were transfected with CKIP-1 or empty vector (mock) together with PKCθ and FLAG-CARMA1 (left panel), or together with HA-Bcl10 and FLAG-CARMA1 (right panel). Cell lysates were immunoprecipitated by anti-FLAG antibody, followed by Western blotting with indicated antibodies. (B) HEK293T cells were transfected with CKIP-1 truncated form together with PKCθ and FLAG-CARMA1. Cell lysates were immunoprecipitated by anti-FLAG antibody, followed by Western blotting with indicated antibodies.</p