The Phospholipid Scramblases 1 and 4 Are Cellular Receptors for the Secretory Leukocyte Protease Inhibitor and Interact with CD4 at the Plasma Membrane

Secretory leukocyte protease inhibitor (SLPI) is secreted by epithelial cells in all the mucosal fluids such as saliva, cervical mucus, as well in the seminal liquid. At the physiological concentrations found in saliva, SLPI has a specific antiviral activity against HIV-1 that is related to the perturbation of the virus entry process at a stage posterior to the interaction of the viral surface glycoprotein with the CD4 receptor. Here, we confirm that recombinant SLPI is able to inhibit HIV-1 infection of primary T lymphocytes, and show that SLPI can also inhibit the transfer of HIV-1 virions from primary monocyte-derived dendritic cells to autologous T lymphocytes. At the molecular level, we show that SLPI is a ligand for the phospholipid scramblase 1 (PLSCR1) and PLSCR4, membrane proteins that are involved in the regulation of the movements of phospholipids between the inner and outer leaflets of the plasma membrane. Interestingly, we reveal that PLSCR1 and PLSCR4 also interact directly with the CD4 receptor at the cell surface of T lymphocytes. We find that the same region of the cytoplasmic domain of PLSCR1 is involved in the binding to CD4 and SLPI. Since SLPI was able to disrupt the association between PLSCR1 and CD4, our data suggest that SLPI inhibits HIV-1 infection by modulating the interaction of the CD4 receptor with PLSCRs. These interactions may constitute new targets for antiviral intervention

Arbeidsorganisatie en kwaliteit van arbeid

status: publishe

Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq

Abstract Background There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever-growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puzzle. An important mechanism of gene regulation is the binding of transcription factors (TFs) to specific DNA sequence motifs across the genome. However, these sequences are hindered by the packaging of DNA to chromatin. Thus, the accessibility of these loci for TF binding is highly regulated and determines where and when TFs bind. We present a workflow for measuring chromatin accessibility in Arabidopsis thaliana and define organ-specific regulatory sites and binding motifs of TFs at these sites. Results We coupled the recently described isolation of nuclei tagged in specific cell types (INTACT) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) as a genome-wide strategy to uncover accessible regulatory sites in Arabidopsis based on their accessibility to nuclease digestion. By applying this pipeline in Arabidopsis roots, we revealed 41,419 accessible sites, of which approximately half are found in gene promoters and contain the H3K4me3 active histone mark. The root-unique accessible sites from this group are enriched for root processes. Interestingly, most of the root-unique accessible sites are found in nongenic regions but are correlated with root-specific expression of distant genes. Importantly, these gene-distant sites are enriched for binding motifs of TFs important for root development as well as motifs for TFs that may play a role as novel transcriptional regulators in roots, suggesting that these accessible loci are functional novel gene-distant regulatory elements. Conclusions By coupling INTACT with ATAC-seq methods, we present a feasible pipeline to profile accessible chromatin in plants. We also introduce a rapid measure of the experiment quality. We find that chromatin accessibility at promoter regions is strongly associated with transcription and active histone marks. However, root-specific chromatin accessibility is primarily found at intergenic regions, suggesting their predominance in defining organ identity possibly via long-range chromatin interactions. This workflow can be rapidly applied to study the regulatory landscape in other cell types, plant species and conditions

Zorg Proeftuinen Vlaanderen. Een inhoudelijke vergelijking van de platformen en projecten bij de start

nrpages: 195status: publishe

Disruption of the CD4/PLSCR1 interaction by SLPI.

<p>A) In vitro inhibition of the CD4/PLSCR1 interaction by SLPI. GST or GST-PLSCR1 (left panel, coomassie blue) was incubated with equal amounts of lysates from Jurkat CD4-positive T cells in the presence of the indicated concentrations of either GST-SLPI or GST-ARF1 (left panel) used as a control. Bound proteins were analyzed by Western blot with anti-CD4 (right panel). B) Mapping of the PLSCR1 determinants required for binding to CD4 and SLPI. L40 yeast strain expressing either the cytoplasmic domain of CD4 (CD4c) or SLPI fused to LexA in combination with each of the deleted forms of the Gal4AD-PLSCR1 hybrids indicated on the left was analyzed for histidine auxotrophy and beta-gal activity. The interactions between hybrid proteins were scored as follows: (+), cell growth on medium without histidine and development of a β-gal activity; (−), no growth on medium without histidine and no β-gal activity.</p

Interaction of PLSCR1 and PLSCR4 with the CD4 receptor.

<p>A) In vitro interaction. Lysates from Jurkat CD4-positive T cells were incubated with equal amounts of GST or GST-PLSCR1 (upper panel, coomassie blue) immobilized on GSH-sepharose beads. Bound proteins were then analyzed by immunoblotting with anti-CD4 (lower panel). B) Co-immunoprecipitation of endogenous proteins from T lymphocytes. Jurkat T cells were lyzed and CD4 was precipitated with either anti-CD4 (OKT4) or a control isotypic antibody. Precipitates were analyzed by Western blot with anti-CD4 (upper panel) or anti-PLSCR1 (lower panel). C) Co-precipitation of overexpressed CD4 and PLSCR1 proteins. 293T cells expressing HA-tagged PLSCR1 (lower panel, Cell lysate) in combination with wild-type CD4 (WT) or a mutant of CD4 deleted of its cytoplasmic domain (ΔCT) were lyzed and the CD4 forms were precipitated with anti-CD4. Precipitates were then analyzed by Western blot with anti-CD4 (upper panel) or anti-HA (middle panel). D) Co-precipitation of overexpressed CD4 and PLSCR4 proteins. 293T cells expressing GFP- PLSCR1, GFP-PLSCR3 or GFP-PLSCR4 (lower panels, Cell lysate) in combination with CD4 WT (right panels) or CD4 ΔCT (left panels) were lyzed and the CD4 forms were precipitated with anti-CD4. Precipitates were then analyzed as in (C). Of note, the differences in migration observed between PLSCR1 (318 a.a.), PLSCR3 (295 a.a.) and PLSCR4 (329 a.a.) is likely related to the respective amino acid lengths of the GFP fusion proteins <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005006#pone.0005006-Zhou1" target="_blank">[23]</a>. E) Interactions in the two-hybrid system. L40 yeast strain expressing the LexA-CD4c hybrid in combination with the indicated Gal4AD hybrids was analyzed for histidine auxotrophy and β-gal activity. Transformants were patched on medium with histidine (upper panels) and then replica-plated on medium without histidine (middle panels) and on Whatman filter for β-gal assay (lower panels).</p

Mapping of the CD4 determinants required for PLSCR1 binding by co-immunoprecipitation assay.

<p>A) Schematic representation of the human CD4 mutants. The extracellular and transmembrane (TM) domains of CD4 are represented in grey and hatched, respectively. The a.a. sequences of the cytoplasmic tail of the CD4 mutants are aligned with that of the wild-type CD4 (CD4 WT). Dashes (−) indicate a.a. identities with the wild type protein and a.a. substitutions are identified. B) Co-immunoprecipitation assay. Protein extracts were prepared 48 h post transfection from 293T cells co-expressing HA-PLSCR1 together with wild type or mutated CD4 as indicated at the top. Crude extracts were then subjected to CD4 immunoprecipitation followed by Western blot analysis with anti-CD4 (upper panels) and anti-HA (lower panels).</p

Mapping of the CD4 determinants required for PLSCR1 binding by ELISA.

<p>A) Primary a.a. sequences of the CD4 long (405–433) and short (405–426) peptides used in the ELISA test. The primary sequence of the entire cytoplasmic domain of CD4 is shown at the top; the 2 Cys residues required for p56Lck binding and mutated in Ala in both peptides are indicated in red. B) ELISA interaction test. 96-well plates were coated with the CD4c long (left panel) or short (right panel) peptides at a final concentration of 0.5 µM. After washings and blocking of non-specific binding sites, GST or GST-PLSCR1 was incubated at concentrations ranging from 1 nM to 300 nM. Binding was then revealed with an anti-GST antibody and a secondary peroxidase-conjugated anti-mouse IgG. The peroxidase substrate solution was incubated for 10 min and the optical density was measured at 450 nm.</p

Anti-HIV-1 activity of recombinant SLPI.

<p>A) Inhibition of virus replication. Primary T lymphocytes were isolated from peripheral blood mononuclear cells and used for infection with the HIV-1JR-CSF isolate in the presence of increasing concentrations (0–50 µg/ml) of purified GST-SLPI (see inset, coomassie blue) or GST (50 µg/ml). After washing, infected cells were cultured for 6 days and the viral production was quantified by measuring the p24 production in the cell-culture medium. B) Inhibition of virus transfer from dendritic cells to T lymphocytes. Dentritic cells were derived from purified primary monocytes, and incubated with either HIV-1Bal (R5 strain, upper panel) or HIV-1NDK (×4 strain, lower panel) for 1 h at 37°C in the presence of 50 µg/ml of purified GST-SLPI or GST. After washing, IL-2 activated-lymphocytes were added in a 1/5 ratio and maintained in co-culture for 72 h. Viral production was quantified by measuring the p24 production in the cell culture medium.</p