EMBO/SourceData huggingface dataset:
Figure legend: "(a,b) Ubiquitination of Mfn1 following treatment with CCCP (10 μM) is reduced in the mitochondrial fraction of both SH-SY5Y cells stably expressing Fbxo7 short hairpin RNA (Fbxo7 KD) compared to an empty vector control line (a) and in patient fibroblasts with homozygous R378G mutation compared to fibroblasts from healthy controls (b). Arrowheads indicate ubiquitinated Mfn1. IB, immunoblot."
NCBI gene IDs:
"Fbxo7: 25793"
Figure legend: "(c,d) Fbxo7 expression restores elevated Mfn steady-state levels in parkin (c) but not PINK1 (d) mutant Drosophila. Histograms show mean ± s.e.m. of densitometry analysis of Mfn immunoblots above, normalized to complex Vα (CxVα). Control genotypes are park25/+; da-GAL4/+ (c) and PINK1B9/+; da-GAL4/+ (d)."
NCBI gene IDs:
"GAL4: 
da: 34413
Fbxo7: 38443
parkin: 40336
PINK1: 31607"
Figure legend: "(e) Mitochondria in control Drosophila S2R+ cells stained with MitoTracker Red show a heterogeneous morphology, with a mixture of tubules and fragmented mitochondria. RNAi knockdown of parkin or PINK1 causes excessive fusion and elongated mitochondria compared to control double-stranded RNA (Caenorhabditis elegans gene ZK686.3). Expression of Fbxo7 restores parkin but not PINK1 knockdown phenotype to WT appearance. Scale bar shows 5 μm. (f) Quantification of mitochondrial morphology in dsRNA treated cells. Scoring system: 1, fragmented; 2, WT; 3, tubular; 4, hyper-fused (clumped). Histograms indicate mean ± s.e.m. Two-tailed Student t-tests (***P 0.001, *P 0.05). All western blots were performed a minimum of three times and images are representative of 100 cells scored per condition. Full-length blots are presented in Supplementary Figure 9."
NCBI gene IDs:
"Fbxo7: 38443
parkin: 40336
PINK1: 31607
ZK686.3: 176089"
Figure legend: "(a) Treatment with CCCP (10 μM) results in an increase in LC3-II in the mitochondrial but not the cytosolic fraction of cells stably expressing the empty shRNA vector (control), and this is delayed in stable Fbxo7 knockdown (KD) SH-SY5Y cells."
NCBI gene IDs:
"Fbxo7: 25793"
Figure legend: "(c) Mitochondrial accumulation of p62 following CCCP treatment is inhibited by Fbxo7 siRNA. Flag-Parkin overexpressing SH-SY5Y cells were transfected with scrambled (scr) or Fbxo7 siRNA as indicated and treated with either DMSO or CCCP (10 μM) for 6 h. Colocalization of p62 with HtrA2, a mitochondrial marker, was assessed by Pearson's correlation coefficient (Rr) on a cell-by-cell basis. Histogram shows the percentage of cells in which Rr was greater than 0.5. Data are represented as mean ± s.e.m., *P 0.05. Scale bars, 10 μm."
NCBI gene IDs:
"Fbxo7: 25793
Parkin: 5071"
Figure legend: "(d) Mitophagy was analyzed in untransfected (UT) SH-SY5Y cells or in stable Flag-Parkin overexpressing SH-SY5Y cells transfected with either scrambled (scr) or Fbxo7 siRNA. Histogram indicates the percentage of cells with no remaining mitochondria following 24 h treatment with CCCP (10 μM) for each condition. Complex Vβ subunit (CxVβ) was used as a mitochondrial marker. Data are presented as mean ± s.e.m., **P 0.01. Scale bars, 10 μm."
NCBI gene IDs:
"Fbxo7: 25793"
Figure legend: "(e) Mitochondrial mass was measured in Flag-Parkin overexpressing SH-SY5Y cells transfected with scrambled (scr) or Fbxo7 siRNA and treated for 24 h with either dimethylsulfoxide (DMSO) vehicle or CCCP (10 μM). For representative images, see Supplementary Figure 8d. Full-length blots are presented in Supplementary Figure 9."
NCBI gene IDs:
"Fbxo7: 25793
Parkin: 5071"
Figure legend: "Western blot analysis of nuclear extracts of ring (R), trophozoite (T), and schizont (S) stages from a synchronous population of SMC3-3HA-glmS parasites. SMC3-3HA is detected with an anti-HA antibody. An antibody against histone H3 is used as a control. Molecular weights are shown to the right. SMC3-3HA has a predicted molecular weight of 147.3 kDa (of which 3.3 kDa correspond to the 3HA tag)."
NCBI gene IDs:
"HA: 
glmS: 938736
SMC3: 812569"
Figure legend: "(C) Immunofluorescence assays of fixed RBCs infected with trophozoite or schizont stage SMC3-3HA-glmS parasites. DNA was stained with DAPI (blue) and SMC3-3HA was detected with anti-HA (green in B and magenta in C) antibody. HP1 was detected with anti-HP1 antibody (green in C). DIC, differential interference contrast. Scale bars equal 10 µm (B) and 5 µm (C)."
NCBI gene IDs:
"HA: 
glmS: 938736
SMC3: 812569"
Figure legend: "Western blot analysis of nuclear extracts at 12, 24, and 36 hpi from a clonal population of SMC3-3HA-glmS parasites in the absence (-) or presence (+) of glucosamine (GlcN). SMC3-3HA is detected with an anti-HA antibody. An antibody against histone H3 is used as a control. Molecular weights are shown to the right."
NCBI gene IDs:
"HA: 
glmS: 938736
SMC3: 812569"
Figure legend: "Growth curve showing parasite growth rate (parasitemia at Day X/parasitemia at Day 1) over five days for WT and two clones of SMC3-3HA-glmS parasites in the absence or presence of glucosamine (GlcN). Glucosamine treatment was started 96 h (two IDC cycles) before Day 1 to ensure SMC3 knockdown during the days sampled Uninfected red blood cells (Blood) served as reference of background. Error bars indicate standard deviation of three technical replicates (n = 3). A two-way ANOVA with Tukey post hoc test was used for statistical analysis. No significant differences were found."
NCBI gene IDs:
"HA: 
glmS: 938736
SMC3: 812569"
Figure legend: "RNA-seq of an SMC3-3HA-glmS clone shows smc3 transcript levels (FPKM) at 12 (blue, q = 8.5 x 10-3), 24 (coral, q = 1.3 x 10-39), and 36 (green, q = 4.1 x 10-54) hpi in the absence (filled circles) or presence (empty circles) of glucosamine (GlcN). Error bars represent standard deviation of three technical replicates except for the untreated 12 hpi parasites, for which there were two replicates. P-values are calculated with a Wald test for significance of coefficients in a negative binomial generalized linear model as implemented in DESeq2 q = Bonferroni corrected P-value. Asterisks indicate q values &lt; 0.5."
NCBI gene IDs:
"HA: 
glmS: 938736
SMC3: 812569
smc3: 812569"
Figure legend: "ChIP-seq data showing enrichment of SMC3 (y-axis = ChIP/Input) at 12 (blue), 24 (coral), and 36 (green) hpi in clonal SMC3-3HA-glmS parasites at the rhoptry-associated protein 2 (rap2, PF3D7_0501600) and the glideosome-associated protein 45 (gap45, PF3D7_1222700) gene loci. The x-axis is DNA sequence, with the gene represented by a black box with white arrowheads to indicate transcription direction. One replicate (clone A) was used for ChIP-seq. ATAC-seq data from closely corresponding time points (15, 25, and 35 hpi) are shown in grey, with the y-axis representing ATAC-seq (RPM)/gDNA (RPM)."
NCBI gene IDs:
"HA: 
glmS: 938736
SMC3: 812569
PF3D7_0501600: 812869
rap2: 812869
rhoptry-associated protein 2: 812869
gap45: 811270
glideosome-associated protein 45: 811270
PF3D7_1222700: 811270"
Figure legend: "RNA-seq of an SMC3-3HA-glmS clone shows transcript levels (FPKM) for rap2 (PF3D7_0501600) at 12 (q = 3 x 10-2) and 24 (q = 3.3 x 10-2) hpi and gap45 (PF3D7_1222700) at 12 (q = 8 x 10-1) and 24 (q = 1.6 x 10-2) hpi in the absence (black) or presence (grey) of glucosamine (GlcN). Error bars represent standard deviation of three technical replicates except for the untreated 12 hpi parasites, for which there were two replicates. P-values are calculated with a Wald test for significance of coefficients in a negative binomial generalized linear model as implemented in DESeq2 (Love et al, 2014). q = Bonferroni corrected P-value."
NCBI gene IDs:
"HA: 
glmS: 938736
SMC3: 812569
PF3D7_0501600: 812869
rap2: 812869
gap45: 811270
PF3D7_1222700: 811270"
Figure legend: "Expression values of rap2 (PF3D7_0501600) and gap45 (PF3D7_1222700) genes across the IDC (indicated on the x-axis by hpi) from the transcriptomics time course Data corresponding to 12 (blue), 24 (coral), and 36 (green) hpi time points are highlighted."
NCBI gene IDs:
"PF3D7_0501600: 812869
rap2: 812869
gap45: 811270
PF3D7_1222700: 811270"
Figure legend: "Full-length TLN (but not APP) accumulates in a distinct compartment in PS1−/−hippocampal neurons. Double-immunofluorescence staining for endogenous TLN (green, B36.1) and APP (red, mAb C1 6.1) in wild-type (top) and PS1−/− (bottom) hippocampal neurons (15-d culture). The inset shows an overview of the neuron. In wild-type neurons TLN labeling is essentially localized to the somatodendritic plasmalemma in contrast to APP, which is found in intracellular compartments. In addition, PS1 deficiency causes TLN, but not APP, to cluster in large somatic accumulations. Bars, 10 μm."
NCBI gene IDs:
"PS1: 19164"
Figure legend: "(A) Western blot analysis of endogenous TLN and APP in wild-type and PS1−/− hippocampal neurons. PS1 deficiency results in the accumulation of APP-CTF. No TLN-CTF (estimated ± 7 kD) was detected, neither was it detected after SFV-induced exogenous overexpression. Also, overexpression of a TLNΔE fragment did not generate a PS1-dependent TLN intracellular domain."
NCBI gene IDs:
"TLN: 15898
PS1: 19164"
Figure legend: "(B) Different constructs fused to the Gal4VP16 domain were used in a γ-secretase reporter assay. Control transfections (pIPspAdApt empty vector and pIPspAdApt-APP without Gal4VP16) show no luciferase activity. APP-Gal4VP16 and NotchΔE-Gal4VP16 activate the luciferase gene upon cleavage and are inhibited by DAPT, L658,458, or compound 32 (125 nM). No luciferase activity was detected using TLNΔE or APP in which the transmembrane domain was replaced by that of TLN (APP/TLNTMR chimaera), indicating that this region is not cleaved by γ-secretase."
NCBI gene IDs:
"APP: 351
TLN: 7087
Notch: 4855///4854///4853///4851"
Figure legend: "(D) Adenoviral reintroduction of human PS1 suppresses TLN accumulations. 30-35% of PS1−/− neurons display TLN accumulations, in contrast to &lt;5% in PS1+/+ and +/− cultures as well as in cultures expressing human PS1 in a PS1−/− background. However, suppression of TLN accumulations was obtained by adenoviral introduction of human PS1. A clear dose-dependent inhibition was seen with increasing MOI of adenoviral (AV) human PS1, but also the familial Alzheimer's disease-linked PS1G384A and dominant-negative PS1D257A mutants. Control adenoviral infections with eGFP did not have a significant effect. After 9-11 d post-infection (15 d post-plating), neurons displayed significant PS1 protein expression as demonstrated by double staining for TLN and human PS1(mAb 5.2). Bars, 20 μm."
NCBI gene IDs:
"PS1: 5663"
Figure legend: "Wild-type and PS1−/− cortical neurons were transduced with SFV-TLN (A) or -APP (B), pulse labeled for 15 min with [35S]methionine, and chased for different time periods. ImmunoprecipitatedTLN and APP were treated with EndoH and analyzed by SDS-PAGE and phosphorimaging. The accumulation of an EndoH-resistant band indicates progressive maturation during Golgi passage; however, the ratio of EndoH-resistant to -sensitive TLN (A, top) and APP (B, top) revealed no difference (mean ± SEM, n = 3). Instead, the half-life of overexpressed TLN (A, bottom), but not full-length APP (B, bottom), is significantly prolonged in neurons−/−neurons (mean ± SEM, n = 3)."
NCBI gene IDs:
"APP: 351
TLN: 15898
PS1: 5663"
Figure legend: "(C) Wild-type and PS1−/− hippocampal neurons (12 d) were scraped, pelleted, and treated with 10 mU EndoH, followed by Western blot detection of APP, TLN, PS1, nicastrin (NCT), synaptophysin, and ductin. TLN levels are increased almost fourfold in PS1−/− neurons. No EndoH-sensitive TLN was detected in PS1−/− neurons, indicating a complete maturation. APP-CTF shows a dramatic accumulation (44-fold; mean ± SEM, n = 3)."
NCBI gene IDs:
"PS1: 19164"
Figure legend: "(B and C) Double immunostaining of wild-type and PS1−/− hippocampal neurons for TLN (green) and autophagic vacuole-associated Apg12p (B) and LC3 (C). To detect both sets of pAbs, an alternative method was developed using biotinylated anti-TLN (see Materials and methods). Each experiment included controls for specificity (not depicted). In wild-type neurons, both Apg12p and LC3 (B and C, top row) were broadly distributed in cell bodies and neurites, but did not colocalize with TLN. Colocalization was only observed in multiple TLN accumulations in PS1−/− hippocampal neurons (second row in B and C, respectively). For Apg12p, coimmunostaining was also noticed in small discrete structures in the proximal dendrites (B, bottom row). Bars, 10 μm."
NCBI gene IDs:
"PS1: 19164"
Figure legend: "(A) Intracellular sorting and maturation of catD. Wild-type and PS1−/− neurons were metabolically labeled and chased for the indicated time periods. Phosphorimaging of immunoprecipitated radiolabeled catD did not reveal a difference in the ratio of proteolytically processed 46-kD intermediate vs. 52-kD precursor (mean ± SEM, n = 3)."
NCBI gene IDs:
"PS1: 19164"
Figure legend: "(B-D) TLN localizes to autophagic vacuoles of catD−/−hippocampal neurons. Lysotracker staining revealed sparsely distributed small-sized organelles in wild-type and PS1−/− neurons in contrast to catD−/−neurons where high numbers of large Lysotracker-positive organelles were found (B, arrowheads). Although TLN accumulations in PS1−/− were fully negative for Lysotracker, some acidic organelles tended to closely associate (C, arrowheads, middle). In catD−/− neurons, TLN was clearly detected in the large acidic organelles (C, bottom). Bars, 20 μm. (D) At the immuno-EM level, the large acidic organelles seen in catD−/−neurons represent dense autophagic vacuole-like structures (star) that label positive for TLN (10-nm gold). M, mitochondrion. Bars, 200 nm."
NCBI gene IDs:
"catD: 13033
PS1: 19164"
Figure legend: " B, C. Effects of deleting β′ ZBD on transcriptional activities of RNAP on different promoters. The fliCp (B) was used as template for σ28-dependent transcription, and the lacUV5p (C) was used in σ70-dependent transcription. RNA products indicated by solid triangles were quantified and the signal obtained from 100 nM wild-type RNAP was normalized to 1 in each test respectively. "
NCBI gene IDs:
"fliCp: 949101
lacUV5p: 945006"
Figure legend: " D. Transcriptional activities of ZBD mutated σ28-RNAP on fliCp. RNA products indicated by solid triangles were quantified. "
NCBI gene IDs:
"fliCp: 949101"
Figure legend: " E. Binding of σ28-RNAP with fliCp as detected by EMSA (left). The heparin-resistant RNAP-promoter open complex is indicated as \"RPo\", and the heparin-sensitive RNAP-promoter closed complex is shown as \"RPc\". Percentages of RNAP-promoter open complex (RPo) and closed complex (RPc) in EMSA performed using σ28-RNAP and fliCp (right). "
NCBI gene IDs:
"fliCp: 949101"
Figure legend: " F. DNase I footprinting of the fliCp complex with σ28-RNAP. Promoter DNA was labeled on the non-template strand. The promoter region protected by RNAP is indicated by a red box at the bottom panel. "
NCBI gene IDs:
"fliCp: 949101"
Figure legend: " B, C. Promoter activities of tarp (B) and fliCp (C) in E. coli wild-type (Ec-WT) and its mutants expressing ZBD-mutated RNAP (Ec-K74A, Ec-K87A and Ec-K74A-K87A) shown as mean ± SD from three replicates. "
NCBI gene IDs:
"fliCp: 949101
tarp: 946399"
Figure legend: " E. Relative mRNA levels of flagellar genes in Ec-K74A-K87A strain comparing with that in Ec-WT (normalized to 1 for each gene). Diagram for the role of σ28 (fliA gene) in flagella regulon hierarchy Clarke &amp; Sperandio, 2005Fitzgerald, 2014(; ) is shown in the left panel. Data are mean ± SEM from three replicates. "
NCBI gene IDs:
"fliA: 948824"
Figure legend: "F. Motilities of Ec-K74A-K87A strains with over-expression of wild-type rpoC gene (Ec-K74A-K87A-C) or carrying the control plasmid (Ec-K74A-K87A-V)."
NCBI gene IDs:
"rpoC: 948487"
Figure legend: " G. Activities of fliCp in Ec-K74A-K87A-C and Ec-K74A-K87A-V strains. L-arabinose was used at final concentration of 0.002%. Data are mean ± SD from three colonies. "
NCBI gene IDs:
"fliCp: 949101"
Figure legend: " B. Activities of chimeric σ28-R4m in initiating transcription from tarp-35m, when reconstituted with wild-type (WT) or ZBD mutated RNAP core enzyme. "
NCBI gene IDs:
"tarp: 946399"
Figure legend: " Effects of mutating β′ ZBD on transcriptional activities of σ38-RNAP on osmYp. "
NCBI gene IDs:
"osmYp: 948895"
Figure legend: " Effects of mutating β′ ZBD on transcriptional activities of σ70-RNAP on osmYp. "
NCBI gene IDs:
"osmYp: 948895"
Figure legend: "A-CConfirmation by mass spectrometry that Rab8A (A), Rab8B (B) and Rab13 (C) Ser111 is phosphorylated upon PINK1 activation after CCCP treatment. Flp‐In T‐Rex HEK293 cells expressing empty‐FLAG, WT PINK1‐FLAG and KI (D384A) PINK1‐FLAG were transfected either with HA‐Rab8A (A), HA‐Rab8B (B) or HA‐Rab13 (C) induced with doxycycline and stimulated with 10 μM of CCCP for 3 h. Whole‐cell lysates (10 mg) were immunoprecipitated with anti‐HA agarose, resolved by SDS-PAGE and stained with colloidal Coomassie blue (second panel). Coomassie‐stained bands migrating with expected molecular mass of HA‐Rabs were excised, in‐gel digested with trypsin and subjected to high‐performance liquid chromatography with LC‐MS/MS on an LTQ‐Orbitrap mass spectrometer. Upper panel shows the extracted ion chromatogram (XIC) analysis of Ser111‐containing phosphopeptides (8A, NIEEHApSADVEK; 8B, NIEEHApSSDVER; 13, SIKENApSAGVER) with the combined signal intensity of the 2+ and 3+ forms of the peptide indicated on the y‐axis. Note that the Ser111 phosphopeptide was only detected in samples from WT PINK1‐FLAG‐expressing cells following CCCP stimulation."
NCBI gene IDs:
"PINK1: 65018
Rab13: 5872
Rab8A: 4218
Rab8B: 51762"
Figure legend: "DCharacterisation of Rab8A, Rab8B and Rab13 phospho‐Ser111 antibodies. Flp‐In T‐Rex HEK293 cells expressing empty‐FLAG, WT PINK1‐FLAG and KI (D384A) PINK1‐FLAG were transfected with either WT or Ser111Ala‐mutant (S111A) HA‐Rab8A, HA‐Rab8B or HA‐Rab13, induced with doxycycline and stimulated with 10 μM of CCCP for 3 h. Whole‐cell lysates (0.25 mg) were immunoprecipitated with anti‐HA agarose and immunoblotted with Rab8A, Rab8B or Rab13 phospho‐Ser111 antibodies. Part of the immunoprecipitates was used to immunoblot for HA antibody as loading controls."
NCBI gene IDs:
"PINK1: 65018
Rab13: 5872
Rab8A: 4218
Rab8B: 51762"
Figure legend: "PINK1 is essential for CCCP‐mediated Rab8A Ser111 phosphorylation. WT and PINK1 KO HeLa cells were transfected with either WT or Ser111Ala (S111A) mutant constructs of HA‐Rab8A, HA‐Rab8B or HA‐Rab13. Some PINK1 KO HeLa cells were reintroduced with PINK1 by transfection of WT PINK1‐3xFLAG or KI (D384A) PINK1‐3xFLAG as indicated. After transfection for at least 24 h, cells were treated with DMSO as a vehicle control or CCCP for 20 h. Whole‐cell lysates (1 mg) were immunoprecipitated with anti‐HA agarose and immunoblotted with Rab8A, Rab8B or Rab13 phospho‐Ser111 antibody. Part of the immunoprecipitates was used to immunoblot for HA antibody as loading controls. For the lower panel, whole‐cell lysates (30 μg) were immunoblotted with total PINK1 antibody to confirm PINK1 expression and with GAPDH as loading controls."
NCBI gene IDs:
"PINK1: 65018
Rab13: 5872
Rab8A: 4218
Rab8B: 51762"
Figure legend: "Endogenous Rab8A Ser111 phosphorylation is PINK1 dependent. WT and PINK1 KO HeLa cells were treated with DMSO as a vehicle control or CCCP for 20 h. Some PINK1 KO HeLa cells were reintroduced with PINK1 by transfection of WT PINK1‐3xFLAG or KI (D384A) PINK1‐3xFLAG as indicated for at least 24 h before CCCP treatment. Whole‐cell lysates (1 mg) were immunoprecipitated with anti‐Rab8A pre‐bound with protein A agarose followed by immunoblot with Rab8A phospho‐Ser111 antibody. Part of the immunoprecipitates was used to immunoblot with anti‐total Rab8A antibody as loading controls."
NCBI gene IDs:
"PINK1: 65018"
Figure legend: "Absence of Rab8A Ser111 phosphorylation in human mutant PINK1 patient fibroblasts. Primary skinfibroblasts were derived from a patient with homozygous PINK1 Q456X mutation or unaffected control. Cells were incubated with DMSO or CCCP for 20 h, and whole‐cell lysates (1 mg) were immunoprecipitated with anti‐Rab8A antibody conjugated to protein A agarose and immunoblotted with total or Rab8A phospho‐Ser111 antibody. Lysates (1 mg) were also subjected to immunoprecipitation with polyclonal anti‐PINK1 antibody and immunoblotted with monoclonal PINK1 antibody. Equal loading of protein extracts was confirmed by GAPDH."
NCBI gene IDs:
"PINK1: 65018"
Figure legend: "Absence of Rab8A Ser111 phosphorylation in PINK1 knockout MEFs. MEFs were derived from PINK1 knockout embryos or wild‐type controls (see Materials and Methods). Cells were incubated with DMSO or CCCP for 20 h, and whole‐cell lysates (1 mg) were immunoprecipitated with anti‐Rab8A antibody conjugated to protein A agarose and immunoblotted with total or Rab8A phospho‐Ser111 antibody. Lysates (1 mg) were also subjected to immunoprecipitation with a polyclonal anti‐mouse‐specific PINK1 antibody and immunoblotted with a different anti‐mouse‐specific PINK1 antibody. Equal loading of protein extracts was confirmed by GAPDH."
NCBI gene IDs:
"PINK1: 68943"
Figure legend: "Rab8A is not required for the activation of Parkin E3 ligase activity at mitochondria in response to PINK1 activation by CCCPWild‐type (WT) or Rab8A knockout (KO) HeLa cells were transfected with WT or Cys431Phe (C341F)‐mutant Parkin. After transfection for 24 h, cells were treated with DMSO as a vehicle control or 10 μM CCCP for 6 h. Mitochondrial enriched extracts (mitochondrial lysate) were incubated with ubiquitin‐binding resins derived from his‐halo‐ubiquilin1 UBA domain tetramer (UBAUBQLN1). Captured ubiquitylated proteins were subject to immunoblotting with anti‐CISD1 and anti‐mitofusin 2 antibodies. Mitochondrial lysate and total lysate were also subjected to immunoblotting with indicated antibodies for loading and protein expression controls. Phospho‐Ser111 Rab8A was detected after Rab8A immunoprecipitation from 200 μg of mitochondrial lysate with anti‐Rab8A antibody."
NCBI gene IDs:
"Parkin: 5071
Rab8A: 4218"
Figure legend: "In vitro phosphorylation analysis of Rab8A by PINK1. WT or S111A‐mutant Rab8A (1.2 μg) was incubated in the presence of MBP‐fused WT or KI (D359A) TcPINK1 (1.1 μg) and Mg2+‐[γ‐32P] ATP for the indicated time. Samples were subjected to SDS-PAGE, and proteins were detected by colloidal Coomassie blue staining (lower panel). The [γ‐32P] incorporation to substrate was detected by autoradiography (upper panel). Cerenkov counting was used to calculate the stoichiometry of substrate phosphorylation as mol of [γ‐32P] incorporation/mol of substrate. Ubiquitin was used as a positive control of the TcPINK1 substrate."
NCBI gene IDs:
"PINK1: Q9BXM7///65018
Rab8A: 4218"
Figure legend: "Time‐course comparison of PINK1‐mediated Rab8A, Rab8B and Rab13 Ser111 phosphorylation vs. Parkin Ser65 phosphorylation. Flp‐In T‐Rex HEK293 cells expressing WT PINK1‐FLAG were transfected with either WT or Ser111Ala‐(S111A) mutant HA‐Rab8A, HA‐Rab8B or HA‐Rab13, induced with doxycycline and stimulated with CCCP for the indicated time. In parallel, Flp‐In T‐Rex HEK293 cells expressing WT PINK1‐FLAG were transfected with either WT or Ser65 Ala (S65A)‐mutant Parkin. Whole‐cell lysates (0.25 mg) were immunoprecipitated with anti‐HA agarose and immunoblotted with indicated phospho‐Ser111 antibodies. Part of the immunoprecipitates was used to immunoblot for HA antibody as loading controls. For the lower panel, whole‐cell lysates (30 μg) were immunoblotted with indicated antibodies."
NCBI gene IDs:
"Parkin: 5071
PINK1: 65018
Rab13: 5872
Rab8A: 4218
Rab8B: 51762"
Figure legend: "Time‐course comparison of endogenous PINK1‐mediated Rab8A, Rab8B and Rab13 Ser111 phosphorylation vs. Parkin Ser65 phosphorylation. HeLa cells were transfected with either WT or S111A‐mutant HA‐Rab8A, HA‐Rab8B or HA‐Rab13 for at least 24 h before CCCP treatment for the indicated time. Whole‐cell lysates (1 mg) were immunoprecipitated with anti‐HA agarose and immunoblotted with indicated phospho‐Ser111 antibodies. In parallel, HeLa cells were transfected with either WT or S65A‐mutant Parkin and whole‐cell lysates (30 μg) were immunoblotted with indicated antibodies."
NCBI gene IDs:
"Parkin: 5071
Rab13: 5872
Rab8A: 4218
Rab8B: 51762"