Journal: Journal of Bacteriology

Article Title: Treponema denticola PrcB Is Required for Expression and Activity of the PrcA-PrtP (Dentilisin) Complex ▿

doi: 10.1128/JB.00274-10

Figure Lengend Snippet: T. denticola strains used in this study

Article Snippet: Cultures were examined by phase-contrast microscopy for purity and typical strain morphology before use. table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 T. denticola strain Relevant features Source or reference a 35405 Parent for mutagenesis ATCC 33520 ATCC OTK 20 P0760 prcB , polar mutation 5 CF417 prcB -6×His Δ prcA This study CF499 prcB -6×His This study CF522 Δ prcB , nonpolar mutation This study Open in a separate window a ATCC, American Type Culture Collection, Rockville, MD.

Techniques: Mutagenesis

Journal: Journal of Bacteriology

Article Title: Treponema denticola PrcB Is Required for Expression and Activity of the PrcA-PrtP (Dentilisin) Complex ▿

doi: 10.1128/JB.00274-10

Figure Lengend Snippet: Protease locus in T. denticola parent and prcB mutant strains. The genes of the protease operon, prcB, prcA, and prtP, are shown as gray arrows. The location of the protease operon promoter region is indicated by “P.” The protease mRNA transcript is shown as a thin arrow above the genes transcribed in each strain. The location and orientation of the erm cassette are shown by a black arrow. The T. denticola strains are 35405 (wild-type parent), P0760 (erm insertion at the 5′ end of prcB), CF417 (prcB modified to encode a C-terminal His tag; erm insertion replaces the 5′ end of prcA), CF499 (prcB modified to encode a C-terminal His tag; erm insertion is upstream of the protease locus), and CF522 (ΔprcB; promoter region is intact; erm insertion as in CF499).

Article Snippet: Cultures were examined by phase-contrast microscopy for purity and typical strain morphology before use. table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 T. denticola strain Relevant features Source or reference a 35405 Parent for mutagenesis ATCC 33520 ATCC OTK 20 P0760 prcB , polar mutation 5 CF417 prcB -6×His Δ prcA This study CF499 prcB -6×His This study CF522 Δ prcB , nonpolar mutation This study Open in a separate window a ATCC, American Type Culture Collection, Rockville, MD.

Techniques: Mutagenesis, Modification

Journal: Journal of Bacteriology

Article Title: Treponema denticola PrcB Is Required for Expression and Activity of the PrcA-PrtP (Dentilisin) Complex ▿

doi: 10.1128/JB.00274-10

Figure Lengend Snippet: Protein expression in prcB mutants. Results of Western immunoassays, gelatin zymography, and chromogenic substrate cleavage assays are shown. Samples for immunoblots were heated whole-cell extracts, and samples for protease activity assays were unheated extracts (zymograms) or cells in growth medium. (A) PrcB-6×His was detected in CF417 and CF499 as a 22-kDa protein (molecular size scale not shown). CF417 expressed neither PrcA nor PrtP, while CF499 expressed native protease complex proteins and activity. (B) The ΔprcB mutant CF522 expressed PrcA in uncleaved form (70 kDa), but no PrtP protein or protease activity was detected. (C) PrtP-dependent SAAPFNA hydrolysis, assayed by the change in absorbance at 405 nm. Data shown are mean values for triplicate samples from a representative experiment. T. denticola strains are as in Fig. ​Fig.2:2: 35405 (ATCC 35405; parent strain), CF417 (prcB-6×His polar mutation), CF499 (prcB-6×His nonpolar mutation), CF522 (ΔprcB), and P0760 (erm insertion at 5′ end of prcB).

Article Snippet: Cultures were examined by phase-contrast microscopy for purity and typical strain morphology before use. table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 T. denticola strain Relevant features Source or reference a 35405 Parent for mutagenesis ATCC 33520 ATCC OTK 20 P0760 prcB , polar mutation 5 CF417 prcB -6×His Δ prcA This study CF499 prcB -6×His This study CF522 Δ prcB , nonpolar mutation This study Open in a separate window a ATCC, American Type Culture Collection, Rockville, MD.

Techniques: Expressing, Western Blot, Zymography, Activity Assay, Mutagenesis

Journal: Journal of Bacteriology

Article Title: Treponema denticola PrcB Is Required for Expression and Activity of the PrcA-PrtP (Dentilisin) Complex ▿

doi: 10.1128/JB.00274-10

Figure Lengend Snippet: RT-PCR analysis of prtP transcription in T. denticola parent and mutant strains. Lanes: 1, 35405 (parent); 2, CF417 (prcB-6×His polar mutation); 3, CF499 (prcB-6×His nonpolar mutation); 4, CF522 (ΔprcB nonpolar mutation); 5, P0760 (prcB polar insertion mutation). The structure of the protease locus in the parent and mutant strains is shown in Fig. ​Fig.2.2. RT-PCRs were done using matched primer sets specific for internal fragments of prtP or flaA, as indicated. Panels show PCR amplicons obtained using prtP- or flaA-specific primer sets and the indicated templates, including negative (no RT) and positive (genomic DNA) controls.

Article Snippet: Cultures were examined by phase-contrast microscopy for purity and typical strain morphology before use. table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 T. denticola strain Relevant features Source or reference a 35405 Parent for mutagenesis ATCC 33520 ATCC OTK 20 P0760 prcB , polar mutation 5 CF417 prcB -6×His Δ prcA This study CF499 prcB -6×His This study CF522 Δ prcB , nonpolar mutation This study Open in a separate window a ATCC, American Type Culture Collection, Rockville, MD.

Techniques: Reverse Transcription Polymerase Chain Reaction, Mutagenesis

Journal: bioRxiv

Article Title: Targeting the PI5P4K lipid kinase family in cancer using novel covalent inhibitors

doi: 10.1101/819961

Figure Lengend Snippet: (A) Chemical structures of compound JNK-IN-7 as previously reported in and novel compound THZ-P1-2 with its reversible and desthiobiotinylated counterparts. ( B) THZ-P1-2 potently inhibits PI5P4Kα kinase activity in the ADP-Glo luminescence assay. The curve obtained is representative of two independent experiments and the IC50 value is an average of values obtained from both experiments with three technical replicates each. (C) THZ-P1-2 shows potent inhibition of kinase activity of all three PI5P4K isoforms in a radiometric TLC assay measuring radiolabeled PI-4,5-P 2 . TLC image shown is representative of two independent experiments. ( D) Quantification of (C). Radiolabeled PI-4,5-P 2 spots were imaged by autoradiography and quantified by densitometry.

Article Snippet: A construct of human PI5P4Kα covering residues 35-405 in the pNIC28Bsa4 vector (Addgene #42494) was overexpressed in E. coli BL21 (DE3) in TB medium in the presence of 50 μg/ml of kanamycin.

Techniques: Activity Assay, Luminescence Assay, Inhibition, Autoradiography

Journal: bioRxiv

Article Title: Targeting the PI5P4K lipid kinase family in cancer using novel covalent inhibitors

doi: 10.1101/819961

Figure Lengend Snippet: (A) list of selected targets, including PI5P4Kγ (PIP4K2C), from KiNativ profiling of JNK-IN-7 at 1 μM for 3 hours in A375 cells. A higher percent inhibition of kinase labeling by ATP-biotin is indicates stronger binding and inhibition of the target kinase. Full list is available in . (B) JNK-IN-7 inhibits kinase activity of all three PI5P4K isoforms in a radiometric TLC assay measuring radiolabeled PI-4,5-P 2 . JNK-IN-7 was incubated with purified protein for 30min, followed by a 10min kinase reaction, quenching, lipid extraction and TLC development. (C) Quantification of (B). Radiolabeled PI-4,5-P 2 spots were imaged by autoradiography and quantified by densitometry. (D) Zero charge masses of recombinant PI5P4Kα and γ incubated with JNK-IN-7 for 2 hours at 37°C demonstrates covalent labeling of PI5P4K isoforms as determined by intact mass spectrometry. See Supplemental Intact MS Spectra for representative raw MS spectra used for charge deconvolution. (E) Subsequent protease digestion and tandem mass spectrometry confirms that THZ-P1-2 covalently labels cysteine residues on all three PI5P4K isoforms. The peptide for PI5P4Kβ was exclusively observed to be singly labeled at either Cys-307 or Cys-318. See Supplemental Intact MS Spectra for representative raw MS spectra used for charge deconvolution.

Article Snippet: A construct of human PI5P4Kα covering residues 35-405 in the pNIC28Bsa4 vector (Addgene #42494) was overexpressed in E. coli BL21 (DE3) in TB medium in the presence of 50 μg/ml of kanamycin.

Techniques: Inhibition, Labeling, Binding Assay, Activity Assay, Incubation, Purification, Autoradiography, Recombinant, Mass Spectrometry

Journal: bioRxiv

Article Title: Targeting the PI5P4K lipid kinase family in cancer using novel covalent inhibitors

doi: 10.1101/819961

Figure Lengend Snippet: (A) Electrospray mass spectrometry of recombinant PI5P4Kα/β/γ incubated with THZ-P1-2 demonstrates covalent labeling of PI5P4K isoforms. (B) Subsequent protease digestion and tandem mass spectrometry confirms that THZ-P1-2 covalently labels cysteine residues. (C) Crystal structure of PI5P4Kα in complex with THZ-P1-2, colored according to B factor and shown with covalent warhead extended out towards the covalently-targeted cysteine, C293 (labeled; not resolved in crystal structure). (D) Ligand interaction map of THZ-P1-2 with residues in the ATP-binding pocket of PI5P4Kα. (E) Modeled THZ-P1-2 binding showed for all three isoforms based on alignment of published PI5P4Kβ and γ structures with obtained PI5P4Kα structure. PI5P4Kα (magenta), PI5P4Kβ (blue), PI5P4Kγ (orange).

Article Snippet: A construct of human PI5P4Kα covering residues 35-405 in the pNIC28Bsa4 vector (Addgene #42494) was overexpressed in E. coli BL21 (DE3) in TB medium in the presence of 50 μg/ml of kanamycin.

Techniques: Mass Spectrometry, Recombinant, Incubation, Labeling, Binding Assay

Journal: bioRxiv

Article Title: Targeting the PI5P4K lipid kinase family in cancer using novel covalent inhibitors

doi: 10.1101/819961

Figure Lengend Snippet: (A) Protease digestion and tandem mass spectrometry following intact mass labeling confirms that THZ-P1-2 covalently labels cysteine residues on all three PI5P4K isoforms. The peptide for PI5P4Kβ was exclusively observed to be singly labeled at either Cys-307 or Cys-318. Related to . See Supplemental Intact MS Spectra for representative raw MS spectra used for charge deconvolution. (B) THZ-P1-2-R was found not to covalently label recombinant PI5P4Kα and γ when incubated with purified protein for 2 hours at 37°C. Mass labeling plot shown here is compared to mass shift observed with THZ-P1-2 from . (C) Surface representation of co-crystal structure of PI5P4Kα in complex with THZ-P1-2. Related to . (D) Zoom-in of ligand electron density within the active site of PI5P4Kα. See for diffraction data collection and refinement statistics.

Article Snippet: A construct of human PI5P4Kα covering residues 35-405 in the pNIC28Bsa4 vector (Addgene #42494) was overexpressed in E. coli BL21 (DE3) in TB medium in the presence of 50 μg/ml of kanamycin.

Techniques: Mass Spectrometry, Labeling, Recombinant, Incubation, Purification

Journal: bioRxiv

Article Title: Targeting the PI5P4K lipid kinase family in cancer using novel covalent inhibitors

doi: 10.1101/819961

Figure Lengend Snippet: (A) THZ-P1-2-R and dtb-THZ-P1-2 were found to inhibit PI5P4Kα in an ADP-Glo assay, with a slight loss in potency with THZ-P1-2-R. Both compounds were incubated with PI5P4Ka for 15min before proceeding with a 1 hour reaction with ATP and development with ADP-Glo reagents. Plots are shown in comparison with THZ-P1-2 from . (B) THZ-P1-2 engages PI5P4K isoforms at 2h and 4h timepoints, exhibiting prolonged engagement when a washout is performed. HEK293T cells were treated with DMSO or THZ-P1-2 at time, t=0 and cells were washed 2X with PBS at either 2 or 4h and harvested at the end of 6h. A streptavidin pulldown was then conducted in lysates after normalization of protein content with a BCA assay. (C) THZ-P1-2 inhibits the Type 1 PI4P5K kinases at a lower extent but shows potent inhibition on PIKfyve by ADP-Glo. In vitro kinase assays were performed by Carna Biosciences. (D) THZ-P1-2 causes vacuolar enlargement, characteristic of PIKfyve inhibition, at a concentration of 10 μ M but not 1 μ M, compared to PIKfyve inhibitor apilimod at 10 nM treatment. Vero cells were treated with DMSO or compound for 6h and imaged. (E) Incubation of Vero cells with 1 μM THZ-P1-2 was unable to impair the PIKfyve inhibitory phenotype of apilimod. Preincubation: Vero cells were incubated with DMSO/THZ-P1-2 for 1 or 6h, washed with PBS to completely remove compound, treated with DMSO/apilimod and imaged after 6h. Coincubation: Vero cells were incubated with DMSO/THZ-P1-2 for 1 or 6h, and then co-treated with DMSO/apilimod and imaged after 6h.

Article Snippet: A construct of human PI5P4Kα covering residues 35-405 in the pNIC28Bsa4 vector (Addgene #42494) was overexpressed in E. coli BL21 (DE3) in TB medium in the presence of 50 μg/ml of kanamycin.

Techniques: Glo Assay, Incubation, BIA-KA, Inhibition, In Vitro, Concentration Assay

Journal: bioRxiv

Article Title: Targeting the PI5P4K lipid kinase family in cancer using novel covalent inhibitors

doi: 10.1101/819961

Figure Lengend Snippet: (A) Similar to genetic loss of PIP4K2A/B , inhibition of PI5P4K activity with THZ-P1-2 increases LAMP1-positive lysosomal size, number and contact with LC3B-positive autophagosomes. HeLa cells were cultured overnight with either DMSO, 0.25 μM, 0.5 μM or 1.0 μM THZ-P1-2 and stained for LC3B (magenta) or LAMP1 (green) with nuclei in blue. Scale bars, 10 μM. (B) Inhibition of PI5P4K activity with THZ-P1-2 increases TFEB nuclear localization. HeLa cells were cultured overnight with either DMSO, 0.25 μM, 0.5 μM or 1.0 μM THZ-P1-2 and stained for TFEB (green) with nuclei in blue. Scale bars, 10 μM. (C) Quantification of results in (B). The intensity of TFEB immunofluorescence was quantified in the nucleus and the cytoplasm, and used to calculate the ratio. Statistical significance determined by ANOVA (***p < 0.0005) with Dunnett multiple comparison post-test. Each group was compared to control control HeLa cells treated with DMSO, (n ≥ 30). (D) Expression of PI5P4K cysteine to serine mutants alleviates lysosomal dysfunction induced by THZ-P1-2 treatment. HeLa cells were infected with viruses expressing GFP, GFP-PI5P4Kα, GFP-PI5P4Kα C293S, GFP-PI5P4Kβ, or GFP-PI5P4Kβ C307S C318S and treated with either DMSO or 250 nM THZ-P1-2 overnight. Expression of both the PI5P4Kα and PI5P4Kβ cysteine to serine mutants alleviated dysfunctional lysosomes (green) with nuclei in blue. Scale bars, 10 μM. (E) Quantification of results in (D). The number of lysosomes was quantified per cell. Statistical significance determined by ANOVA (***p < 0.0005) with Dunnett multiple comparison post-test. Each group was compared to control HeLa cells expressing GFP and treated with DMSO, (n ≥ 30). (F) HeLa cells expressing GFP, GFP-PI5P4Kα, GFP-PI5P4Kα C293S, GFP-PI5P4Kβ, or GFP-PI5P4Kβ C307S C318S were treated with either DMSO or 250 nM THZ-P1-2 overnight for 16 hours and subsequently harvested for qPCR of TFEB targets. Fold change is calculated by comparison to HeLa cells expressing GFP treated with DMSO. *p < 0.05, Student’s t-test, (n ≥ 8).

Article Snippet: A construct of human PI5P4Kα covering residues 35-405 in the pNIC28Bsa4 vector (Addgene #42494) was overexpressed in E. coli BL21 (DE3) in TB medium in the presence of 50 μg/ml of kanamycin.

Techniques: Inhibition, Activity Assay, Cell Culture, Staining, Immunofluorescence, Expressing, Infection

Journal: Molecular oral microbiology

Article Title: The C- terminal region of the Major Outer Sheath Protein (Msp) of Treponema denticola inhibits neutrophil chemotaxis

doi: 10.1111/omi.12180

Figure Lengend Snippet: Msp impairs neutrophil chemotaxis in whole bacteria. In a transwell chemotaxis assay, murine neutrophils were exposed to T. denticola 35405 wild type or MHE (Msp mutant) bacteria for 1 hour to allow chemotaxis toward the bacteria through a membrane. Cells that migrated across the membrane were fixed, stained with crystal violet, and counted. Neutrophils exposed to the wild type and MHE bacterial strains were compared to each other, with more neutrophils migrated toward MHE than the wild type strain. Neutrophils alone and unstimulated with fMLP served as a negative control, while neutrophils stimulated with fMLP as the positive control for neutrophil chemotaxis and were compared to each other. Results were normalized to the control +fMLP. Graphs represents mean ± SEM of 3 independent experiments (*** P < 0.001 and **** P < 0.0001 by unpaired t test).

Article Snippet: All Escherichia coli strains were grown in Luria-Bertani (LB) broth with shaking or on LB agar at 37 °C with appropriate antibiotics. table ft1 table-wrap mode="anchored" t5 caption a7 Component Relevant Characteristics Source Bacteria Treponema denticola 35405 Wild type strain R. Ellen 84 MHE Msp mutant of strain 35405 J.C. Fenno 59 OTK Wild type strain J.C. Fenno 55 Escherichia coli M15 Expression of recombinant Msp and N, V, and C, strain 35405 Qiagen C41 (DE3) Expression of recombinant CA and CB Msp, strain 35405 Lucigen BL21 (DE3) pLysS Expression of recombinant Msp, strain OTK A. Sharma Plasmids pQE30 3461 bp plasmid, adds N-terminal 6xHis tag H. Jenkinson 54 rMsp 1590 bp 35405-Msp gene cloned into pQE30 H. Jenkinson 54 rN-Msp 567 bp N-terminal fragment of 35405 Msp cloned into pQE30 H. Jenkinson 54 rV-Msp 171 bp V-region fragment of 35405 Msp cloned into pQE30 H. Jenkinson 54 rC-Msp 816 bp C-terminal fragment of 35405 Msp cloned into pQE30 H. Jenkinson 54 pET23b 3665 bp plasmid, adds N-terminal T7 tag and C-terminal 6xHis tag W. Hofman p23-CA 405 bp CA fragment cloned into pET23b This study p23-CB 411 bp CB fragment cloned into pET23b This study p23-OTK 1690 bp OTK-Msp gene cloned into pET23b This study Open in a separate window Bacterial strains and plasmid constructs

Techniques: Chemotaxis Assay, Bacteria, Mutagenesis, Membrane, Staining, Negative Control, Positive Control, Control

Journal: Molecular oral microbiology

Article Title: The C- terminal region of the Major Outer Sheath Protein (Msp) of Treponema denticola inhibits neutrophil chemotaxis

doi: 10.1111/omi.12180

Figure Lengend Snippet: Bacterial strains and plasmid constructs

Article Snippet: All Escherichia coli strains were grown in Luria-Bertani (LB) broth with shaking or on LB agar at 37 °C with appropriate antibiotics. table ft1 table-wrap mode="anchored" t5 caption a7 Component Relevant Characteristics Source Bacteria Treponema denticola 35405 Wild type strain R. Ellen 84 MHE Msp mutant of strain 35405 J.C. Fenno 59 OTK Wild type strain J.C. Fenno 55 Escherichia coli M15 Expression of recombinant Msp and N, V, and C, strain 35405 Qiagen C41 (DE3) Expression of recombinant CA and CB Msp, strain 35405 Lucigen BL21 (DE3) pLysS Expression of recombinant Msp, strain OTK A. Sharma Plasmids pQE30 3461 bp plasmid, adds N-terminal 6xHis tag H. Jenkinson 54 rMsp 1590 bp 35405-Msp gene cloned into pQE30 H. Jenkinson 54 rN-Msp 567 bp N-terminal fragment of 35405 Msp cloned into pQE30 H. Jenkinson 54 rV-Msp 171 bp V-region fragment of 35405 Msp cloned into pQE30 H. Jenkinson 54 rC-Msp 816 bp C-terminal fragment of 35405 Msp cloned into pQE30 H. Jenkinson 54 pET23b 3665 bp plasmid, adds N-terminal T7 tag and C-terminal 6xHis tag W. Hofman p23-CA 405 bp CA fragment cloned into pET23b This study p23-CB 411 bp CB fragment cloned into pET23b This study p23-OTK 1690 bp OTK-Msp gene cloned into pET23b This study Open in a separate window Bacterial strains and plasmid constructs

Techniques: Plasmid Preparation, Bacteria, Mutagenesis, Expressing, Recombinant, Clone Assay