Structure of autophagy-related protein Atg8 from the silkworm Bombyx mori

The crystal structure of autophagy-related protein Atg8 from the silkworm B. mori has two additional helices at the N-terminus before the expected ubiquitin fold.

Abstract

Autophagy-related protein Atg8 is ubiquitous in all eukaryotes. It is involved in the Atg8–PE ubiquitin-like conjugation system, which is essential for autophagosome formation. The structures of Atg8 from different species are very similar and share a ubiquitin-fold domain at the C-terminus. In the 2.40 Å crystal structure of Atg8 from the silkworm Bombyx mori reported here, the ubiquitin fold at the C-terminus is preceded by two additional helices at the N-­terminus.

1. Introduction  

Autophagy is essential for cell survival in all eukaryotes and is involved in the degradation of cytoplasmic components and intracellular proteins by lysosomes (Reggiori & Klionsky, 2002 ▶). Cell signals such as starvation can stimulate autophagy and induce the formation of a double-membrane structure called the autophagosome, which docks and fuses with the lysosome, whereupon the inner contents of the autophagosome are released into the lysosome and are consumed by hydrolases (Shintani & Klionsky, 2004 ▶; Reggiori & Klionsky, 2002 ▶). Recent studies have revealed a wide variety of physiological roles of autophagy and its relevance to diseases such as liver diseases, muscular disorders, neurodegeneration, pathogen infections and cancer (Cuervo, 2004 ▶).

Several autophagy-related genes (ATGs) have been identified in Saccharomyces cerevisiae. Two ubiquitin-like conjugation systems (the Atg8–PE system and the Atg12–Atg5–Atg16 system) are essential for autophagosome formation (Klionsky et al., 2003 ▶; Amar et al., 2006 ▶). In the Atg8–PE system, the removal of the carboxyl-terminal arginine from newly synthesized Atg8 by a cysteine protease, Atg4, exposes a glycine residue at the carboxyl-terminus. The uncovered glycine is then activated and covalently conjugated to phosphatidylethanolamine (PE) by the E1-like enzyme Atg7 and the E2-like enzyme Atg3 (Ichimura et al., 2000 ▶). The Atg8–PE system controls the expansion of the autophagosome precursor, the phagophore (Xie et al., 2008 ▶), and directly determines the growth of autophagosomal membranes (Nakatogawa et al., 2007 ▶).

Recently, several autophagy-related genes have been identified in Bombyx mori (Zhang et al., 2009 ▶). BmATG8 (Genbank accession No. FJ416330), which encodes a homologue of yeast Atg8, was found to be up-regulated in the silk gland in fifth-instar B. mori larvae, suggesting that BmAtg8 may play an important role in maturation of the silk gland (Zhang et al., 2009 ▶).

Here, we report the crystal structure of BmAtg8 at 2.40 Å resolution. BmAtg8 consists of the ubiquitin fold at the C-terminus, which is conserved among species from yeast to mammals, with two additional helices at the N-terminus.

2. Materials and methods  

2.1. Cloning and protein expression  

The gene encoding residues 1–116 of BmAtg8 was amplified by PCR from the total RNA of B. mori. The amplified DNA was cloned into pET28a-derived vector plasmid using primers with NdeI and NotI restriction sites. The resulting construct was verified by sequencing and contained an MHHHHHHG tag at the N-terminus of the protein. Escherichia coli BL21 (DE3) cells were transformed with this construct and were cultured in 400 ml 2×YT medium containing 10 µg ml⁻¹ kanamycin at 310 K until the OD₆₀₀ reached 0.6. Protein expression was induced using isopropyl β-d-1-thio­galactopyranoside at a final concentration of 0.2 mM at 310 K for 4 h. Cells were harvested by centrifugation at 7330g for 10 min and resuspended in lysis buffer (20 mM Tris–HCl pH 8.5, 50 mM NaCl). The suspension was sonicated and the supernatant was collected by centrifugation at 12 000g for 30 min at 277 K.

2.2. Purification  

The supernatant was loaded onto 2 ml Ni–NTA affinity resin (GE Healthcare Bioscience) with lysis buffer at 289 K. After washing with 20 ml 10 mM imidazole in lysis buffer, the target protein of about 14 kDa was eluted with lysis buffer containing 250 mM imidazole and was then further purified on a HiLoad Superdex 75 column (GE Healthcare Bioscience) equilibrated with lysis buffer at 289 K. The fractions containing the target protein were verified using 15% SDS–PAGE.

2.3. Crystallization and data collection  

Purified protein solution (in 20 mM Tris–HCl pH 8.5, 50 mM NaCl) was concentrated to 20 mg ml⁻¹ by ultrafiltration (Millipore Amicon) into lysis buffer with a final concentration of 4 mM dithiothreitol (DTT). Crystallization conditions were screened by the sitting-drop vapour-diffusion method at 291 K using Crystal Screens I and II and Index I and II (Hampton Research). Crystals obtained in a condition consisting of 2.0 M ammonium sulfate, 0.1 M sodium citrate pH 5.6 and 0.2 M sodium/potassium tartrate were reproduced and grown to a useful size by the hanging-drop vapour-diffusion method. The drops consisted of 1 µl protein solution and 1 µl reservoir solution and were equilibrated against 500 µl reservoir solution. The crystal used for data collection was flash-frozen in liquid nitrogen using a cryoprotectant consisting of the reservoir solution plus 25%(v/v) glycerol. Diffraction data were collected to 2.40 Å resolution at 100 K using an in-house Rigaku MM007 X-ray generator (λ = 1.5418 Å) with a MAR Research 345 dtb detector (MAR Research, Germany) at the School of Life Sciences, University of Science and Technology of China (USTC; Hefei, People’s Republic of China).

2.4. Structure determination and refinement  

The structure was determined by molecular replacement with the program MOLREP (Vagin & Teplyakov, 1997 ▶) from the CCP4 suite (Collaborative Computational Project, Number 4, 1994 ▶) using the structure of GABA-A receptor-associated protein (GABARAP; PDB code 1kjt; Bavro et al., 2001 ▶) as a search model. The initial model was refined by using the maximum-likelihood method and TLS refinement to refine the anisotropic B factors as implemented in REFMAC5 (Murshudov et al., 1997 ▶) as part of the CCP4 program suite and was rebuilt interactively using σ_A-weighted electron-density maps with coefficients 2mF _o − Fc and mF _o − Fc in the program Coot (Emsley & Cowtan, 2004 ▶). The final model was validated with the programs PROCHECK (Laskowski et al., 1993 ▶) and MolProbity (Chen et al., 2010 ▶). Structure factors and coordinates have been deposited in the Protein Data Bank (PDB; http://www.rcsb.org/pdb) under accession code 3m95.

3. Results and discussion  

3.1. Overall structure  

The crystal structure of BmAtg8 was refined to a resolution of 2.40 Å. There are two subunits (A and B) in the asymmetric unit, but the symmetry relating them was not imposed during refinement. The majority of residues are fitted well in the electron-density map, except for the N-terminal His tag of both subunits. Statistics of the X-ray data-collection and refinement statistics are summarized in Table 1 ▶.

Table 1. Crystal parameters, data-collection and structure-refinement statistics.

Values in parentheses are for the highest resolution bin.

Data processing
Resolution range ()	27.082.40 (2.462.40)
Space group	P41
Unit-cell parameters (, )	a = b = 96.77, c = 44.31, = = = 90.00
Unique reflections	14385 (765)
Completeness (%)	92.7 (90.2)
Mean I/(I)	14.4 (1.7)
R merge † (%)	8.3 (32.9)
Refinement statistics
Resolution range ()	27.082.40
R factor‡/R free § (%)	23.11/27.31
Mean B factor (2)	48.69
No. of protein atoms	1949
No. of water atoms	69
R.m.s.d.¶ bond lengths ()	0.015
R.m.s.d.¶ bond angles ()	1.448
Ramachandran plot††
Residues in most favoured regions (%)	95.15
Residues in additional allowed regions (%)	4.85
Residues in disallowed regions (%)	0

^† R _merge = , where I _i(hkl) is the intensity of an observation and I(hkl) is the mean value for its unique reflection; summations are over all reflections.

^‡ R factor = , where F _obs and F _calc are the observed and calculated structure-factor amplitudes, respectively.

^§ R _free was calculated with 5% of the data excluded from the refinement.

^¶Root-mean-square deviation from ideal values.

^††Categories were defined by MolProbity.

The overall structure of BmAtg8 consists of a four-stranded β-­sheet (β1–β4) flanked by two pairs of α-helices (α1–α2 and α3–α4), one on each side of the sheet (Fig. 1 ▶). The core domain, a ubiquitin fold, consists of four β-strands (β1–β4) with two of the α-helices (α3–α4) on one side of the sheet. In BmAtg8, two additional α-helices (α1 and α2) cover the other side of the sheet via both polar and hydrophobic interactions.

Figure 1.

The overall structure of BmAtg8. α-Helices are coloured cyan and β-strands are coloured magenta. This figure was prepared using PyMOL (DeLano, 2002 ▶).

3.2. Structure comparison  

Several crystal structures of Atg8 homologues have been reported. Multiple sequence alignment indicates that Atg8 is highly conserved from yeast to mammals (Fig. 2 ▶ a). We found that BmAtg8 shows high structural similarity to the search model GABARAP (PDB code 1kjt; Bavro et al., 2001 ▶), microtubule-associated protein light chain 3 (LC3; PDB code 1ugm; Sugawara et al., 2004 ▶), Trypanosoma brucei Atg8 (TbAtg8; PDB code 3h9d; Koopmann et al., 2009 ▶) and S. cerevisiae Atg8 (ScAtg8; PDB code 2zpn; Noda et al., 2008 ▶), with root-mean-square deviations (r.m.s.d.s) of 0.5, 0.9, 1.1 and 0.8 Å over 110 C^α atoms, respectively (Fig. 2 ▶ b). The helices α1 and α2 sustain their orientation via tight interactions with the ubiquitin core by means of several hydrogen bonds and salt bridges. In detail, residues Phe3, Gln4, Tyr5, Lys6, Ile21, Arg22, Tyr25, Arg28 and Glu34 contribute to the hydrogen bonding. Four salt bridges were found: between Lys6 and Asp100, between Arg14 and Asp102, between Lys15 and Glu101 and between Glu17 and Lys48 (Fig. 3 ▶). Most of these residues are highly conserved from yeast to mammals. This implies that these conserved residues are essential for the protein to maintain its structural integrity and biological function (Sugawara et al., 2004 ▶). In BmAtg8, residues His9 and Ser10 on the loop between α1 and α2 also contribute to the stabilization of the N-terminal helices. His9 can form hydrogen bonds to Tyr5 and Arg14. Ser10, which is not con­served in the homologues, forms hydrogen bonds to Lys13 and Arg14.

Figure 2.

Structure comparison. (a) Structure-based sequence alignment of microtubule-associated protein light chain 3 (LC3; 33% identity), T. brucei Atg8 (TbAtg8; 46% identity), S. cerevisiae Atg8 (ScAtg8; 56% identity) and GABARAP (90% identity) with BmAtg8. The sequences of homologues of BmAtg8 were obtained from the PDB. The secondary structure of LC3 is shown at the top and that of BmAtg8 is shown at the bottom. Alignments were performed using the programs MULTALIN (Corpet, 1988 ▶) and ESPript (Gouet et al., 2003 ▶). Conserved residues are marked by blue boxes and identical residues are shown in red. (b) Overall structure superposition of BmAtg8 (red) with GABARAP (green), LC3 (magenta), TbAtg8 (orange) and ScAtg8 (cyans). This figure was prepared using PyMOL (DeLano, 2002 ▶).

Figure 3.

Interactions between the ubiquitin fold and the N-terminal helices. The N-terminal helices are coloured cyan and the ubiquitin fold is coloured magenta. The residues contributing to the interactions are labelled. This figure was prepared using PyMOL (DeLano, 2002 ▶).

Two hydrophobic pockets are found to exist in all Atg8 homologues. One pocket comprises Glu17, Ile21, Pro30, Ile32, Lys48 and Leu50 and is located between helix α2 and the core domain and the other comprises Tyr49, Val51, Pro52, Phe60, Leu63 and Ile64 and is located in the ubiquitin fold. Most residues in the hydrophobic pockets are also conserved in different species. As reported pre­viously (Noda et al., 2008 ▶), these pockets are involved in the interaction between LC3 and p62: the side chains of residues Trp338 and Leu341 in p62 insert deeply into these pockets and an intermolecular β-­sheet is formed by p62 and β2 in LC3. This suggests that these regions in BmAtg8 are potential binding sites that recognize other protein partners in a similar manner.

In conclusion, BmAtg8 contains a ubiquitin fold which has been found in all Atg8 proteins from yeast to mammals. The high conservation in the structure of Atg8 illustrates that the Atg8 protein plays a central role in the autophagy pathway of eukaryotes.

Supplementary Material

PDB reference: autophagy-related protein Atg8, 3m95