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Mol Biol Cell. May 1999; 10(5): 1367–1379.
PMCID: PMC25280
Apg7p/Cvt2p: A Novel Protein-activating Enzyme Essential for Autophagy
Isei Tanida,* Noboru Mizushima, Miho Kiyooka, Mariko Ohsumi, Takashi Ueno,* Yoshinori Ohsumi, and Eiki Kominami*§
*Department of Biochemistry, Juntendo University School of Medicine, Tokyo 113-8421, Japan; Department of Cell Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan; and Department of Bioscience, Teikyo University of Science and Technology, Yamanashi 409-0193, Japan
Randy W. Schekman, Monitoring Editor
§Corresponding author. E-mail address: kominami/at/med.juntendo.ac.jp.
Received November 3, 1998; Accepted February 16, 1999.
In the yeast Saccharomyces cerevisiae, the Apg12p–Apg5p conjugating system is essential for autophagy. Apg7p is required for the conjugation reaction, because Apg12p is unable to form a conjugate with Apg5p in the apg7/cvt2 mutant. Apg7p shows a significant similarity to a ubiquitin-activating enzyme, Uba1p. In this article, we investigated the function of Apg7p as an Apg12p-activating enzyme. Hemagglutinin-tagged Apg12p was coimmunoprecipitated with c-myc–tagged Apg7p. A two-hybrid experiment confirmed the interaction. The coimmunoprecipitation was sensitive to a thiol-reducing reagent. Furthermore, a thioester conjugate of Apg7p was detected in a lysate of cells overexpressing both Apg7p and Apg12p. These results indicated that Apg12p interacts with Apg7p via a thioester bond. Mutational analyses of Apg7p suggested that Cys507 of Apg7p is an active site cysteine and that both the ATP-binding domain and the cysteine residue are essential for the conjugation of Apg7p with Apg12p to form the Apg12p–Apg5p conjugate. Cells expressing mutant Apg7ps, Apg7pG333A, or Apg7pC507A showed defects in autophagy and cytoplasm-to-vacuole targeting of aminopeptidase I. These results indicated that Apg7p functions as a novel protein-activating enzyme necessary for Apg12p–Apg5p conjugation.
Autophagy is the process of bulk degradation of cytoplasmic components by the lysosomal/vacuolar system (Seglen and Bohley, 1992 blue right-pointing triangle; Dunn, 1994 blue right-pointing triangle). The phenomenon is dramatically enhanced under nutrient starvation conditions. In the initial step of the macroautophagy, a cup-shaped membrane sac surrounds cytosolic components to form an autophagosome (Baba et al., 1994 blue right-pointing triangle). The outer membrane of the autophagosome fuses with a lysosome/vacuole (Baba et al., 1995 blue right-pointing triangle). A transient single-membrane structure, the autophagic body, is released into the lumen and subsequently degraded in the lysosome/vacuole. Although biochemical and cell–biological approaches have revealed several aspects of autophagy in mammalian cells, the molecular mechanism of autophagy remains unclear.
In the yeast Saccharomyces cerevisiae, macroautophagy was first described by Takeshige et al. (1992) blue right-pointing triangle, and the process is similar to that in higher eukaryotes (Baba et al., 1994 blue right-pointing triangle, 1995 blue right-pointing triangle). Taking advantage of yeast genetics, autophagy-defective mutants (14 apg mutants and 9 aut mutants) have been isolated in two different laboratories (Tsukada and Ohsumi, 1993 blue right-pointing triangle; Thumm et al., 1994 blue right-pointing triangle; Harding et al., 1996 blue right-pointing triangle). Surprisingly, most of the apg and aut mutants overlap genetically and phenotypically with some cvt mutants, which have defects in the cytoplasm-to-vacuole targeting of aminopeptidase I (API)1. These results suggest that the APG and AUT gene products function even in a vegetative growth (APG1/CVT10/AUT3, APG7/CVT2, APG8/CVT5/AUT7, APG9/CVT7/AUT9, APG14/CVT12, APG15/CVT11, and CVT17/AUT5) (Harding et al., 1996 blue right-pointing triangle; Scott et al., 1996 blue right-pointing triangle). Several APG and AUT genes have been identified, and most encode novel proteins (APG1/CVT10/AUT3, APG5, APG6, APG7/CVT2, APG12, APG13, APG14, AUT1, AUT2, and AUT7) (Kametaka et al., 1996 blue right-pointing triangle; Funakoshi et al., 1997 blue right-pointing triangle; Matsuura et al., 1997 blue right-pointing triangle; Schlumpberger et al., 1997 blue right-pointing triangle; Straub et al., 1997 blue right-pointing triangle; Kametaka et al., 1998 blue right-pointing triangle; Lang et al., 1998 blue right-pointing triangle; Mizushima et al., 1998a blue right-pointing triangle). Biochemical characterization of the gene products has revealed some molecular aspects of autophagy: Apg1p/Aut3p is a novel protein kinase (Matsuura et al., 1997 blue right-pointing triangle; Straub et al., 1997 blue right-pointing triangle). Apg6p/Vps30p and Apg14p form a protein complex (Kametaka et al., 1998 blue right-pointing triangle). Aut2p interacts with Aut7p/Apg8p, a homologue of rat microtubule-associated protein light chain 3 (Lang et al., 1998 blue right-pointing triangle).
Recently, we found that the Apg12p–Apg5p conjugation system is essential for autophagy (Mizushima et al., 1998a blue right-pointing triangle). Apg12p has no significant homology to ubiquitin or ubiquitin-related modifiers; however, Apg12p is conjugated to Apg5p through an isopeptide bond between the C-terminal Gly residue of Apg12p and the Lys149 residue of Apg5p. Ubiquitination is a posttranslational modification to present the degradation signal for proteolytic attack by 26S proteasomes (reviewed by Finley and Chau, 1991 blue right-pointing triangle; Hershko and Ciechanover, 1992 blue right-pointing triangle; Hershko, 1996 blue right-pointing triangle; Hochstrasser, 1996a blue right-pointing triangle,b blue right-pointing triangle; Haas and Siepmann, 1997 blue right-pointing triangle; Varshavsky, 1997 blue right-pointing triangle). Ubiquitin is activated by a ubiquitin-activating enzyme (E1) in an ATP-dependent manner in which a thioester bond is formed between the C terminus of ubiquitin and a Cys residue within the E1 enzyme (Ciechanover et al., 1982 blue right-pointing triangle; Haas et al., 1982 blue right-pointing triangle). The ubiquitin is transferred from the E1 enzyme to a Cys residue within a ubiquitin-conjugating enzyme (E2). Finally, ubiquitin is covalently attached to a target protein by an isopeptide linkage directly from E2 or by a ubiquitin-protein ligase (E3) (Hershko et al., 1983 blue right-pointing triangle; Bartel et al., 1990 blue right-pointing triangle; Scheffner et al., 1993 blue right-pointing triangle, 1995 blue right-pointing triangle; Peters et al., 1996 blue right-pointing triangle; Zachariae et al., 1996 blue right-pointing triangle).
Recent discoveries have revealed that the ubiquitin-related modifiers other than ubiquitin play essential roles in eukaryotes (reviewed by Johnson and Hochstrasser, 1997 blue right-pointing triangle; Saitoh et al., 1997 blue right-pointing triangle; Dolan, 1998 blue right-pointing triangle; Hochstrasser, 1998 blue right-pointing triangle). A mammalian ubiquitin-related protein, SUMO-1 [small ubiquitin-related modifier; also called GMP1, PIC1, UBL1, or sentrin (Boddy et al., 1996 blue right-pointing triangle; Matunis et al., 1996 blue right-pointing triangle; Okura et al., 1996 blue right-pointing triangle; Shen et al., 1996 blue right-pointing triangle)] is covalently attached to the RanGAP1 and PML proteins (Matunis et al., 1996 blue right-pointing triangle; Mahajan et al., 1997 blue right-pointing triangle; Muller et al., 1998 blue right-pointing triangle). This posttranslational modification affects the subcellular localization of these proteins (Mahajan et al., 1998 blue right-pointing triangle; Matunis and Blobel, 1998 blue right-pointing triangle; Muller et al., 1998 blue right-pointing triangle). A yeast SUMO-1 homologue, Smt3p, is activated by an E1-like heterodimer Aos1p/Uba2p (Dohmen et al., 1995 blue right-pointing triangle; Johnson et al., 1997 blue right-pointing triangle). The E2 enzyme for Smt3p and SUMO-1 are Ubc9p and its mammalian homologue (Gong et al., 1997 blue right-pointing triangle; Johnson and Blobel, 1997 blue right-pointing triangle; Lee et al., 1998 blue right-pointing triangle; Schwarz et al., 1998 blue right-pointing triangle). Another family of ubiquitin-related proteins is RUB1 and NEDD8 (Kumar et al., 1993 blue right-pointing triangle; Callis et al., 1995 blue right-pointing triangle; Hochstrasser, 1996 blue right-pointing triangle; Kamitani et al., 1997 blue right-pointing triangle; Lammer et al., 1998 blue right-pointing triangle; Liakopoulos et al., 1998 blue right-pointing triangle). A major substrate of RUB1/NEDD8 is Cdc53p/Cullin in yeast and mammalian cells, which play an essential role in regulating the cell cycle (Lammer et al., 1998 blue right-pointing triangle; Liakopoulos et al., 1998 blue right-pointing triangle; Osaka et al., 1998 blue right-pointing triangle). In Arabidopsis thaliana, the auxin response depends on the RUB1 modification of nuclear proteins (del Pozo et al., 1998 blue right-pointing triangle). RUB1 and NEDD8 are activated by E1-like heterodimers: Ula1p (Enr2p)/Uba3p in yeast, an APP-BP1 (a 59-kDa β-amyloid-protein-precursors-binding protein)/human UBA3 homologue in humans, and AXR1/ECR1 in A. thaliana (Leyser et al., 1993 blue right-pointing triangle; Chow et al., 1996 blue right-pointing triangle; del Pozo et al., 1998 blue right-pointing triangle; Liakopoulos et al., 1998 blue right-pointing triangle; Osaka et al., 1998 blue right-pointing triangle). The E2 enzyme for RUB1 and NEDD8 are Ubc12p and its mammalian homologue (del Pozo et al., 1998 blue right-pointing triangle; Liakopoulos et al., 1998 blue right-pointing triangle; Osaka et al., 1998 blue right-pointing triangle).
These findings strongly suggest that there must be E1- and E2-like enzymes for the Apg12p–Apg5p conjugation system in yeast. Candidates in the Apg12p conjugation system are Apg7p/Cvt2p and Apg10p. In apg7 and apg10 mutants, no Apg12p–Apg5p conjugate is observed, indicating that Apg7p and Apg10p play indispensable roles in the Apg12p conjugation system (Mizushima et al., 1998a blue right-pointing triangle). A region of Apg7p (residues 322 to 407 out of 633 amino acids) shows significant homology to the corresponding region of a ubiquitin-activating enzyme, Uba1p, although the other regions show no homology (McGrath et al., 1991 blue right-pointing triangle; Mizushima et al., 1998a blue right-pointing triangle). We took particular interest in Apg7p/Cvt2p and investigated functions of Apg7p through both biochemical and molecular biological techniques. In this study, we provide several lines of evidence showing that Apg7p is an Apg12p-activating enzyme.
Strains, Media, Materials, and Genetic Techniques
Escherichia coli strain DH5α as the host for plasmids and protein expression was grown in Luria Broth medium in the presence of antibiotics as required (Ausubel et al., 1995 blue right-pointing triangle). The S. cerevisiae strains and plasmids used in this study are listed in Table Table1.1. All yeast strains were cultured in rich medium (YPD, pH 5.0: 1% yeast extract, 2% polypeptone, 2% glucose, 20 mg/l adenine, 20 mg/l tryptophan, 20 mg/l uracil, and 50 mM succinate/NaOH, pH 5.0), MVD medium (0.67% yeast nitrogen base without amino acids, 0.5% casamino acids, and 2% glucose), or SD medium (0.67% yeast nitrogen base without amino acids, 2% glucose, and appropriate amino acids as described by Kaiser et al. [1994]). Nitrogen-starvation medium contained 0.17% yeast nitrogen base without amino acids and ammonium sulfate and 2% glucose. Solid medium contained 2% Bacto agar. Standard genetic and molecular biological techniques were performed as described by Kaiser et al. (1994) blue right-pointing triangle and Ausubel et al. (1995) blue right-pointing triangle. The PCR was performed with a program temperature control system PC-701 (ASTEC, Fukuoka, Japan). The DNA sequence was determined by an ABI 373A DNA sequencer (PE Applied Biosystems, Foster City, CA). Restriction enzymes were purchased from TOYOBO (Osaka, Japan) and New England Biolabs (Beverly, MA). Oligonucleotides were synthesized by Sawady Technology (Tokyo, Japan) or ESPEC oligo-service (Ibaraki, Japan). pYO324 was a kind gift from Y. Ohya, pRS series vectors were kind gifts from P. Hieter, and pGAD-C1 vector, pGBD-C1 vector, and PJ69-4A strain were kind gifts from P. James (Sikorski and Hieter, 1989 blue right-pointing triangle; James et al., 1996 blue right-pointing triangle; Homma et al. 1998 blue right-pointing triangle). pGEX-3X and cyanogen bromide-activated Sepharose beads were purchased from Amersham Pharmacia Biotech (Uppsala, Sweden); pGEM-T was from Promega (Madison, WI).
Table 1
Table 1
Yeast strains and plasmids
Gene Disruption of the APG7 Gene
Gene disruption with the PCR product was performed as described by Lorenz et al. (1995) blue right-pointing triangle. Briefly, PCR was performed with APG7-pRSF primer (5′-GTCGTCAGAAAGGGTCTTAAGTTATGCACCAGCTTTTAAATCATTTCTGGTATCACGAGGCCCTTTCGTC-3′), APG7pRSR primer (5′-GCAATCTCATCAGATTCATCATCTTCCCATTCAAAAACATCGTTGCCTAGGTGCGGTATTTCACACCGC-3′), and pRS30X plasmids as a template. The amplified PCR product was transformed into a yeast strain. APG7 gene disruption was confirmed by PCR with APG7Bgl2ATG primer (5′-AGATCTATGTCGTCAGAAAGGGTCTTAAG-3′) and APG7SalISTOP primer (5′-GTCGACTATTAAGCAATCTCATCAGATTCATC-3′).
Plasmid Construction and Site-directed Mutagenesis
A BamHI fragment (3.9 kb) containing the APG7 gene (ORF YHR171w) was introduced into the BamHI site of pRS314 and pYO324 (pAPG7-314 and pAPG7-324, respectively). To construct an expression plasmid for c-myc–tagged Apg7p, SacI and ApaI sites were introduced just before the termination codon of the APG7 gene by nested PCR with APG7SAF primer (5′-GAATCTGATGAGATTGC-TGAGCTCGGGCCCTAATATTTTGCATATAATAGC-3′), APG7SAR primer (5′-GCTATTATATGCAAAATATTAGGGCCCGAGCTCAG-CAATCTCATCAGATTC-3′), M13-47 primer (5′-CGCCAGGGTTT-TCCCAGTCACGAC-3′), and M13-RV primer (5′-GAGCGGATAA-CAATTTCACACAGG-3′). The amplified DNA fragment was cloned into pGEM-T Vector (pAPG7SA-GEMT). A StuI–SacI fragment (0.12 kb) of pAPG7-GEMT, a SacI–ApaI fragment (0.16 kb) of pMPY-3xMYC, and an ApaI–SalI fragment (1.0 kb) of pAPG7-GEMT were replaced with the StuI–SalI region of pAPG7-314 and pAPG7-324 (pAPG7myc-314 and pAPG7myc-324). The junction and PCR-amplified region were confirmed by DNA sequencing. The plasmid complemented the apg7Δ mutation.
Site-directed mutagenesis of the APG7 gene (Gly333 and Cys507 changed to Ala) was performed by nested PCR with APG7E1928F primer (5′-CTTTAAAAATTGCTGACCAATCCGTGG-3′), APG7X2298F primer (5′-GAGCATTAATAAAAGAGCATG-3′), APG7G333AR primer (5′-CAACCTAGTGTAGCAGCACCTAGTAGTAG-3′), APG7C507AR primer (5′-CTAGTTACTGTGGCCATTTGATCC-3′), APG7S2855R primer (5′-CCTGCTTTATGACTGACAAACCGC-3′), and pAPG7-314 as a template. The amplified EcoRI–StuI fragment (0.8 kb) was replaced with the same region of pAPG7myc-314. The mutation site and PCR-amplified region were confirmed by DNA sequencing. The resultant plasmids were designated pAPG7G333Amyc-314 and pAPG7C507Amyc-314.
For the two-hybrid experiment, a BglII site was introduced just before the start codon of the APG7 gene by PCR with APG7Bgl2ATG primer, APG7SalISTOP primer, and pAPG7-314 as a template. The PCR product was cloned into pGEM-T. The AflII–SalI fragment (~1.9 kb) of the clone was replaced with the AflII–SalI fragment (~3.8 kb) of pAPG7myc-314 (pAPG7BS-GEMT). The BglII–SalI fragment of pAPG7BS-GEMT was subcloned into the BamHI–SalI sites of the pGBD-C1 vector (pGBD-APG7). The AflII–SalI fragment of pGBD-APG7 was replaced with the AflII–SalI fragment from pAPG7G333Amyc-314 or pAPG7C507Amyc-314 to construct pGBD-APG7G333A and pGBD-APG7C507A, respectively. The whole APG12 coding region was PCR-amplified and then introduced into the PstI site of pGAD-C1 (pGAD-APG12).
Antibodies
To express the GST-Apg7p fusion protein in E. coli, an EcoRV fragment (0.6 kb) and an EcoRV–EcoRI fragment (1.6 kb) of pAPG7-316 were subcloned into the SmaI and SmaI–EcoRI sites of pGEX-3X, respectively (pGEX-APG7N and pGEX-APG7C). GST-Apg7p fusion proteins were expressed in DH5α cells carrying pGEX-APG7N and pGEX-APG7C according to manufacturer’s protocol (Amersham Pharmacia Biotech). The GST–C-terminal region of Apg7p was expressed in cells carrying pGEX-APG7C and purified on glutathione Sepharose 4B. The GST–N-terminal region of Apg7p was expressed in cells carrying pGEX-APG7N but was included in the inclusion bodies. The protein was extracted from the inclusion bodies with extraction buffer (8 M urea, 50 mM Tris-Cl, pH 9.5), subjected to SDS-PAGE, and excised from the gel. Polyclonal antibodies against the carboxyl and amino terminal fragments of Apg7p were raised in Japanese white rabbits using purified proteins as antigens (αApg7C and αApg7N, respectively). The IgG fraction was precipitated with 50% saturated ammonium sulfate and dissolved in TBS buffer (150 mM NaCl, 20 mM Tris-Cl, pH 7.5). Anti-Apg7p antibodies were purified on a GST-Apg7p Sepharose column. A polyclonal anti-API antibody was a kind gift from D. J. Klionsky. An anti-hemagglutinin (HA) mouse mAb (16B12) was purchased from Berkeley Antibody Company (Berkeley, CA), an anti–c-myc mouse mAb (9E10)-Agarose conjugate was from Santa Cruz Biotechnology (Santa Cruz, CA), and anti-yeast 3-phosphoglycerate kinase and anti-yeast Dol-P-Man synthase mouse mAbs were from Molecular Probes (Eugene, OR).
Immunoprecipitation
Cells (OD600 = 10) grown to early logarithmic phase in MVD or YPD pH 5.0 medium were harvested and converted to spheroplasts in spheroplasting solution (1% yeast extract, 2% polypeptone, 0.5% glucose, 1 mg/ml Zymolyase 100T). The spheroplasts were harvested in 1.3 M sorbitol as a cushion, lysed with lysis buffer (1% SDS, 150 mM NaCl, 20 mM sodium phosphate, pH 7.5), vortexed, boiled for 5 min, and chilled on ice. When indicated, 1 mM DTT was added to the lysate before boiling. Ten volumes of IP buffer (2% Triton X-100, 150 mM NaCl, 20 mM sodium phosphate, pH 7.5) were added to the cell lysate, and the mixture was centrifuged at 10,000 × g for 5 min at 4°C to remove debris. The supernatant was precleared with 50 μl Protein A-Agarose (20% slurry, Santa Cruz Biotechnology). Fifty microliters of Agarose beads conjugated with anti–c-myc antibody (9E10) (20% slurry, Santa Cruz Biotechnology) were added to the lysate, and the mixture was incubated for 2 h at 4°C. The immunoprecipitate–bead complex was washed six times with ice-cold RIPA buffer (10 mM Tris-Cl, pH 7.4, 1% Nonidet P40, 0.1% sodium deoxycholate, 0.1% SDS, 150 mM NaCl, 1 mM EDTA). Proteins were eluted from the beads with 0.1N glycine-HCl, pH 2.5, and precipitated by incubation with 10% TCA on ice for 1 h. The sediment was washed twice in cold acetone, subjected to reducing SDS-PAGE, transferred to a polyvinylidene difluoride membrane (Millipore, Bedford, MA), and analyzed by Western blotting. All solutions contained a protease-inhibitor mixture for use with fungal and yeast extracts (Sigma, St. Louis, MO).
Other Techniques
Two-hybrid analysis was performed as described by James et al. (1996) blue right-pointing triangle. A biochemical assay monitoring autophagy in yeast by alkaline phosphatase processing was performed as described by Noda et al. (1998) blue right-pointing triangle. Subcellular fractionation of yeast cells was performed as described by Huang and Chiang (1997) blue right-pointing triangle. Advanced BLAST search was performed on the National Center for Biotechnology Information web site (http://www.ncbi.nlm.nih.gov/BLAST/). Multiple alignment of amino acids sequences was performed using a CLUSTAL W program by the computer laboratory in the National Institute for Basic Biology.
Apg12p Interacts with Apg7p via a Thioester Bond
A significant homology between Apg7p and Uba1p suggests that Apg7p functions as an Apg12p-activating enzyme. In this case, Apg12p should first form a transient enzyme–substrate complex with Apg7p as demonstrated with Uba1p and ubiquitin. To examine this possibility, we constructed a strain of yeast expressing both c-myc–tagged Apg7p and HA-tagged Apg12p (YIT702 strain), and immunoprecipitated the c-myc–tagged Apg7p with anti–c-myc antibody. Western analysis using αApg7N antibody recognized c-myc–tagged Apg7p (~78 kDa) in the immunoprecipitates (Figure (Figure1A,1A, WB αApg7N). HA-tagged Apg12p was also detected in the same immunoprecipitate with anti-HA antibody (Figure (Figure1A,1A, WB αHA). The results correspond to those of the two-hybrid experiment (Figure (Figure2).2). PJ69-4A strain (trp1-901 leu2-3112 gal4Δ gal80Δ GAL2-ADE2 GAL1-HIS3) expressing both GAL4AD-Apg12p and GAL4BD-Apg7p grew well on SD-Ade-His-Trp-Leu plate, whereas strains expressing GAL4AD and GAL4BD, GAL4AD-Apg12p and GAL4BD, or GAL4AD and GAL4BD-Apg7p did not. These results suggest that Apg12p interacts with Apg7p.
Figure 1
Figure 1
Apg12p conjugates with Apg7p via a thioester bond. (A) Apg12p was coimmunoprecipitated with Apg7p. pAPG7myc-314 plasmid (CEN) was transformed into apg7Δ cells producing HA-tagged Apg12p to express c-myc–tagged Apg7p. A transformant was (more ...)
Figure 2
Figure 2
Apg7p interacts with Apg12p in vivo. pGBD-APG7 (TRP1) and pGAD-APG12 (LEU2) were transformed into PJ69-4A strain (gal4Δ gal80Δ trp1 leu2 GAL2-ADE2 GAL1-HIS3) to express GAL4BD-Apg7p and GAL4AD-Apg12p, respectively. pGAD-C1 and pGBD-C1 (more ...)
We next determined whether this interaction is mediated by a thioester bond. When the lysate was treated with 1 mM DTT before immunoprecipitation, no Apg12p coimmunoprecipitated with the c-myc–tagged Apg7p (Figure (Figure1B,1B, DTT+). In contrast, Apg12p coimmunoprecipitated with c-myc–tagged Apg7p when the lysate was not treated with DTT (Figure (Figure1B,1B, DTT−). Furthermore, when a lysate of cells overexpressing both Apg7p and Apg12p (YIT703 strain) was analyzed on a nonreducing gel, two bands of Apg7p were detected by Western analysis using αApg7N antibody (Figure (Figure1C,1C, pAPG7myc-324/pAPG12HA-426, βME−). When a sample was treated with a thiol-reducing reagent, β-mercaptoethanol, the upper band disappeared, indicating that the upper band is a thioester conjugate of Apg7p. The conjugates were hardly detected in a lysate of cells expressing Apg7p and Apg12p on centromere-type plasmids (Figure (Figure1C,1C, pAPG7myc-314/pAPG12HA-316, YIT702 strain). This is probably due to the low amount of the conjugate form of Apg7p in the strain. These results indicate that Apg12p binds with Apg7p via a thioester bond.
The ATP-binding Domain of Apg7p Is Essential for the Interaction with Apg12p to Form the Apg5p–Apg12p Conjugate
Apg12p–Apg5p conjugation was reconstituted in an ATP-dependent manner in vitro (Mizushima et al. 1998a blue right-pointing triangle). A Uba1p-homologous region in Apg7p contains a putative ATP-binding domain (GXGXXG; residues 331 to 336) (Figure (Figure3A)3A) (Wierenga and Hol, 1983 blue right-pointing triangle; McGrath et al., 1991 blue right-pointing triangle). According to Wierenga and Hol (1983) blue right-pointing triangle, the second Gly of the ATP-binding domain will be essential for function. To investigate whether the ATP-binding domain is essential for Apg7p function, we used the site-directed mutagenesis to change the Gly333 of Apg7p to Ala (Figure (Figure3A).3A). The mutant protein was expressed in an amount quite similar to wild-type Apg7p (Figure (Figure3B);3B); however, it could not precipitate HA-tagged Apg12p (Figure (Figure3C).3C). This result indicates that the ATP-binding domain of Apg7p is essential for the conjugation of Apg12p with Apg7p.
Figure 3
Figure 3
The ATP-binding domain and active site cysteine of Apg7p are essential for conjugation with Apg12p via a thioester bond. (A) Point mutation sites are schematically represented. Gly333 in a predicted ATP-binding domain of Apg7p was changed to Ala by site-directed (more ...)
If Apg7p functions as an activating enzyme for Apg12p–Apg5p conjugation, the loss of conjugation of Apg7pG333A with Apg12p may result in a defect in the formation of the Apg12p–Apg5p conjugate. In wild-type cells expressing HA-tagged Apg12p, the HA-tagged Apg12p–Apg5p conjugate was recognized, whereas no conjugate was recognized in apg7Δ cells expressing HA-tagged Apg12p, as described previously (Figure (Figure4,4, pAPG7myc-314/pAPG12HA-316 and pRS314/pAPG12HA-316) (Mizushima et al., 1998a blue right-pointing triangle). In cells expressing Apg7pG333A, very little conjugate was recognized (Figure (Figure4,4, pAPG7G333Amyc-314/pAPG12HA-316). These results suggest the ATP-binding domain of Apg7p is essential for the formation of the Apg12p–Apg5p conjugate.
Figure 4
Figure 4
Apg7pG333A and Apg7pC507A show significant defects in the formation of the Apg12p–Apg5p conjugate. The conjugate in cell lysates expressing HA-tagged Apg12p was detected by Western blotting using αHA antibody as described previously ( (more ...)
Cys507 of Apg7p Is an Active Center Cysteine Essential for Its E1 Function
The active center cysteine (Cys600) of yeast Uba1p is essential for the function of a ubiquitin-activating enzyme. If Apg7p is a protein-activating enzyme for Apg12p, a Cys residue of Apg7p will be essential for Apg12p–Apg7p conjugation. The active center cysteine of Apg7p is strongly suggested to be Cys507, because the amino acid sequence of a neighboring region of Apg7p (MCTV) is identical to the corresponding regions in wheat UBA1 (MCTV; GenBank accession number [Ac.No.] P20973) and A. thaliana UBA1 (MCTV; GenBank Ac.No. U80808), and homologous to the corresponding regions in yeast Uba1p (LCTL; GenBank Ac.No. X55386), human UBA1 (ICTL; GenBank Ac.No. M58028), and mouse UBA1 (ICTL; GenBank Ac.No. D10576) (Hatfield et al., 1990 blue right-pointing triangle, 1997 blue right-pointing triangle; Hatfield and Vierstra, 1992 blue right-pointing triangle; Handley et al., 1991 blue right-pointing triangle; McGrath et al., 1991 blue right-pointing triangle; Imai et al., 1992 blue right-pointing triangle).
To investigate whether the Cys residue is essential for Apg7p function, we changed the Cys507 of Apg7p to Ala by site-directed mutagenesis and expressed both c-myc–tagged Apg7pC507A and HA-tagged Apg12p in the apg7Δ mutant with centromere-type plasmids (YIT7C507A strain) (Figure (Figure3A).3A). Immunoprecipitation using anti–c-myc antibody showed that no HA-tagged Apg12p was coimmunoprecipitated with c-myc–tagged Apg7pC507A (Figure (Figure3C),3C), although Apg7pC507A was stably expressed in the YIT7C507A strain (Figure (Figure3B).3B). We further examined the formation of the Apg12p–Apg5p conjugate. No HA-tagged Apg12p–Apg5p conjugate was recognized in the lysate of the YIT7C507A strain (Figure (Figure4,4, pAPG7C507Amyc-314/pAPG12HA-316). These results indicate that Cys507 of Apg7p is an active site cysteine essential for the Apg12p-activating enzyme to form the Apg12p–Apg5p conjugate.
The ATP-binding Domain and Active Site Cysteine of Apg7p Are Essential for Autophagy
If the formation of the Apg12p–Apg5p conjugate via Apg7p is essential for autophagy in yeast, cells expressing Apg7pG333A and Apg7pC507A will show defects in autophagy. We first examined the accumulation of autophagic bodies in cells under starvation conditions in the presence of PMSF. Nomarski optics showed that no autophagic bodies accumulated in YIT7G333A and YIT7C507A cells cultured in nitrogen-starvation medium in the presence of PMSF similar to the result seen with apg7Δ cells (Figure (Figure5A,5A, b–d). In contrast, many autophagic bodies were seen in apg7Δ cells expressing wild-type Apg7p under the same conditions (Figure (Figure5A,5A, a).
Figure 5
Figure 5
The ATP-binding domain and active site cysteine of Apg7p are essential for autophagy. (A) Gly333 and Cys507 in Apg7p are essential for the accumulation of autophagic bodies under nitrogen-starvation conditions. Cells grown to early-logarithmic phase in (more ...)
We next investigated Apg7pG333A and Apg7pC507A for defects in autophagy using a biochemical assay monitoring autophagy-dependent alkaline phosphatase processing (Noda and Ohsumi, 1998 blue right-pointing triangle). The principle of this assay is as follows. A modified version of vacuolar alkaline phosphatase, Pho8Δ60p, remains in the cytosol as a proform (inactive form). When autophagy is enhanced, Pho8Δ60p in the cytosol is transferred to the vacuole and processed to the active form. This processing is monitored by assaying the activity of alkaline phosphatase in the cell lysate.
pAPG7G333Amyc-314 and pAPG7C507Amyc-314 were introduced into an apg7Δ tester strain (YTS2; apg7Δ pho8::pho8Δ60). Alkaline phosphatase activity was measured in the transformants under rich or nitrogen-starvation conditions. Under rich conditions, the alkaline phosphatase activities in cells expressing Apg7pG333A and Apg7pC507A were as low as that of wild-type Apg7p, indicating that autophagy was suppressed (Figure (Figure5B,5B, +N). When apg7Δ cells expressing wild-type Apg7p were incubated in nitrogen-starvation medium for 4 h at 30°C, the activity increased drastically (Figure (Figure5B,5B, −N), indicating that autophagy is induced by nitrogen starvation; however, the activities in apg7Δ cells expressing Apg7pG333A and Apg7pC507A were not enhanced, indicating that autophagy is suppressed in the mutant cells.
A defect in autophagy results in a loss of cell viability under nutrient starvation conditions (Tsukada and Ohsumi, 1993 blue right-pointing triangle). We further examined the loss of viability of YIT7G333A and YIT7C507A strains using phloxine B. Phloxine B specifically stains dead cells. The colonies of YIT7G333A and YIT7C507A cells turned red (gray in monochrome) on nitrogen-starvation plates containing 10 μg/ml phloxine B, whereas the color of apg7Δ mutant colonies expressing wild-type Apg7p was pink (white in monochrome) (Figure (Figure5C).5C). The results indicate that the viability of YIT7G333A and YIT7C507A cells was markedly decreased under nitrogen-starvation conditions. From these results, we conclude that the ATP-binding domain and Cys507 are essential for the function of Apg7p in autophagy.
The ATP-binding Domain and Active Site Cysteine of Apg7p Are Essential for Cytoplasm-to-Vacuole Targeting of API
The apg7 mutant also has a defect in the cytoplasm-to-vacuole targeting of API. API is synthesized in the cytoplasm as a precursor form (Klionsky et al., 1992 blue right-pointing triangle). After targeting to the vacuole, the precursor is processed to the mature form in the vacuole (Klionsky et al., 1992 blue right-pointing triangle). We examined whether Gly333 and Cys507 in Apg7p are also essential for the targeting. We prepared lysates of cells in logarithmic phase and detected the precursor and mature forms of API by Western blotting using αAPI antibody. In wild-type cells, the mature form of API was detected in addition to the precursor, indicating that the precursor transferred from the cytoplasm to the vacuole to be processed into the mature form (Figure (Figure6,6, pAPG7myc-314/pRS316 and pAPG7myc-314/pAPG12HA-316). In contrast, the processing of API was markedly decreased in cells expressing Apg7pG333A and completely inhibited in cells expressing Apg7pC507A, as in the case of apg7Δ cells (Figure (Figure6,6, pAPG7G333Amyc-314/pAPG12HA-316, pAPG7C507Amyc-314/pAPG12HA-316, and pRS314/pAPG12HA-316). These results indicate that the ATP-binding domain and Cys507 of Apg7p are essential for the cytoplasm-to-vacuole targeting of API under rich conditions.
Figure 6
Figure 6
The ATP-binding domain and active center cysteine of Apg7p are essential for cytoplasm-to-vacuole targeting of API. The processing of API in cells growing logarithmically was measured as described by Mizushima et al. (1998a) blue right-pointing triangle. Lanes correspond to those (more ...)
Apg7p Is Present in Cytosol
It has been shown that most free Apg5p, Apg5p–Apg12p conjugate, and more than half of Apg12p are present in the 100,000 × g pellet (Mizushima et al., 1998a blue right-pointing triangle). To determine the intracellular localization of Apg7p, a lysate of wild-type cells was fractionated by centrifugation as described previously (Huang and Chiang, 1997 blue right-pointing triangle). Apg7p in each fraction was detected by Western blotting using αApg7C antibody. Apg7p in vegetatively growing cells was present mainly in the 100,000 × g supernatant (Figure (Figure7,7, wild type, Vegetative Growth). Under nitrogen-starvation conditions, the amount and localization of Apg7p remained unchanged (Figure (Figure7,7, wild type, Nitrogen Starvation). Similar results were obtained with the immunoprecipitation of fractions prepared from cells expressing c-myc–tagged Apg7p. These results indicate that Apg7p is mainly present in the cytoplasm.
Figure 7
Figure 7
Apg7p is present in the cytosol. A wild-type strain (YW5–1B) was cultured in MVD+Ura+Trp medium, transferred to nitrogen-starvation medium, and incubated for 30 min. Cells growing vegetatively were converted to spheroplasts in (more ...)
In this article, we have characterized Apg7p as an Apg12p-activating enzyme and demonstrated its indispensable role in the yeast autophagy. Apg12p, a novel modifier protein, binds to Apg7p via a thioester bond. This binding requires both the active site cysteine (Cys507) and the ATP-binding domain. Accordingly, both the cysteine residue and the ATP-binding domain are essential for Apg12p–Apg5p conjugation and for autophagy as well. From these results, we conclude that Apg7p is a novel E1-like enzyme that activates Apg12p and is essential for autophagy.
Although we clearly showed the E1-like function of Apg7p, only the C-terminal region of Apg7p (residues 322 to 407) shows homology to Uba1p. According to the similarity boxes within other E1-like enzymes as described by Johnson et al. (1997) blue right-pointing triangle and Liakopoulos et al. (1998) blue right-pointing triangle, Apg7p has an ATP-binding domain within box I and an active site cysteine within box III that are essential for E1 function (Figure (Figure8A);8A); however, box III of Apg7p is not similar to those of Uba1p, Uba2p, or Uba3p. Also, neither similarity box II nor IV is present within Apg7p. Phylogenetic analysis of the regions containing box I and box III in the E1 enzymes also suggested that the relationship of Apg7p to the corresponding regions in UBA1, UBA2, and UBA3 family proteins is distant (Figure (Figure8B)8B) (Hatfield et al., 1990 blue right-pointing triangle, 1997 blue right-pointing triangle; Handley et al., 1991 blue right-pointing triangle; McGrath et al., 1991 blue right-pointing triangle; Imai et al., 1992 blue right-pointing triangle; Dohmen et al., 1995 blue right-pointing triangle; Liakopoulos et al., 1998 blue right-pointing triangle; Mizushima et al., 1998a blue right-pointing triangle; Osaka et al., 1998 blue right-pointing triangle; Yuan et al., 1998 blue right-pointing triangle). The comparison of the similarity boxes and phylogenetic analysis showed that Apg7p is distinct from other E1-like enzymes. It is of interest to know whether Apg7p functions as a heterodimer, because the Aos1p/Uba2p and Ula1p/Uba3p complexes function as heterodimers (del Olmo et al., 1997 blue right-pointing triangle; Johnson et al., 1997 blue right-pointing triangle; Liakopoulos et al., 1998 blue right-pointing triangle). At present, we have no answer.
Figure 8
Figure 8
Apg7p is distantly related to Uba1p and its relatives. (A) Schematic representation of the similarity domains among UBA1, UBA2, UBA3, and APG7. The putative active site cysteines are located within similarity box III (UBA domain), as indicated. The essential (more ...)
A working hypothesis of the Apg12p conjugation system consistent with these results is proposed in Figure Figure9.9. The C-terminal Gly of Apg12p is activated by Apg7p in an ATP-dependent manner. The Apg12p–Apg7p conjugate forms via the C-terminal Gly of Apg12p and Cys507 of Apg7p. The reaction probably occurs in the cytosol or the cytoplasmic side of an Apg12p-associated compartment(s), because Apg7p is mainly present in the cytoplasm (Figure (Figure7)7) (Kim et al., 1999 blue right-pointing triangle). By analogy to ubiquitination and related modifications, there may be novel E2 and E3 enzymes for the conjugation system. One such candidate for E2 is Apg10p, because the Apg12p–Apg5p conjugate is not observed in an apg10 mutant. Cloning of the APG10 gene and biochemical analysis will reveal the function of Apg10p. Screening other candidates will be performed using an Apg12p-affinity column, an Apg7p-affinity column, or two-hybrid screening.
Figure 9
Figure 9
Working hypothesis for the function of Apg7p in the Apg12p conjugation system. Apg12p associates with Apg7p. The C-terminal Gly of Apg12p conjugates with Cys507 in Apg7p via a thioester bond in an ATP-dependent manner. The reaction occurs in the cytoplasm (more ...)
It remains to be determined at which step in autophagy the Apg12p conjugation system works. Apg7p is mainly present in the cytosol, whereas more than half of Apg12p is localized in membrane compartment(s) or a large complex. The Apg12p–Apg7p binding probably occurs in the cytosol or the cytoplasmic side of an Apg12p-associated structure(s). Recently, Yuan et al. (1999) blue right-pointing triangle suggested that a quite similar conjugation system is required for microautophagy in Pichia pastoris. Microautophagy is the sequestration of cytoplasmic components (peroxisomes in this case) by an invagination of the vacuolar membrane. In a conjugation-deficient mutant (gsa7), the sequestration is not accomplished completely, probably because of defects in the membrane fusion step. Gsa7p, a P. pastoris homologue of Apg7p, was shown to be conjugated to a small protein through a thioester bond. Although a modifier and substrate(s) have not been identified, it strongly suggests that the Apg12p conjugation system is essential for microautophagy. Because the process of microautophagy is quite different from that of macroautophagy, it would be interesting if similar machinery is involved in both processes.
We have identified a human Apg12p homologue and have observed that the Apg12p homologue also conjugates with a human Apg5p homologue, which has been identified as an apoptosis-specific protein (Hammond et al. 1998 blue right-pointing triangle; Mizushima et al. 1998b blue right-pointing triangle). A BLAST search of Apg7p in the Expressed Sequence Tag database showed potential mammalian homologues of Apg7p. Recently, an Apg7p homologue in P. pastoris, Gsa7p, and a human Gsa7p/Apg7p homologue were identified by Yuan et al. (1999) blue right-pointing triangle. The human Gsa7p/Apg7p homologue is expressed in various tissues as revealed by Northern analysis (Tanida and Kominami, unpublished observations). These findings suggest that the Apg12p conjugation system generally functions in eukaryotes. By analogy to the Apg5p homologue, an Apg7p homologue may play a significant role in the autophagic and apoptotic pathways in mammalian cells. Cloning and biochemical analyses of Apg7p homologues will reveal the function of the novel protein conjugation system in mammalian cells.
Apg7p is distantly related to UBA1, UBA2, and UBA3 family proteins (Figure (Figure8A).8A). Nevertheless, Apg7p functions as an E1 enzyme for Apg12p–Apg5p conjugation. These findings suggest that the ubiquitin-like protein modification system will form a ubiquitous regulatory system in eukaryotes, not specific to ubiquitin and ubiquitin-like proteins. Further analyses of potential E1 enzymes may reveal a novel regulatory system by posttranslational modification.
ACKNOWLEDGMENTS
We thank D.J. Klionsky (University of California Davis) for providing information, helpful discussion, and antibody, W.A. Dunn, Jr. (University of Florida) for providing information, A. Ogiwara (National Institute for Basic Biology) for analyzing sequence data, Y. Ohya (University of Tokyo), P. James (University of Wisconsin), and P. Hieter (Johns Hopkins University) for plasmids and strains, K. Ishidoh, J. Ezaki, D. Muno (Juntendo University), and members of Y. Ohsumi’s laboratories for helpful discussions. This work was supported in part by grants-in-aid 09680629 (to T.U.) for Scientific Research, grants-in-aid 08278103 (to E.K.) for Scientific Research on Priority areas from the Ministry of Education, Science, Sports, and Culture of Japan, and The Science Research Promotion Fund from the Japan Private School Promotion Foundation (to E.K.).
Abbreviations used:
Ac.No.accession number
APIaminopeptidase I
GAL4ADGAL4 activation domain
GAL4BDGAL4 DNA binding domain
HAhemagglutinin

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