Journal: Communications Biology

Article Title: An inducible CRISPR interference library for genetic interrogation of Saccharomyces cerevisiae biology

doi: 10.1038/s42003-020-01452-9

Figure Lengend Snippet: a Schematic of amPL43 expression vector for inducible CRISPRi library in S. cerevisiae . b The expression fold change of each target: ERG25 (three replicates), ERG11 (five replicates), and Sec14 (four replicates), as a result of presence of sgRNA, without induction after 24 hours, as measured by qPCR. The mean for each sample is represented by a solid line. c The expression fold change of each target: ERG25 (three replicates), ERG11 (three replicates), and Sec14 (two replicates), as a result of gRNA induction by ATc, was calculated over time by qPCR. The mean for each sample is represented by a solid line. d Schematic depicting the genomic region of PTA1 and ERV46. The gRNAs targeting the region between the two genes, depending on their proximity to each gene, could affect both genes. e Histogram depicting the number of gRNAs per gene in two library replicates. The dashed blue line denotes the median: ~6. f Scatter plot depicting the frequency of reads per gRNA between select biological replicates of the CRISPRi library. Pearson Correlation R value is reported for each pair.

Article Snippet: AmPl43 was also deposited to Addgene (Addgene ID: 161830).

Techniques: Expressing, Plasmid Preparation

Journal: Cell reports

Article Title: Rab11-Rab8 cascade dynamics in primary cilia and membrane tubules.

doi: 10.1016/j.celrep.2024.114955

Figure Lengend Snippet: Figure 1. Rab8 ciliary trafficking is promoted by Rabin8 and Rab11 (A) Immunoblot analysis comparing lysates from RPE WT, tRFP-Rab8a, tRFP-Rab8a+GFP-Rab11a, tRFP-Rab8a+GFP-Rabin8, tRFP-Rab8a+GFP-Ra- bin8+miRFP-Rab11a, tRFP-Rab8a+GFP-Rabin8+miRFP-Rab14 cells ± Dox probed with Rab8a antibody; RPE WT, tRFP-Rab8a+GFP-Rabin8, tRFP-Rab8a+GFP-Rabin8+miRFP-Rab11a, tRFP-Rab8a+GFP-Rabin8+miRFP-Rab14, cells ± Dox probed with Rabin8 antibody; and RPE WT, tRFP-Ra- b8a+GFP-Rab11a, tRFP-Rab8a+GFP-Rabin8+miRFP-Rab11a cells ± Dox and probed with Rab11a antibody. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) antibody was used as a loading control. * corresponds to the endogenous protein detected in RPE WT cells and the arrows indicates the endogenous and exogenous levels in established fluorescent-tagged RPE cells.

Article Snippet: Multisite gateway cloning with LR Clonase II+ (#12538120, Invitrogen) was used to generate BFP-Rab11b and BFP-Rab14 fusion constructs Cell Reports 43, 114955, November 26, 2024 19 cloned into a gateway compatible pCS2+30 vector with an NH2-terminal FLAG-TEV-Stag tag sequence. pENTR Rab11aS25N, Rab11bS25N, Rab5aS34N and Rab14S25N were generated using QuickChange II mutagenesis kit (Catalog no. 200524, Agilent Technologies) and subcloned in pDEST53 to generate GFP-Rab5aSN, GFP-Rab14SN, GFP-Rab11bSN. pENTR Rab11aQ67L, Rab11bQ67L and Rab14Q70L were generated using QuickChange II mutagenesis kit, and along with pENTR Rab11a, Rab11b and Rab14 were subcloned in pDEST-tRFP, a vector previously described in3, to generate tRFP-Rab11a, tRFP-Rab11aQL, tRFPRab11b, tRFP-Rab11bQL, tRFP-Rab14 and tRFP-Rab14QL. mNeonGreen-Rab8a, mCherry-Rab11a, Rabin8 and Rabin8E192A were subcloned into pCS2+ (Addgene, Kit#1000000107) or pCS2-GFP (#86723, Addgene).

Techniques: Western Blot, Control

Journal: Cell reports

Article Title: Rab11-Rab8 cascade dynamics in primary cilia and membrane tubules.

doi: 10.1016/j.celrep.2024.114955

Figure Lengend Snippet: Figure 5. Rabin8 GEF activity is required for Rab8 LTM localization, ciliary trafficking, and ciliogenesis (A) (Right) Quantification of tRFP-positive LTMs in fixed RPE cells stably expressing tRFP-Rab8a and GFP-Rabin8 WT or GEF mutants (E192A and F201A) treated with Dox for 24 h, followed by CytoD for 30 min. (Left) Representative images from a single xy-plane of a z stack captured on an SDCM. Mean ± SEM for 100 cells from n = 3 experiments. (B) Quantification of mNeonGreen-Rab8a and mCherry-Rab11a colocalized on LTMs in yolk sac cells from 24 hfp zebrafish embryos co-injected with Rabin8 or Rabin8 E192A mRNA. Mean ± SEM for n = 10 (Rabin8) and n = 9 (Rabin8 E192A) independent experiments. (C) Quantification of ciliation in cells described in (A) following serum starvation for 24 h and stained with AcTub. Mean ± SEM for 100 cells from n = 3 experiments.

Article Snippet: Multisite gateway cloning with LR Clonase II+ (#12538120, Invitrogen) was used to generate BFP-Rab11b and BFP-Rab14 fusion constructs Cell Reports 43, 114955, November 26, 2024 19 cloned into a gateway compatible pCS2+30 vector with an NH2-terminal FLAG-TEV-Stag tag sequence. pENTR Rab11aS25N, Rab11bS25N, Rab5aS34N and Rab14S25N were generated using QuickChange II mutagenesis kit (Catalog no. 200524, Agilent Technologies) and subcloned in pDEST53 to generate GFP-Rab5aSN, GFP-Rab14SN, GFP-Rab11bSN. pENTR Rab11aQ67L, Rab11bQ67L and Rab14Q70L were generated using QuickChange II mutagenesis kit, and along with pENTR Rab11a, Rab11b and Rab14 were subcloned in pDEST-tRFP, a vector previously described in3, to generate tRFP-Rab11a, tRFP-Rab11aQL, tRFPRab11b, tRFP-Rab11bQL, tRFP-Rab14 and tRFP-Rab14QL. mNeonGreen-Rab8a, mCherry-Rab11a, Rabin8 and Rabin8E192A were subcloned into pCS2+ (Addgene, Kit#1000000107) or pCS2-GFP (#86723, Addgene).

Techniques: Activity Assay, Stable Transfection, Expressing, Injection, Staining

Journal: The Journal of Biological Chemistry

Article Title: Allosteric regulation of the Golgi-localized PPM1H phosphatase by Rab GTPases modulates LRRK2 substrate dephosphorylation in Parkinson’s disease

doi: 10.1016/j.jbc.2025.110679

Figure Lengend Snippet: AlphaFold 3 model of PPM1H bound to its pRab10 substrate and non-pRab10 allosteric regulator (loops #1 and #2 were removed for simplicity; see A for comparison). The PPM1H FLAP domain, amphipathic helix, and Leu66 and R388 residues are indicated. PPM1H ( blue ); pRab10 ( beige ); and Rab10 ( goldenrod ). pRab, phosphoRab.

Article Snippet: Recombinant DNA , pET15b His SUMO mNeon R338A PPM1H , Addgene in progress , 245124 RRID: Addgene_245124 , New , Human.

Techniques: Comparison

Journal: The Journal of Biological Chemistry

Article Title: Allosteric regulation of the Golgi-localized PPM1H phosphatase by Rab GTPases modulates LRRK2 substrate dephosphorylation in Parkinson’s disease

doi: 10.1016/j.jbc.2025.110679

Figure Lengend Snippet: PPM1H binds nonphosphorylated Rab8A and Rab10 but not Rab12 via Leu66. Microscale thermophoresis of mNeon PPM1H and mNeon L66R PPM1H with Rab10 Q68L ( A and D ), Rab8A Q67L ( B , E ), or Rab12 Q101L ( C and F ). Purified Rab proteins were serially diluted, and mNeon PPM1H or mNeon L66R PPM1H was added (final concentration of 100 nM). Graphs show the mean ± SD from three independent measurements, each using different protein preparations. Values are summarized in .

Article Snippet: Recombinant DNA , pET15b His SUMO mNeon R338A PPM1H , Addgene in progress , 245124 RRID: Addgene_245124 , New , Human.

Techniques: Microscale Thermophoresis, Purification, Concentration Assay

Journal: The Journal of Biological Chemistry

Article Title: Allosteric regulation of the Golgi-localized PPM1H phosphatase by Rab GTPases modulates LRRK2 substrate dephosphorylation in Parkinson’s disease

doi: 10.1016/j.jbc.2025.110679

Figure Lengend Snippet: Binding properties of Rab8A and thiophosphorylated Rab8A to PPM1H. A and B , thiophosphorylated Rab8A Q67L does not rely on L66 for PPM1H binding. C and D , thio-phosphorylated Q67L Rab8A but not nonphosphorylated Rab8A binds much less tightly to a PPM1H FLAP domain mutated PPM1H R338A. E and F , GTP-bound WT Rab8A binds more strongly than GDP-bound WT Rab8A to PPM1H. Various Rab8A or pRab8A proteins were serially diluted and incubated with 100 nM mNeon PPM1H variants as in . Graphs represent mean ± SD from three independent experiments using separate protein preparations. pRab, phosphoRab.

Article Snippet: Recombinant DNA , pET15b His SUMO mNeon R338A PPM1H , Addgene in progress , 245124 RRID: Addgene_245124 , New , Human.

Techniques: Binding Assay, Incubation

Journal: The Journal of Biological Chemistry

Article Title: Allosteric regulation of the Golgi-localized PPM1H phosphatase by Rab GTPases modulates LRRK2 substrate dephosphorylation in Parkinson’s disease

doi: 10.1016/j.jbc.2025.110679

Figure Lengend Snippet: Rab8A associates with liposome-bound PPM1H. Sucrose gradient coflotation of His-Rab8A Q67L (full length, nonprenylated) with mNeon PPM1H ( A , B ) or mNeon L66R PPM1H ( C , D ) in the presence and absence of 50 nm liposomes. The distribution of PPM1H and Rab8A across the gradient was determined by immunoblot; fractions were collected from the top . Quantification of three independent experiments is shown (±SD).

Article Snippet: Recombinant DNA , pET15b His SUMO mNeon R338A PPM1H , Addgene in progress , 245124 RRID: Addgene_245124 , New , Human.

Techniques: Liposomes, Western Blot

Journal: The Journal of Biological Chemistry

Article Title: Allosteric regulation of the Golgi-localized PPM1H phosphatase by Rab GTPases modulates LRRK2 substrate dephosphorylation in Parkinson’s disease

doi: 10.1016/j.jbc.2025.110679

Figure Lengend Snippet: Rab10 associates with liposome-bound PPM1H. Sucrose gradient coflotation of Rab10 Q68L (full length) with mNeon PPM1H ( A ) or mNeon L66R PPM1H ( C ) in the presence and absence of 50 nm liposomes. The distribution of PPM1H and Rab10 across the gradient was determined by immunoblot; fractions were collected from the top . Quantification of three independent experiments is shown (±SD).

Article Snippet: Recombinant DNA , pET15b His SUMO mNeon R338A PPM1H , Addgene in progress , 245124 RRID: Addgene_245124 , New , Human.

Techniques: Liposomes, Western Blot

Journal: The Journal of Biological Chemistry

Article Title: Allosteric regulation of the Golgi-localized PPM1H phosphatase by Rab GTPases modulates LRRK2 substrate dephosphorylation in Parkinson’s disease

doi: 10.1016/j.jbc.2025.110679

Figure Lengend Snippet: PPM1H’s N-terminal residues contribute to Rab8A and Rab10 binding. Microscale thermophoresis of mNeon Δ37 PPM1H with His Rab8A Q67L ( A ) or Rab10 Q68L ( B ). C , sucrose gradient coflotation of His Rab8A Q67L with mNeon Δ37 PPM1H in the presence and absence of 50 nm diameter NTA(Ni) containing liposomes. D , quantification of three independent experiments is shown (±SD). Ni, nickel; NTA, nitrilotriacetic acid.

Article Snippet: Recombinant DNA , pET15b His SUMO mNeon R338A PPM1H , Addgene in progress , 245124 RRID: Addgene_245124 , New , Human.

Techniques: Binding Assay, Microscale Thermophoresis, Liposomes

Journal: The Journal of Biological Chemistry

Article Title: Allosteric regulation of the Golgi-localized PPM1H phosphatase by Rab GTPases modulates LRRK2 substrate dephosphorylation in Parkinson’s disease

doi: 10.1016/j.jbc.2025.110679

Figure Lengend Snippet: Rab8A, but not Rab12, inhibits PPM1H activity. A , anti-pRab10 immunoblot analysis of dephosphorylation by PPM1H ( upper gel ) or L66R PPM1H ( lower gel ). B and C , data were plotted as PPM1H activity, with maximum activity equal to the amount of pRab10 dephosphorylation seen in the absence of non-pRab inhibitor (lanes 3 and 4 of each gel) compared with reactions lacking PPM1H (lanes 1 and 2). D , rate of pRab10 phosphatase activity (monitored at t = 0, 8, 15, and 30 min) for mNeon-PPM1H, mNeon-L66R PPM1H, and mNeon Δ37 PPM1H. E , quantification of pRab10 intensity from ( D ), with maximum intensity detected at 0 min normalized to a value of 1. Error bars represent SD from three independent experiments; representative gels are shown. Black line , mNeon L66R PPM1H activity; red line , mNeon PPM1H activity; and blue line , mNeon Δ37 PPM1H activity. pRab, phosphoRab.

Article Snippet: Recombinant DNA , pET15b His SUMO mNeon R338A PPM1H , Addgene in progress , 245124 RRID: Addgene_245124 , New , Human.

Techniques: Activity Assay, Western Blot, De-Phosphorylation Assay

Journal: The Journal of Biological Chemistry

Article Title: Allosteric regulation of the Golgi-localized PPM1H phosphatase by Rab GTPases modulates LRRK2 substrate dephosphorylation in Parkinson’s disease

doi: 10.1016/j.jbc.2025.110679

Figure Lengend Snippet: A model for PPM1H membrane recruitment and allosteric regulation. For details, see text.

Article Snippet: Recombinant DNA , pET15b His SUMO mNeon R338A PPM1H , Addgene in progress , 245124 RRID: Addgene_245124 , New , Human.

Techniques: Membrane