Ubiquitination and dynactin regulate TMEPAI lysosomal trafficking

Luo, Shenheng; Jing, Lei; Zhao, Tian; Li, Yuyin; Liu, Zhenxing; Diao, Aipo

doi:10.1038/srep42668

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Published: 20 February 2017

Ubiquitination and dynactin regulate TMEPAI lysosomal trafficking

Shenheng Luo¹^na1,
Lei Jing¹^na1,
Tian Zhao¹,
Yuyin Li¹,
Zhenxing Liu¹ &
…
Aipo Diao¹

Scientific Reports volume 7, Article number: 42668 (2017) Cite this article

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Abstract

The transmembrane prostate androgen-induced protein (TMEPAI) has been reported to be elevated in various tumor cells, is localized to the lysosome and promotes lysosome stability. The molecular mechanism of TMEPAI trafficking however to the lysosome is unknown. Here we report that clathrin and CI-M6PR mediate TMEPAI transport from the Golgi directly into the endo-lysosomal pathway. TMEPAI is ubiquitinated at its C-terminal region and ubiquitination modification of TMEPAI is a signal for its lysosomal trafficking. Moreover, TMEPAI binds the ubiquitin binding proteins Hrs and STAM which is required for its lysosomal transport. In addition, TMEPAI interacts with the dynactin pointed-end complex subunits dynactin 5 and dynactin 6. The aa 132–155 domain is essential for specific TMEPAI binding and deletion of this binding site leads to mis-trafficking of TMEPAI to the plasma membrane. These results reveal the pathway and mechanism regulating transport of TMEPAI to the lysosome, which helps to further understand the role of TMEPAI in tumorigenesis.

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Introduction

Protein trafficking in the secretory and endocytic pathways is a multistep process involving the transport of proteins from a particular intracellular or extracellular compartment to another. This is regulated by an array of pathways including membrane trafficking, protein translocation, and endocytosis or exocytosis¹. Membrane trafficking has become an increasingly studied area of cellular machinery. The membrane bound organelles have different functions designed to facilitate protein transport and for providing distinct compartments specifically for its target proteins. In addition, the functional organization of the cell is maintained by the selectivity of the vesicular transport which plays a central role in the transport of molecules between different membrane-enclosed compartments. Lysosomes are ubiquitous organelles which function as the primary degradative compartments of cells. The integrity of the lysosome structure and its function is maintained by lysosomal membrane proteins (LMPs) and hydrolases. Lysosome biogenesis requires the involvement of both secretory and endocytosis pathways. Degradative cargo and newly synthesized lysosomal proteins target to the lysosome from an endo-lysosome system with or without passing through the plasma membrane, indicating two distinct trafficking pathways. Firstly the trans-Golgi network (TGN) feeds directly into the endo-lysosome system, and the best-characterized direct intracellular pathway is the clathrin-dependent transport of lysosomal hydrolases mediated by mannose-6-phosphate receptors (M6PRs)^2,3. The second route is following the constitutive secretory pathway to the plasma membrane which subsequently reaches the lysosomes by endocytosis. Increasing evidence suggests that there are multiple TGN exits for LMPs, LMPs and that these can travel to the lysosomes through both direct and indirect pathways^4,5.

Ubiquitination was originally described as a protein degradation signal to the 26 S proteasome^6,7. More attention has been attracted however to the discovery that ubiquitination is also found to modulate numerous biological processes in yeast and mammalian cells, including vesicular trafficking, signaling transduction, endocytosis, cell-cycle modification, DNA damage repair and gene transcription^8,9. The process of ubiquitinylation involves the sequential transfer of the evolutionarily conserved 76 amino acid protein ubiquitin, between ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2) and ubiquitin-protein ligase (E3), to the specific lysine residues of the target proteins. Proteins can either be mono, multi, or poly-ubiquitinated according to the degree of ubiquitin linkage to the lysine residues of the substrate or of ubiquitin itself¹⁰. The different forms of ubiquitin modification on a protein dictate its distinct functions. Poly-ubiquitination provides the main targeting signals for degradation to the proteasome, whereas the mono-ubiquitination and multi-ubiquitination, act as a sorting signal that regulate the intracellular protein trafficking from TGN to endosomes or lysosomes and endocytosis of plasma membrane proteins^11,12. The function of The Nedd4 family of E3 ubiquitin ligases in regulating endocytosis and of the sorting of transmembrane proteins has been demonstrated^13,14. In mammalian cells, ubiquitination of GGA3 by Nedd4 regulates the sorting of LAPTM5 from the Golgi to endosomes/lysosomes¹⁵.

The endosomal sorting complex required for transport (ESCRT) system is critical for the degradation of ubiquitinated proteins and comprises a major pathway for multivesicular body (MVB) formation. The ubiquitinated proteins can be recognized by intracellular proteins that contain one or more ubiquitin-binding domains, such as Hrs and STAM which are two components of the ESCRT subunit ESCRT-0, and provide an additional targeting module that promote their binding to cargo-enriched endosomes¹⁶. Thus, ESCRT-0 is the detection module for initiating the ESCRT pathway at endosomes^17,18, and ubiquitination is a vital modification for sorting ubiquitinated cargoes into ESCRT-mediated MVB vesicles and their subsequent transfer to lysosomes¹⁹.

In addition to sorting signal of ubiquitination, microtubules provide the tracks for protein transporting, along which cargo is carried to its destination. Microtubule-based transport is of critical importance for the localization and motility of endomembranes. Motor proteins consisting of dynein, kinesin and myosin co-ordinate to physically move cargo along the microtubule network. Dynactin is a multisubunit protein complex that is required for dynein activity through the direct binding of dynein with p150^Glued²⁰ and allows the motor to traverse the microtubule lattice over long intracellular distances. It has been suggested that dynactin contributes to microtubule anchoring²¹ since impairment of dynactin structure or its function commonly leads to the redistribution of endomembrane compartments from the cell center to the periphery^22,23. Loss of p25 (dynactin 5) significantly weakened the physical interaction between dynein and early endosomes²⁴, leading subsequent redistribution of early endosome²⁵.

Transmembrane prostate androgen-induced protein (TMEPAI), also known as PMEPA1 (prostate transmembrane protein androgen induced 1) or STAG1 (solid tumor-associated 1 protein), has been reported to be overexpressed in various tumor cells^26,27,28. TMEPAI is a type Ib transmembrane protein containing 287 amino acids containing a transmembrane domain at the N-terminus and two PY motifs (PPxY) which interact with E3 ubiquitin ligase Nedd4²⁹. Previous studies have shown that TMEPAI localizes to the lysosome and downregulates TGF-β signaling by competing with SARA (Smad anchor for receptor activation) for R-Smad binding to sequester R-Smad phosphorylation³⁰ and promoting lysosomal degradation of TGF-β receptor (TβR)³¹. TMEPAI promotes lysosome stability and autophagy³². Moreover, it has been reported that the E3 ubiquitin ligase Nedd4-binding defective mutant of TMEPAI was translocated to the plasma membrane³¹. The molecular mechanism of TMEPAI trafficking to the lysosome and of E3-binding defective mutant TMEPAI (2YA) translocation to the plasma membrane is unknown. Here, we further investigated and demonstrated that clathrin and CI-M6PR mediated TMEPAI transport from the Golgi directly into the endo-lysosomal pathway, and ubiquitination modification of TMEPAI is a signal for its lysosomal trafficking. In addition, the dynactin complex is involved in the transport of TMEPAI to the lysosome.

Results

Clathrin and CI-M6PR modulate TMEPAI transport from the Golgi to the lysosome

It has been reported that TMEPAI was mainly localized to the lysosome, while the Nedd4-binding defective mutant of TMEPAI was translocated to the plasma membrane³¹. We further verified that endogenous TMEPAI was mainly localized to the lysosome, partially overlapped with TfR and not colocalized with the Golgi (Fig. 1A), whilst the TMEPAI (2YA) was localized to the plasma membrane (Fig. 1B). Lysosomal proteins can reach the lysosome through either direct or indirect pathways which are distinguishable in whether the transport process passes through the plasma membrane or not. To determine if the intracellular transport of TMEPAI is via a plasma membrane route, the endocytosis inhibitors dynasore and genistein were used to define the trafficking pathway of TMEPAI to the lysosome. Dynasore acts as an inhibitor of endocytic pathways and depends on dynamin 2 by rapidly blocking coated vesicle formation³³. Genistein is a tyrosine-kinase inhibitor that causes local disruption of the actin network at the site of endocytosis and inhibits the recruitment of dynamin 2³⁴. Our results showed that TMEPAI remained in the lysosome with no apparent alternation after treatment with endocytosis inhibitor (Fig. 1C), and the function of dynasore and genestein in inhibiting endocytosis was verified (Fig. 1D). Furthermore, depletion of dynamin 2 by RNA interference and expression of dynamin 2 GDP mutant (K44A) also did not affect the lysosomal localization of TMEPAI (data not shown). These results indicate that TMEPAI transports to the lysosome without passing through the plasma membrane.

**Figure 1: TMEPAI transports to lysosome without passing through plasma membrane.**

Dynasore and genistein both act on dynamin 2, an essential protein engaged in clathrin-mediated endocytosis³⁵. Clathrin serves to mediate vesicle-coating on TGN exits³⁶. To determine the potential involvement of clathrin in both TMEPAI and its mutant form in sorting from TGN, clathrin-shRNA targeting the clathrin heavy chain was performed in order to deplete clathrin and block clathrin coated vesicles (CCVs) formation. Depletion of clathrin showed an enrichment of TMEPAI and its mutant TMEPAI (2YA) was observed in the Golgi labelling with the Golgi marker Golgin 84) (Fig. 2A,B), together with the redistribution to the Golgi and plasma membrane of transferrin receptor (TfR), a receptor coated by clathrin during its exit from TGN and internalization on plasma membrane, and depletion of clathrin also resulted in the redistribution of Lamp2 to the perinuclear region. Western blot analysis was used to confirm the efficient depletion of clathrin (Fig. 2C). These results indicate that TMEPAI lysosomal transport is clathrin-dependent.

**Figure 2: Clathrin regulates TMEPAI intracellular localization.**

Mannose-6-phosphate receptors (M6PRs), as well as clathrin are involved in lysosomal protein trafficking. There are two types of M6PRs, cation-independent mannose-6-phosphate receptors (CI-M6PR) and cation-dependent mannose-6-phosphate receptors (CD-M6PR), both of which deliver newly synthesized acid hydrolases to the endo-lysosomal pathway and then return them to the TGN. To investigate whether M6PRs regulate TMEPAI transport, M6PR levels were reduced by M6PR-shRNA lentivirus infection. Depletion of CI-M6PR resulted in TMEPAI retention to the Golgi (Fig. 3A), whereas no effect was observed on TMEPAI (2YA) localization on the plasma membrane (Fig. 3B). The localization of control proteins TfR and Lamp2 were not affected by the depletion of CI-M6PR. The CI-M6PR RNAi efficiency was confirmed by Western blot analysis (Fig. 3C). In addition, the localization of both TMEPAI and its mutant remained unchanged on CD-M6PR depletion (data not show). Together, these results suggest that CI-M6PR modulates TMEPAI intracellular transport to the lysosome.

**Figure 3: CI-M6PR involves in TMEPAI intracellular trafficking to the lysosome.**

Ubiquitination regulates TMEPAI lysosomal transport

Since TMEPAI sorting to the lysosome requires interaction with Nedd4³¹, the lysosomal sorting defect of the TMEPAI mutant lacking the Nedd4 binding sites is due to either blocking the TMEPAI-Nedd4 interaction or to ubiquitination modification of TMEPAI. We next tested whether TMEPAI ubiquitination is involved in its sorting to the lysosome. To determine if the ubiquitination of TMEPAI is mono- or poly-ubiquitination, His-tagged ubiquitin protein and methylated ubiquitin protein defective in mediating poly-ubiquitination were used in an in vitro ubiquitination assay. Both the wide-type ubiquitin and ubiquitin mutant resulted in a similar pattern of Nedd4-mediated ubiquitin ligation, which suggested that Nedd4 catalyzes mono-ubiquitination of TMEPAI (Fig. 4A). Further, we analyzed the potential ubiquitination sites on the TMEPAI protein sequence using the online ubiquitination sites prediction tool of UbiPred (http://iclab.life.nctu.edu.tw/ubipred/index.php), and found that potential ubiquitination sites presented at the C-terminal tail of TMEPAI (277-KEKDKQKGHPL-287). We then generated TMEPAI mutants TMEPAI-KR with four Lysine (K) residues mutated to Arginine (R) and produced the TMEPAI cytoplasmic recombinant protein His-HA-TMEPAI-WT, the mutants His-HA-TMEPAI-2YA and His-HA-TMEPAI-KR for additional in vitro ubiquitination experiments. Ubiquitination of TMEPAI-2YA and TMEPAI-KR were inhibited compared to TMEPAI-WT (Fig. 4B). Moreover, in vivo ubiquitination performed by immunoprecipitation of A549 cells stably expressing Flag-tagged TMEPAI-WT, TMEPAI-2YA and TMEPAI-KR showed that ubiquitination of both TMEPAI-2YA and TMEPAI-KR was disrupted (Fig. 4C). To examine whether the ubiquitination site is required for TMEPAI sorting to the lysosome, A549 stably expressing TMEPAI-KR-Flag was double labeled with anti-Flag antibody and WGA-FITC, indicating that TMEPAI-KR-Flag was present on the plasma membrane (Fig. 4D). These results indicated that ubiquitination of TMEPAI at its C-terminal is responsible for transport to the lysosome.

**Figure 4: Ubiquitination modulates TMEPAI intracellular localization.**

Ubiquitin binding proteins (UBPs) play an important role in the recognition and recruitment of ubiquitinated protein, and ubiquitinated proteins require binding to specific UBPs for targeting to relevant endomembrane compartment. To investigate whether UBPs serve as an adaptor to supervise TMEPAI trafficking, a series of UBPs including Hrs, STAM, GGA3, Tsg101 and Eap45 were selected to test the TMEPAI interaction by yeast two-hybrid analysis. The yeast two-hybrid results showed that TMEPAI interacted with Hrs and STAM (Fig. 5A). Interaction of TMEPAI between Hrs and STAM was further identified using an immunoprecipitation assay by co-expression of pEF-TMEPAI-WT-Flag and pcDNA3.1⁺ -HA-Hrs or pcDNA3.1⁺ -HA-STAM constructs respectively in HeLa cells (Fig. 5B). Furthermore, since ubiquitinated protein links with ubiquitin binding proteins through ubiquitin (Henne et al.¹⁶), GST-TMEPAI was first in vitro ubiquitinated to produce ubiquitinated GST-TMEPAI (Ub) for the GST pull-down assay, and the results indicated that ubiquitination is critical for TMEPAI interaction with Hrs and STAM (Fig. 5C). We next investigated the roles of Hrs and STAM in regulating TMEPAI intracellular transport. RNA interference of Hrs and STAM was performed in A549 cells and showed that TMEPAI was significantly distributed to the plasma membrane in either Hrs or STAM depleted cells, although with little colocalization with lysosomal marker Lamp2 and early endosome marker EEA1 (Fig. 5D and E). These results together demonstrate that ubiquitination is a sorting signal for TMEPAI lysosomal trafficking and that the ubiquitin binding proteins Hrs and STAM are involved in its lysosomal transport.

**Figure 5: Ubiquitin binding proteins Hrs and STAM regulate TMEPAI lysosomal trafficking.**

Dynactin involvement in TMEPAI intracellular trafficking

Dynactin acts as an important adaptor in combination with dynein and maintains dynein activity to drive membrane vesicles along microtubules for long-distance movement. The dynactin pointed-end complex consists of dynactin 4/p62, dynactin 5/p25 and dynactin 6/p27 and is proposed to be a cargo-targeting module. We initially found that TMEPAI interacted with dynactin 6 by yeast two-hybrid screening, thus we next set out to investigate whether TMEPAI interacts with the other two subunits (dynactin 4 and dynactin 5). Yeast two-hybrid experiments showed that TMEPAI interacted with both dynactin 5 and dynactin 6, but not with dynactin 4, or with another dynactin complex subunit Arp1, which forms the Arp1 rod for binding to membrane vesicles³⁷, indicating that TMEPAI specifically combined with the point-end complex through dynactin 5 and dynactin 6 (Fig. 6A). Interaction of TMEPAI between dynactin 5 and dynactin 6 was further verified by GST pull-down assay using recombinant proteins (Fig. 6B). Since the integrity of dynactin point-end complex is essential for membrane binding, we addressed the question of whether the interaction between TMEPAI and dynactin 5, dynactin 6 might be reinforced when the point-end complex formed. We performed a GST pull-down assay to test the binding of GST-TMEPAI with different combinations of point-end complex subunits recombinant proteins. Interestingly, the interaction of TMEPAI with dynactin 5 and dynactin 6 was not strengthened with a combination of different subunits. In contrast, binding of TMEPAI to dynactin 5 and dynactin 6 was inhibited in the presence of dynactin 4 (Fig. 6C).

**Figure 6: TMEPAI interacts with dynactin 5 and dynactin 6.**

To further identify the binding domain of TMEPAI with dynactin, we analyzed the homology sequence of TMEPAI protein and generated truncated versions of TMEPAI to test their interaction with dynactin 5 and dynactin 6 using the yeast two-hybrid system. The yeast two-hybrid experiments indicated that the N-terminal region of TMEPAI bound to both dynactin 5 and dynactin 6 (Fig. 7A), and further deletion mutation screening showed the aa132–155 domain was required for this interaction, as mutants lacking this region failed to bind dynactin 5 and dynactin 6 (Fig. 7B), but without affecting its binding to Nedd4 (data not shown). Furthermore, GST pull-down assay tests confirmed that GST-TMEPAI bound dynactin 5 and dynactin 6 but not the deletion mutant GST-TMEPAI (Δ132–155) (Fig. 7C). Moreover, we investigated whether the binding of TMEPAI to dynactin 5 and dynactin 6 contributed to its lysosomal localization. We generated TMEPAI mutants TMEPAI (Δ132–155) and TMEPAI (Δ63–86) with deletion of regions aa 132–155 and aa 63–86 respectively, and expressed these in A549 cells before double labelling with anti-Flag antibody and other membrane compartment markers. We observed that the mutant TMEPAI (Δ132–155) was significantly distributed to the plasma membrane, though with little colocalization with lysosomal marker Lamp2 and early endosome marker EEA1. The TMEPAI-WT and deletion mutant TMEPAI (Δ63–86) were localized to the lysosome normally (Fig. 7D). These results suggest that the aa132–155 domain of TMEPAI is required for its interaction with dynactin and lysosomal trafficking.

**Figure 7: Interaction between TMEPAI and dynactin is required for TMEPAI lysosomal localization.**

Discussion

Each protein that enters the endo-lysosomal pathway passes a number of decision stations that determine the rest of its journey. Alternative pathways for the delivery of newly lysosomal proteins to the endo-lysosomal system demand multiple TGN exits with two lysosomal trafficking pathways options. Apart from the clathrin- and M6PR- mediated pathway, the biosynthetic pathways to the lysosome are poorly understood. Identification of distinct sorting mechanisms for direct targeting of lysosome membrane proteins (LMPs) or lysosomal hydrolases to the lysosome raises challenges in lysosomal trafficking research. Even a cross-link between lysosomal hydrolases and LMPs such as LIMP2 has been shown to interact with β-glucocerebrosidase (βGC) and mediate lysosome transport³⁸. Blocking the interaction of TMEPAI with Nedd4 leads to translocation of TMEPAI to the plasma membrane, which raises the question of whether TMEPAI is delivered initially to plasma membrane before being internalized into the endo-lysosomal pathway. We found that endogenous TMEPAI remained in the lysosome location in cells treated with the endocytic inhibitor dynasore and genistein to inhibit the clathrin-dependent endocytosis. This suggests that TMEPAI is directly delivered to the endo-lysosome system from the Golgi, and it seems that TMEPAI is ubiquitinated before travelling into the endosome. A clathrin-dependent or -independent TGN exit pathway could be utilized by LMPs, Lamp1³⁹ and LAPTM5¹⁵ separate from TGN via clathrin-coated vesicles (CCVs). Our study indicated that TMEPAI and its mutant targeted to their respective destination in a CCV-dependent pathway.

LMPs such as Lamp1 and Lamp2 are not modified with mannose 6 phosphate (M6P) groups and therefore are in the M6PR-independent sorting pathway. Instead, they undergo sorting as directed by their cytosolic tails that mediate both endo-lysosomal targeting and rapid endocytosis after travelling to the cell surface. Similar to other TGN sorting and endocytic signals, most lysosomal targeting signals belong to the YXXØ or [DE]XXXL[LI] types with certain features that make them functional for lysosomal trafficking⁴⁰. In order to define whether TMEPAI trafficking to the lysosome is M6PR-mediated, we found that transport of TMEPAI was blocked in the Golgi under conditions of CI-M6PR depletion but not with CD-M6PR. However, the transport of TMEPAI (2YA) mutant to the plasma membrane was M6PR-independent. Although TMEPAI does not contain the typical residues for lysosome sorting signals described above, TMEPAI contains potential glycosylation sites according to the online N-glycosylation prediction software analysis (http://www.cbs.dtu.dk/services/NetNGlyc/), which suggests that glycosylation may serve as a sorting signal for TMEPAI lysosomal trafficking mediated by M6PR.

Ubiquitin, particularly monoubiquitin, has several proteasome independent functions in regulating membrane protein trafficking, including serving as a sorting signal on plasma membrane proteins for internalization and sorting into the endosomal vesicles for delivery into the lysosome. It also regulates biosynthetic membrane proteins trafficking from the Golgi to the endosomes or lysosomes^11,41. The function of The Nedd4 family of E3 ubiquitin ligases in regulating endocytosis and the sorting of transmembrane proteins has been demonstrated in yeast and mammalian cells^13,14. In mammalian cells, ubiquitination of GGA3 by Nedd4 regulates sorting of LAPTM5 from the Golgi to endosomes/lysosomes¹⁵. We found that interaction of TMEPAI with Nedd4 via its two PY motifs is responsible for its mono-ubiquitination. Biosynthetic and endocytic pathways converge at the early endosomes, which receives proteins coming from the TGN and the plasma membrane. In early endosomes, non-ubiquitinated proteins are recycled to the plasma membrane or directed to other membrane compartments, which may provide another explanation for the translocation to the plasma membrane of TMEPAI ubiquitination-defective mutants. In contrast, ubiquitinated proteins are sorted into intraluminal vesicles (ILVs) and develop into multivesicular bodies (MVBs)^11,42. At the endosome, a series of proteins form ESCRT (endosomal sorting complex required for transport) to recruit ubiquitinated cargo to the endosome and sort into the interior of MVBs. These proteins are referred to as the ubiquitin binding proteins (UBPs) including Eps15, which operate at the plasma membrane to early endosome⁴³. GGA3, mediates transport from the Golgi to the endosome¹⁵; Hrs/STAM, functions on interface between endosomes^44,45; Tsg101, primary recruitment to late endosome¹⁹ and other ESCRT subunit complexes, all of which together are presumed to be involved in MVB formation. We found that TMEPAI directly interacts with both Hrs and STAM both by yeast two-hybrid and biochemical essays, and that either depletion of Hrs/STAM leads to redistribution of TMEPAI to the plasma membrane. A possible trafficking pathway of TMEPAI to the plasma membrane following UBP depletion involves TMEPAI being transported to the early endosome without recruitment by Hrs/STAM to ILVs, then recycling back to the Golgi and reaching the plasma membrane through the constitutive pathway.

Dynactin is responsible for dynein activity and drives cargo along microtubules for long distance movement. Our study showed that TMEPAI bound to both dynactin 5 and dynactin 6 simultaneously, but not dynactin 4 and the cargo-binding unit Arp1, indicating a specific association of TMEPAI with dynactin 5 and dynactin 6. Interestingly, dynactin 4 inhibited the binding of TMEPAI to dynactin 5 and dynactin 6, which suggested that dynactin 4 might function as a switch in modulating the binding and regulating the release of TMEPAI from the complex during its transport along the microtubule. Apart from dynein, dynactin also contributes to the activity of another microtubule-based motor protein, kinesin II⁴⁶. Dynactin concentrates at the microtubule plus end and presents on various endo-membranes such as the early endosome and cell periphery⁴⁷. Although dynactin is reported to conduct minus direction transport of microtubules, a recent study implied that dynactin could facilitate the mobility of adenovirus both towards and away from the nucleus⁴⁸. In addition to binding dynein and maintaining its activity, dynactin functions as a cargo-targeting module by the point end complex, as dynactin 5 was discovered to be involved in endosome movement²⁴ and dynactin 6 was found to assist polo-like kinase 1 target kinetochores during mitosis⁴⁹. To investigate the role of dynactin in regulating TMEPAI intracellular trafficking, we identified the aa132–155 domain of TMEPAI as the dynactin binding region, and the dynactin-binding defective mutant TMEPAI (Δaa132–155) was found localized to plasma membrane. Although it has been reported that dynactin 5 and dynactin 6 are required for binding of dynactin and recruitment of dynein to the vesicles that recycle TfR to the cell surface, but not to late endosomes²⁵, how this interaction with the dynactin complex regulates TMEPAI trafficking from the Golgi to lysosomes is still unclear and needs further investigation.

It has been reported that TMEPAI inhibits TGF-β signaling by blocking both R-Smad phosphorylation and by promoting degradation of TβR. This is not observed in the ubiquitination loss mutant TMEPAI (2YA)^30,31, which suggests that ubiquitination contributes to TMEPAI lysosomal localization and the regulation of TGF-β signaling. A recent study has shown that TMEPAI promotes lysosome stability and autophagy and thus enhances cancer cells drug resistance to chemotherapeutics³². Protein expression, protein trafficking and subcellular localization, signaling transduction all co-ordinate to regulate normal cellular function. Our studies demonstrate that modification by ubiquitination and interaction with dynactin regulates TMEPAI intracellular trafficking to the lysosome. These findings extend the known roles of TMEPAI in tumorigenesis and might provide a novel strategy to modulate the transport and intracellular function of TMEPAI as a potential target for cancer treatment.

Methods

Materials and antibodies

All materials were from Sigma unless otherwise stated. Yeast two hybrid system kit and dropout solution screening medium were purchased from Clontech. Rabbit polyclonal antibody to TMEPAI was generated using the His-tagged cytoplasmic domain of TMEPAI as immunogen, antibody was affinity-purified against the GST-TMEPAI covalently coupled to Glutathione Sepharose (GE Healthcare). The specificity of the TMEPAI antibody was assessed by Western blot using the purified recombinant TMEPAI proteins and cell lysates³¹. Mouse anti-HA, Mouse anti-Flag and WGA-FITC were all from Sigma. Mouse anti-β-actin was from Tianjin Sungene Biotech. Sheep anti-Golgin84 and mouse anti-Lamp2 was from Abcam. Goat anti-EEA1 (N-19), mouse anti-TfR/CD71 (3B82A1), mouse anti-Rab7 (B-3), mouse anti-Clathrin HC (TD.1), rabbit anti-CI-M6PR (H-300), mouse anti-Hrs (D-3) and mouse anti-STAM (B-2) were from Santa Cruz Biotechnology. Fluorophore secondary antibodies were purchased from Invitrogen.

Cell culture, transfection and stable cell lines

A549 cells were cultured in F-12K medium, supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin. HeLa cells were maintained in DMEM medium containing 10% FBS, 100 U/ml penicillin, and 100 mg/ml streptomycin. Transfection was performed with Lipofectamine 2000 (Invitrogen) transfection reagent according to the manufacturer’s instructions. A549 cell lines stably expressing TMEPAI-2YA-Flag or TMEPAI-KR-Flag were obtained by transfection with pEF-IRES-puro-TMEPAI-2YA-Flag or pEF-IRES-puro-TMEPAI-KR-Flag recombinant plasmid and selected in 1 μg/ml puromycin for 2 weeks.

Immunofluorescence microscopy

The cells were grown on coverslips and fixed in 4% PFA in PBS at room temperature (RT) for 20 min. Cells were quenched with 10 mM glycine, pH 8.5 (in PBS), and permeabilized with 0.1% TritonX-100 (in PBS) for 5 min at RT. Coverslips were incubated for 2 h at RT with primary antibodies diluted into PBS containing 3% BSA, washed three times with DPBS, incubated for a further 30 min at RT with fluorophore-conjugated secondary antibodies then DNA dye Hoechst 33342 (200 ng/ml) was mixed with the secondary antibodies. Coverslips were mounted in Mowiol and allowed to dry. Immunofluorescent images were viewed and analyzed using an Olympus FV1000 Confocal Microscope with the FV10-ASW 3.0 Viewer software.

RNA interference

Lentiviral vectors expressing clathrin-shRNAs (clathrin-1: 5′-CCGGTAATCCAATTCGAAGACCAATCTCGAGATTGGTCTTCGAATTGGATTATTTTTG-3′); clathrin-2: 5′-CCGGCGGTTGCTCTTGTTACGGATACTCGAGTATCCGTAACAAGAGCAACCGTTTTTG-3′), CI-M6PR-shRNAs (CI-M6PR-1: 5′-CCGGCGGAGGAAATACTACCTCAATCTCGAGATTGAGGTAGTATTTCCTCCGTTTTTG-3′; CI-M6PR-2: 5′-CCGGCCGGACATCCAGCATCATATTCTCGAGAATATGATGCTGGATGTCCGGTTTTTG-3′), Hrs-shRNAs (Hrs-1: 5′-CCGGCCGCATGAAGAGTAACCACATCTCGAGATGTGGTTACTCTTCATGCGGTTTTTG-3′; Hrs-2: 5′-CCGGCTCACGTCCGGAGTAACACTACTCGAGTAGTGTTACTCCGGACGTGAGTTTTTTG-3′), STAM-shRNAs (STAM-1: 5′-CCGGTTAATACGTTGCTTACTTCACTAGCGCTAGTGAAGTAAGCAACGTATTAATTTTTTG-3′; STAM-2: 5′-CCGGATACATGGAATACATCGGATCTTCGCGAAGATCCGATGTATTCCATGTATTTTTTTG-3′) and the non-target shRNA control vector (SHC002) was obtained from Sigma and the knockdown level was tested by Sigma. The lentiviruses were produced according to the manufacturers’ manual. Cells were infected with lentiviruses for 4 days prior to the start of the experiments.

In vitro ubiquitination assay

Purified His-HA-TMEPAI or His-HA-TMEPAI-2YA/KR proteins were incubated with recombinant E1 (Boston Biochem), recombinant UbcH5C (Boston Biochem), GST-Nedd4 and methylated ubiquitin or His-tagged ubiquitin (Boston Biochem) in reaction buffer (50 mM Tris-HCl, pH 7.4, 5 mM MgCl₂, 0.3 mM DTT, 2 mM ATP) for 60 min at 30 °C. The reaction products were analyzed by SDS-PAGE and Western blot.

In vivo ubiquitination assay

A549 cells stably expressing Flag-tagged TMEPAI-WT, TMEPAI-2YA or TMEPAI-KR were washed twice with PBS and lysed in the ice-cold lysis buffer (50 mM Tris-Cl, pH 8.0, 150 mM NaCl, 1% TritonX-100, 0.5% sodium deoxycholate, 0.1% SDS, 1 mM NaVO₄, 10 mM NaF, and protease inhibitors). Lysates were left on ice for 40 min and centrifuged for 10 min at 12000 g at 4 °C. The supernatants were incubated with anti-Flag antibody for 2 h at 4 °C with rotation and further incubated for 2 h at 4 °C after addition of protein A/G Sepharose (Thermo Scientific). Immunoprecipitates were washed 3 times with lysis buffer and once with PBS, and then subjected to SDS-PAGE followed by Western blot analysis.

Western blot

The cells were collected in RIPA buffer (50 mM Tris-Cl, pH 7.4, 150 mM NaCl, 1% TritonX-100, 0.5% sodium deoxycholate, 0.1% SDS, 1 mM NaVO₄, 10 mM NaF, and protease inhibitors) for 40 min. Homogenates were clarified by centrifugation at 12000 g for 10 min at 4 °C and the supernatants were mixed with SDS-loading buffer and heated for 5 min at 95 °C. Samples were adjusted to equal protein concentration and volume, and subjected to SDS-PAGE. Separated proteins were transferred to PVDF membranes followed by blocking with 5% non- fat milk in PBS. The membranes were incubated with primary antibody, and subsequent secondary antibody. Proteins were visualized by Odyssey infrared laser imaging system (LI-COR Biosciences, Lincoln, NE, USA).

Molecular biology and yeast two-hybrid analysis

Standard molecular biology techniques were used for all constructs. For the yeast two-hybrid assay, the full-length and truncated versions of TMEPAI cDNA lacking the trans-membrane domain were inserted into the NdeI and EcoRI sites of the pGBTKT vector. The full-length of human Nedd4, Hrs, STAM, GGA3, Tsg101, Esp45, dynactin 4 (DCTN4), dynactin 5 (DCTN5), dynactin 6 (DCTN 6) and Arp1 cDNA were inserted into the pGADT7 vector (CLONTECH Laboratories, Inc.). The pGBKT7/TMEPAI and pGADT7 related plasmids were co-transformed into the yeast reporter strain Y187 on synthetic medium lacking leucine and tryptophan (double dropout, DDO) (low selection) and then patched onto synthetic medium lacking leucine, tryptophan, histidine, and adenine (quadruple dropout, QDO) (medium selection), as well as onto synthetic medium lacking leucine, tryptophan, histidine, and adenine with 40 μg/ml X-α-gal, 125 ng/ml Aureobasidin A (Aba A) (quadruple dropout with X-α-gal and Aba A, QDO/X/A) (high selection) according to the CLONTECH Laboratories, Inc. yeast protocol handbook.

Protein expression and purification

Plasmids encoding His-HA-tagged TMEPAI-WT, TMEPAI-2YA, TMEPAI-KR, dynactin 4, dynactin 5, and dynactin 6 were transformed into BL21-CodonPlus (DE3)-RIL cells. Cells were induced with 0.5 mM IPTG overnight at 16 °C. Cells were lysed in ice cold lysis buffer (50 mM phosphate sodium buffer, pH 8.0, 150 mM NaCl, 5 mM β-mercaptoethanol, protease inhibitors) and the recombinant proteins were purified with Ni Sepharose beads (GE Healthcare).

GST pull-down assay

Glutathione Sepharose beads coupled with 5 μg GST-fusion protein were incubated with the clarified cell lysates in RIPA buffer (50 mM Tris pH 7.4, 150 mM NaCl, 1% Triton X-100, 1% sodium deoxycholate, 0.1% SDS) with complete protease inhibitors at 4 °C for 3 h with rotation. The beads were washed four times with RIPA buffer and resuspended in SDS-PAGE sample buffer, bound and input proteins were subjected to SDS-PAGE and Western blot using indicated antibodies.

Immunoprecipitation

A549 cell lines stably expressing Flag-tagged TMEPAI-WT, TMEPAI-2YA and TMEPAI-KR were extracted in IP buffer (20 mM Tris-Cl pH 7.4, 0.1 M KCl, 0.1 M NaF, 1 mM DTT, 1% TritonX-100) with complete protease inhibitors and clarified by centrifugation at 12000 g for 10 min, then incubated with anti-Flag M2 Magnetic Beads (Sigma M8823) for 4 h at 4 °C with gentle rotation. The beads were washed with IP buffer four times and eluted by boiling in SDS-PAGE sample buffer and analyzed by Western blot with appropriate antibodies.

Statistical analysis

Statistical analysis was performed using the Student t-test with GraphPad Prism software, and P < 0.05 represented statistically significant difference.

Additional Information

How to cite this article: Luo, S. et al. Ubiquitination and dynactin regulate TMEPAI lysosomal trafficking. Sci. Rep. 7, 42668; doi: 10.1038/srep42668 (2017).

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References

Derby, M. C. & Gleeson, P. A. New insights into membrane trafficking and protein sorting. Int. Rev. Cytol. 261, 47–116 (2007).
CAS PubMed Google Scholar
Klumperman, J. et al. Differences in the endosomal distributions of the two mannose 6-phosphate receptors. J. Cell Biol. 121, 997–1010 (1993).
CAS PubMed Google Scholar
Puertollano, R. et al. Sorting of mannose 6-phosphate receptors mediated by the GGAs. Science 292, 1712–1716 (2001).
CAS PubMed ADS Google Scholar
Janvier, K. & Bonifacino, J. S. Role of the Endocytic Machinery in the Sorting of Lysosome-associated Membrane Proteins. Mol. Biol. Cell 16, 4231–4242 (2005).
CAS PubMed PubMed Central Google Scholar
Saftig, P. & Klumperman, J. Lysosome biogenesis and lysosomal membrane proteins: trafficking meets function. Nat. Rev. Mol. Cell Biol. 10, 623–635 (2009).
CAS PubMed Google Scholar
Francisco, T. et al. Ubiquitin in the peroxi somal protein import pathway. Biochimie 98, 29–35 (2014).
CAS PubMed Google Scholar
Hershko, A. & Ciechanover, A. The ubiquitin system for protein degradation. Annu. Rev. Biochem. 61, 761–807 (1992).
CAS PubMed Google Scholar
Haglund, K. & Dikic, I. The role of ubiquitylation in receptor endocytosis and endosomal sorting. J. Cell Sci. 125, 265–275 (2012).
CAS PubMed Google Scholar
Hammond-Martel, I., Yu, H. & Affar, E. B. Roles of ubiquitin signaling in transcription regulation. Cell. Signal. 24, 410–421 (2012).
CAS PubMed Google Scholar
Staub, O. & Rotin, D. Role of ubiquitylation in cellular membrane transport. Physiol. Rev. 86, 669–707 (2006).
CAS PubMed Google Scholar
Hicke, L. & Dunn, R. Regulation of membrane protein transport by ubiquitin and ubiquitin-binding proteins. Annu. Rev. Cell Dev. 19, 141–172 (2003).
CAS Google Scholar
Xie, F. et al. Regulation of TGF-β superfamily signaling by SMAD mono-ubiquitination. Cells 3, 981–993 (2014).
PubMed PubMed Central Google Scholar
Belgareh-Touzé, N. et al. Versatile role of the yeast ubiquitin ligase Rsp5p in intracellular trafficking. Biochem. Soc. Trans. 36, 791–796 (2008).
Google Scholar
Chen, C. & Matesic, L. E. The Nedd4-like family of E3 ubiquitin ligases and cancer. Cancer Metastasis Rev. 26, 587–604 (2007).
CAS PubMed Google Scholar
Pak, Y. et al. Transport of LAPTM5 to lysosomes requires association with the ubiquitin ligase Nedd4, but not LAPTM5 ubiquitination. J. Cell Biol. 175, 631–645 (2006).
CAS PubMed PubMed Central Google Scholar
Henne, W. M., Buchkovich, N. J. & Emr, S. D. The ESCRT pathway. Dev. Cell 21, 77–91 (2011).
CAS PubMed Google Scholar
Mao, Y. et al. Crystal structure of the VHS and FYVE tandem domains of Hrs, a protein involved in membrane trafficking and signal transduction. Cell 100, 447–456 (2000).
CAS PubMed Google Scholar
Raiborg, C. et al. FYVE and coiled-coil domains determine the specific localisation of Hrs to early endosomes. J. Cell Sci. 114, 2255–2263 (2001).
CAS PubMed Google Scholar
Mosesson, Y. & Yarden, Y. Monoubiquitylation: a recurrent theme in membrane protein transport. Isr. Med. Assoc. J. 8, 233–237 (2006).
CAS PubMed Google Scholar
Karki, S. & Holzbaur, E. L. Affinity chromatography demonstrates a direct binding between cytoplasmic dynein and the dynactin complex. J. Biol. Chem. 270, 28806–28811 (1995).
CAS PubMed Google Scholar
Quintyne, N. J. et al. Dynactin is required for microtubule anchoring at centrosomes. J. Cell Biol. 147, 321–334 (1999).
CAS PubMed PubMed Central Google Scholar
King, S. J. et al. Analysis of the dynein-dynactin interaction in vitro and in vivo . Mol. Biol. Cell 14, 5089–5097 (2003).
CAS PubMed PubMed Central Google Scholar
Wassmer, T. et al. The retromer coat complex coordinates endosomal sorting and dynein-mediated transport, with carrier recognition by the trans-Golgi network. Dev. Cell 17, 110–122 (2009).
CAS PubMed PubMed Central Google Scholar
Zhang, J. et al. The p25 subunit of the dynactin complex is required for dynein-early endosome interaction. J. Cell Biol. 193, 1245–1255 (2011).
CAS PubMed PubMed Central Google Scholar
Yeh, T. Y. et al. Dynactin’s pointed-end complex is a cargo-targeting module. Mol. Biol. Cell 23, 3827–3837 (2012).
CAS PubMed PubMed Central Google Scholar
Fournier, P. G. et al. The TGF-beta Signaling Regulator PMEPA1 Suppresses Prostate Cancer Metastases to Bone. Cancer Cell 27, 809–821 (2015).
CAS PubMed PubMed Central Google Scholar
Singha, P. K. et al. TGF-beta induced TMEPAI/PMEPA1 inhibits canonical Smad signaling through R-Smad sequestration and promotes non-canonical PI3K/Akt signaling by reducing PTEN in triple negative breast cancer. Genes Cancer 5, 320–336 (2014).
PubMed PubMed Central Google Scholar
Vo Nguyen, T. T. et al. TMEPAI/PMEPA1 enhances tumorigenic activities in lung cancer cells. Cancer Sci. 105, 334–341 (2014).
PubMed PubMed Central Google Scholar
Xu, L. L. et al. PMEPA1, an androgen-regulated NEDD4-binding protein, exhibits cell growth inhibitory function and decreased expression during prostate cancer progression. Cancer Res. 63, 4299–4304 (2003).
CAS PubMed Google Scholar
Watanabe, Y. et al. TMEPAI, a transmembrane TGF-beta-inducible protein, sequesters Smad proteins from active participation in TGF-beta signaling. Mol. Cell 37, 123–134 (2010).
CAS PubMed Google Scholar
Bai, X. et al. TMEPAI inhibits TGF-beta signaling by promoting lysosome degradation of TGF-beta receptor and contributes to lung cancer development. Cell. Signal. 26, 2030–2039 (2014).
CAS PubMed Google Scholar
Luo, S. et al. TMEPAI increases lysosome stability and promotes autophagy. Int. J. Biochem. Cell Biol 76, 98–106 (2016).
CAS PubMed Google Scholar
Macia, E. et al. Dynasore, a cell-permeable inhibitor of dynamin. Dev. Cell 10, 839–850 (2006).
CAS PubMed Google Scholar
Vercauteren, D. et al. The use of inhibitors to study endocytic pathways of gene carriers: optimization and pitfalls. Mol. Ther. 18, 561–569 (2010).
CAS PubMed Google Scholar
Sundborger, A. C. & Hinshaw, J. E. Regulating dynamin dynamics during endocytosis. F1000prime reports 6, 85 (2014).
PubMed PubMed Central Google Scholar
Robinson, D. G. & Pimpl, P. Clathrin and post-Golgi trafficking: a very complicated issue. Trends in plant science 19, 134–139 (2014).
CAS PubMed Google Scholar
Muresan, V. et al. Dynactin-dependent, dynein-driven vesicle transport in the absence of membrane proteins: a role for spectrin and acidic phospholipids. Mol. Cell 7, 173–183 (2001).
CAS PubMed Google Scholar
Reczek, D. et al. LIMP-2 is a receptor for lysosomal mannose-6-phosphate-independent targeting of beta-glucocerebrosidase. Cell 131, 770–783 (2007).
CAS PubMed Google Scholar
Honing, S., Griffith, J., Geuze, H. J. & Hunziker, W. The tyrosine-based lysosomal targeting signal in lamp-1 mediates sorting into Golgi-derived clathrin-coated vesicles. EMBO J. 15, 5230–5239 (1996).
CAS PubMed PubMed Central Google Scholar
Bonifacino, J. S. & Traub, L. M. Signals for sorting of transmembrane proteins to endosomes and lysosomes. Annu. Rev. Biochem 72, 395–447 (2003).
CAS PubMed Google Scholar
Hicke, L. Protein regulation by monoubiquitin. Nat. Rev. Mol. Cell Biol. 2, 195–201 (2001).
CAS PubMed Google Scholar
Piper, R. C. & Luzio, J. P. Ubiquitin-dependent sorting of integral membrane proteins for degradation in lysosomes. Curr. Opi. n Cell Biol. 19, 459–465 (2007).
CAS Google Scholar
Polo, S., Confalonieri, S., Salcini, A. E. & Di Fiore, P. P. EH and UIM: endocytosis and more. Sci. STKE 2003, re17 (2003).
PubMed Google Scholar
Katzmann, D. J., Odorizzi, G. & Emr, S. D. Receptor downregulation and multivesicular-body sorting. Nat. Rev. Mol. Cell Biol. 3, 893–905 (2002).
CAS PubMed Google Scholar
Raiborg, C. et al. Hrs sorts ubiquitinated proteins into clathrin-coated microdomains of early endosomes. Nat. Cell Biol. 4, 394–398 (2002).
CAS PubMed Google Scholar
Deacon, S. W. et al. Dynactin is required for bidirectional organelle transport. J. Cell Biol. 160, 297–301 (2003).
CAS PubMed PubMed Central Google Scholar
Habermann, A., Schroer, T. A., Griffiths, G. & Burkhardt, J. K. Immunolocalization of cytoplasmic dynein and dynactin subunits in cultured macrophages: enrichment on early endocytic organelles. J. Cell Sci. 114, 229–240 (2001).
CAS PubMed Google Scholar
Engelke, M. F., Burckhardt, C. J., Morf, M. K. & Greber, U. F. The dynactin complex enhances the speed of microtubule-dependent motions of adenovirus both towards and away from the nucleus. Viruses 3, 233–253 (2011).
CAS PubMed PubMed Central Google Scholar
Yeh, T. Y. et al. Dynactin helps target Polo-like kinase 1 to kinetochores via its left-handed beta-helical p27 subunit. EMBO J. 32, 1023–1035 (2013).
CAS PubMed PubMed Central Google Scholar

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Acknowledgements

We are grateful to Dr. Edward McKenzie (The University of Manchester, UK) for the critical reading of the manuscript. This research is supported by the National Natural Science Foundation of China grant (31471335).

Author information

Shenheng Luo and Lei Jing: These authors contributed equally to this work.

Authors and Affiliations

School of Biotechnology, Tianjin University of Science and Technology, Key Lab of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin, 300457, China
Shenheng Luo, Lei Jing, Tian Zhao, Yuyin Li, Zhenxing Liu & Aipo Diao

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Shenheng Luo
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Lei Jing
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Tian Zhao
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Yuyin Li
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Zhenxing Liu
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Contributions

S.L., L.J., A.D. designed the study. S.L.,.LJ., T.Z., Y.L., Z.L. carried out research experiments. All authors analyzed data. S.L., L.J., A.D. wrote the paper. All the authors have reviewed the final version of the manuscript.

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Correspondence to Aipo Diao.

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Luo, S., Jing, L., Zhao, T. et al. Ubiquitination and dynactin regulate TMEPAI lysosomal trafficking. Sci Rep 7, 42668 (2017). https://doi.org/10.1038/srep42668

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Received: 28 September 2016
Accepted: 13 January 2017
Published: 20 February 2017
DOI: https://doi.org/10.1038/srep42668

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