Myristoylome profiling reveals a concerted mechanism of ARF GTPase deacylation by the bacterial protease IpaJ

Abstract

N-myristoylation is an essential fatty acid modification that governs the localization and activity of cell signaling enzymes, architectural proteins, and immune regulatory factors. Despite its importance in health and disease, there are currently no methods for reversing protein myristoylation in vivo. Recently, the Shigella flexneri protease IpaJ was found to cleave myristoylated glycine of eukaryotic proteins, yet the discriminatory mechanisms of substrate selection required for targeted demyristoylation have not yet been evaluated. Here, we performed global myristoylome profiling of cells treated with IpaJ under distinct physiological conditions. The protease is highly promiscuous among diverse N-myristoylated proteins in vitro but is remarkably specific to Golgi-associated ARF/ARL family GTPases during Shigella infection. Reconstitution studies revealed a mechanistic framework for substrate discrimination based on IpaJ's function as a GTPase "effector" of bacterial origin. We now propose a concerted model for IpaJ function that highlights its potential for programmable demyristoylation in vivo.

Figure 1. IpaJ cleaves majority of myristoylated proteins in vitro

(A) Design of the experiment to analyze protein cleavage by recombinant IpaJ in vitro. Alk-12 labeled myristoylated proteins were conjugated azido-rhodamine for in-gel visualization or with azido-biotin for purification and mass-spectrometric analysis. (B) In-gel fluorescent visualization (left) of myristoylome profile of HeLa cell extracts from untreated or IpaJ treated samples. Total protein is shown (right). * Indicates proteins cleaved by IpaJ. C. Scatter Plot of results from differential mass-spectrometric analysis. Proteins that are known to be N-myristoylated are colored red. Y-axis shows the fold-increase or decrease of protein abundance in IpaJ-treated sample compared to untreated-treated samples. Green shading marks the area of 2-fold deviation of protein abundance in IpaJ-treated lysates. For visualization purpose more than 10 fold over- or under-representation is shown as approximately 10 or −10, respectively. D. Identified N-myristoylated proteins showing the fold increase or decrease of peptide abundance between IpaJ treated and untreated samples.

Figure 2. Myristoylated N-terminus is necessary and sufficient for cleavage by IpaJ

(A) Diagrams of the peptides corresponding to myr-Gly₂-Glu₁₇ and Asn₃-Glu₁₇ control are shown. fSEC analysis of myristoylated peptides after 30 minute of the cleavage reaction. Trace of the Asn₃-Glu₁₇ (blue) control compared myr-Gly₂-Glu₁₇ peptide in untreated (green), IpaJ treated (orange), and IpaJ C64A treated (red) samples are shown. (B) Time course of the myr-Gly₂-Glu₁₇ cleavage by IpaJ. The peptide (1 μM) was incubated with MBP-IpaJΔ50 (50 nM) for indicated period of time (left panel). Areas under the curves were quantified to estimate percent of cleaved substrate (right panel). (C) fSEC analysis of decanoyl and palmitoyl peptide cleavage. Trace of untreated Gly₂-Glu₁₇ harboring 10-carbon decanoyl (left) and 16-carbon palmitoyl (right) is shown in green and cleavage by IpaJ is shown in purple. (D) Full-length human ARF1-6xHis was expressed alone (left) or co-expressed with IpaJ (right) in E. coli BL-21. Expected (theoretical) mass for full-length ARF1 protein is 22757 Da (minor species), and 22625 Da for methionine processed form (major species). (E) In-gel fluorescence assay (top panel) showing Alexa 647-labeled myristoylated ARF1 expressed in E. coli BL-21 after untreated (control) or IpaJ treated samples. Coomassie staining was used to confirm equal loading of ARF1 protein (middle panel).

Figure 3. Defining the N-myristoyl-glycine as the minimal IpaJ substrate

(A) Multiple sequence alignment of N-myristoylated proteins from selected in vitro substrates (top) and ARF/ARL proteins identified in vivo (bottom). Positively charged residues (green), negatively charged residues (red), and sites for protein palmitoylation (blue) are shown. (B and C) fSEC analysis of the minimal myr-Gly-Lys peptide. (B) Trace of myr-Gly-Lys (green) and Lys peptide (orange) are shown. (C) myr-Gly-Lys treated with recombinant wild type IpaJ (purple) or IpaJ C64A mutant (red) are shown. (D) fSEC analysis of the myr-Ala₂-Glu₁₇. Trace of untreated (green) and IpaJ (purple) treated myr-Ala₂-Glu₁₇ peptide is shown. The trace of the IpaJ sample was manually offset by 10 seconds for visualization purposes.

Figure 4. IpaJ has limited number of substrates during infection

(A) Design of the experiment to analyze protein cleavage by IpaJ during Shigella infection. Alk-12 labeled myristoylated proteins were conjugated azido-rhodamine for in-gel visualization or with azido-biotin for purification and mass-spectrometric analysis. (B) In-gel fluorescent visualization of myristoylome profile of uninfected, Shigella WT, or Shigella ΔipaJ infected cells (left). Total protein is shown (right). Arrow indicates proteins cleaved by IpaJ. (C) Representative scatter Plot of results from differential mass-spectrometric analysis. Proteins with N-terminal Glycine are shown in red. Y-axis shows the fold-increase or decrease of protein abundance in WT Shigella infected samples compared to Shigella ΔipaJ treated cells. Green shading marks the area of 2-fold deviation of protein abundance. Myristoylated proteins falling below the green shading are cleaved by IpaJ. For visualization purpose more than 10 fold over- or under-representation is shown as approximately 10 or −10, respectively. (D) Identified N-myristoylated proteins in one representative sample showing the fold increase or decrease of peptide abundance between WT Shigella and Shigella ΔipaJ infected cells.

Figure 5. IpaJ functions as an ARF substrate

(A) Glutathione-pulldown of GST (control) or GST-ARF1Δ17 in the presence of MBP-IpaJΔ50. Proteins by separated with SDS PAGE and visualized by Coomassie staining. (B) Glutathione-pulldown of GST-ARF1Δ17 in the nucleotide free (free), GTP, or GDP bound state in the presence of MBP-IpaJΔ50 (left) or the GAT domain of GGA1 (right). Proteins were separated by SDS PAGE and visualized by Coomassie staining. (C) Glutathione-pulldown of GST-ARF5Δ17 in the nucleotide free (free), GTP, or GDP bound state in presence of MBP-IpaJΔ50 (left) and visualized as in (A). (D and E) Crystal structure of GTP-bound ARF1 (green) in complex with the coatamer subunit gamma-1 (red) (PDB ID: 3TJZ). Binding interface comprises switch I and interswitch regions of ARF1. (E) Specifically, Ile49 and Trp66 (see Figure 5G) participate in this interaction. (F and G) Glutathione-pulldown of GST-ARF1Δ17 harboring the indicated mutations in the presence of MBP-IpaJΔ50. Proteins were visualized as in (A). (H) Homologous competition experiments between GTP-loaded ARF1 GTPase domain (ARF1Δ17) and the indicated effector substrates. Dissociation (K_d) constants are shown.

Figure 6. IpaJ cleaves only Golgi-localized GTPases

(A) Glutathione-pulldown of GST-ARF6Δ13 in the nucleotide free (free), GTP, or GDP bound state in presence of MBP-IpaJΔ50 (left) and visualized as in Figure 5A. (B) In-gel fluorescence showing myristoylated ARF1 or ARF6 after co-expression with IpaJ or IpaJC64A in HeLa cells (top panel). Equal loading of ARF1/ARF6 (middle panel) and expression of IpaJ (lower panel) were confirmed by western blot analysis. Graph shows the quantification of fluorescent signal (in arbitrary units (au) +/− SD) from three experimental repetitions using ImageJ. (C) Fluorescent Microscopy of EGFP-tagged ARF1-, ARF5-, ARL1-, and ARF6 when co expressed with mCherry vector (control) or IpaJ-mCherry (IpaJ). Inset box shows ARF protein localization (middle panel) and cis-Golgi (right panel) visualized by gm130 immunofluorescence. The bottom two rows focus on the plasma membrane localization of ARF6. (D) Fluorescent Microscopy mCherry tagged IpaJC64A and EGFP-tagged ARF1 in HeLa cells left untreated (top row) or treated with Brefeldin A (bottom row). Cis-Golgi was visualized with gm130 antibodies. (E) Fluorescent Microscopy mCherry tagged IpaJC64A and EGFP-tagged ARF6 in HeLa cells. Inset (1) is focused on the cis-Golgi and inset (2) is focused on plasma membrane.

Figure 7. Concerted Model of IpaJ Function at the Golgi apparatus

(A) Model of ARF GTPase function in Golgi regulation. Top panel: GEF-catalyzed nucleotide exchange activates ARF and recruits it onto membrane via the myristoyl switch. GTP-bound ARF recruits downstream effectors to promote formation of transport vesicles. Bottom panel: Type III secreted IpaJ recognizes GTP-ARF and inactivates it by irreversibly releasing it from the membranes via Myristoyl-Glycine Cleavage. (B) Concerted model showing the proposed sequence of events for IpaJ cleavage of myristoylated ARF proteins at the Golgi apparatus. (C) Comparison of the target motifs for IpaJ and the C39 peptidase family. Arrows indicate the protease cleavage sites. Glycines are colored red and myristoyl group colored blue.