Uncovering the Protein Translocon at the Chloroplast Inner Envelope Membrane

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Science  01 Feb 2013:
Vol. 339, Issue 6119, pp. 571-574
DOI: 10.1126/science.1229262


Chloroplasts require protein translocons at the outer and inner envelope membranes, termed TOC and TIC, respectively, to import thousands of cytoplasmically synthesized preproteins. However, the molecular identity of the TIC translocon remains controversial. Tic20 forms a 1-megadalton complex at the inner membrane and directly interacts with translocating preproteins. We purified the 1-megadalton complex from Arabidopsis, comprising Tic20 and three other essential components, one of which is encoded by the enigmatic open reading frame ycf1 in the chloroplast genome. All four components, together with well-known TOC components, were found stoichiometrically associated with different translocating preproteins. When reconstituted into planar lipid bilayers, the purified complex formed a preprotein-sensitive channel. Thus, this complex constitutes a general TIC translocon.

Translocation of nuclear-encoded preproteins across the double envelope membranes of chloroplasts is mediated by two protein translocons, the TOC and TIC complexes (15). Tic20, an integral inner membrane protein with four predicted transmembrane helices, has been proposed to form part of a general protein-conducting channel (6, 7). Recombinant Tic20 has further been reported to have the capacity to form a channel (8). A 1-megadalton (MD) translocation intermediate complex has been recently identified at the inner membrane, in which Tic20 is in close contact with a translocating preprotein (9). Whereas Tic20 forms a stable 1-MD complex in the inner membrane, Tic21 interacts only weakly with the complex, and other known Tic proteins such as Tic110 and Tic40 are not involved in the complex (9). Thus, detailed organization of this 1-MD complex has remained elusive.

Here, we generated transgenic Arabidopsis plants expressing a protein A–tagged Tic20-I (the major Tic20 isoform in Arabidopsis), and the tagged Tic20-I–containing complexes were purified (fig. S1). Three proteins with molecular masses of 214, 100, and 56 kD were specifically copurified with Tic20-I, which were confirmed to form a stable 1-MD complex together with Tic20-I (Fig. 1A). Subsequent mass spectrometric analysis revealed three previously uncharacterized Arabidopsis proteins (fig. S2A).

Fig. 1

The 1-MD complex is composed of Tic20-I and three other Tic proteins. (A) Tic214, Tic100, and Tic56 were copurified with protein A–tagged Tic20-I (PA2-Tic20-I). The purified fraction was separated by two-dimensional blue native (2D-BN) SDS-PAGE followed by silver staining. Tic20-I*, tobacco etch virus (TEV) protease–cleaved PA2-Tic20-I. (B) Wild-type Arabidopsis chloroplasts were solubilized with 1% digitonin in the presence of 1 M NaCl and then separated by 2D-BN SDS-PAGE followed by immunoblotting. (C) Coimmunoprecipitation of the 1-MD TIC complex components. (D and E) The localization and topology of the different TIC complex components were analyzed by alkaline (D) and protease (E) treatment. (D) Chloroplasts were treated with either 10 mM HEPES-KOH, pH 7.5 (hypotonic lysis), or 100 mM Na2CO3 on ice for 30 min, followed by centrifugation to obtain supernatant (S) and membrane pellet (P) fractions. (E) Inverted inner envelope membrane vesicles (26) were treated with or without thermolysin (T-lysin; 100 μg/ml) and with or without Triton X-100 [TX-100; 0.1% (w/v)] on ice for the indicated time periods.

Surprisingly, the 214-kD protein, AtCg01130, is encoded by the previously enigmatic chloroplast gene ycf1 (hypothetical chloroplast open reading frame 1) (1012). The deduced protein, here renamed Tic214, is 1786 amino acids in length with a calculated relative molecular mass Mr of 213,742 and is predicted to contain six N-terminal transmembrane domains (figs. S2B and S3). The 100-kD protein, At5g22640, is a nuclear-encoded protein of 871 amino acids with a calculated Mr of 99,954 (fig. S4). This protein likely has no cleavable transit peptide (fig. S2A) and thus was named Tic100. The 56-kD protein, At5g01590, is also a nuclear-encoded protein of 527 amino acids with a calculated Mr of 61,625 (fig. S5). This protein is most likely synthesized as a preprotein and processed to form a mature protein upon import (fig. S6A) and thus was designated Tic56. Tic100 and Tic56 are highly conserved among most land plants, but show no remarkable overall sequence similarity to any proteins of known function and have no predicted transmembrane segment.

In wild-type chloroplasts, Tic214, Tic100, Tic56, and Tic20-I appeared to form stable 1-MD TIC complexes (Fig. 1, B and C, and fig. S6, B and C), which were shown to associate with preproteins (fig. S7). If we assume that the stoichiometry of the components in the 1-MD complex is 1:1:1:1 (fig. S8), we would expect that the complex represents a trimeric assembly of Tic214, Tic100, Tic56, and Tic20-I (1170 kD). The stoichiometry of Tic20-I:Toc75 (the channel protein of the TOC complex) in the envelope membranes was roughly estimated to be 1:2.5 (fig. S8). Tic20-I and Tic214 likely constitute the membrane-integral part of the 1-MD TIC complex; Tic20-I is entirely buried in the core of the complex, whereas Tic214 is exposed to both sides of the inner membrane (Fig. 1, D and E, and fig. S6D). Tic100 is associated peripherally in the complex at the intermembrane space side, whereas Tic56 is mostly embedded in the complex.

In a search for evidence of direct involvement of the 1-MD TIC complex as a general protein translocation machinery at the inner membrane, we used purified model preproteins in import experiments in vitro to isolate translocation intermediate–associated proteins from Arabidopsis chloroplasts (Fig. 2 and fig. S9) (1315). Almost all major isolated proteins could be assigned to either the well-known TOC components (including Toc159, Toc75, and Toc33) or the 1-MD TIC complex components (including Tic214, Tic100, Tic56, and Tic20-I) (Fig. 2). Association of these TOC and TIC components with preproteins absolutely required adenosine triphosphate (ATP) in the import reactions that could drive preprotein translocation across the envelope membranes (fig. S9B). Tic214, Tic100, Tic56, and Tic20-I were purified at levels comparable to those of TOC components and preproteins (Fig. 2 and fig. S9B). Two different model preproteins, pSTEV and pFdTEV, resulted in essentially similar profiles of associated proteins (Fig. 2), which supports the direct involvement of the 1-MD TIC complex in protein translocation as a general import machinery in concert with the well-established TOC complex.

Fig. 2

Association of the 1-MD TIC complex components with two distinct model preproteins. Arabidopsis chloroplasts were incubated with 100 nM urea-denatured protein A–tagged preproteins pSTEV or pFdTEV in the presence of 0.5 mM ATP for 10 min at 25°C. As a control, incubation without preprotein (–) was also performed. Reisolated chloroplasts were directly solubilized with 1% digitonin, and insoluble material was removed by ultracentrifugation. The resulting supernatant was incubated with immunoglobulin G–sepharose for 2 hours at 4°C. After the beads were washed thoroughly, bound protein complexes were eluted under nondenaturing conditions by TEV cleavage. The denatured samples were separated by 12.5% SDS-PAGE followed by silver staining (left) or immunoblotting (right). ENV, Arabidopsis mixed envelope fraction; TIC, the 1-MD TIC complex purified from PA2-Tic20-I plants; *1, unidentified protein currently under investigation; *2, unknown contaminating protein; AcTEV, TEV protease; pFd and pS, TEV-cleaved preproteins; Tic20-I*, TEV-cleaved PA2-Tic20-I.

By contrast, we observed hardly any specific association of Tic110 or Tic40 with the translocation intermediate complexes (Fig. 2 and fig. S9B). This is surprising because Tic110, an abundant inner membrane protein, was initially identified by a similar method (15) and has long been considered to be a central player (5), together with Tic40, in preprotein translocation across the inner membrane (16). The migration of Tic110 upon SDS–polyacrylamide gel electrophoresis (PAGE) was almost the same as that of Tic100. However, they are completely different proteins, and Tic110 exists as a very distinct 200- to 300-kD entity in the inner membrane (Fig. 1B) (9) most probably without any stably associated proteins (fig. S10). Physical interaction between Tic110 and any component of the 1-MD TIC complex was hardly observed even after chemical cross-linking (Fig. 1C and fig. S11). Thus, although Tic110 might act as a scaffold for stromal molecular chaperones at a later stage during import (17, 18), direct participation of these Tic proteins in preprotein translocation is unclear.

The null mutant of Arabidopsis TIC20-I displays developmental defects during embryogenesis and results in an albino, seedling-lethal phenotype due to a strong defect in protein import into chloroplasts (1921). Null mutants of TIC100 (22) and TIC56 showed very similar phenotypes (Fig. 3, A and B, and figs. S12 and S13). Absence of either Tic100 or Tic56 led to marked reductions of the remaining 1-MD TIC complex components, indicating that they are important for assembly of the complex (Fig. 3C and fig. S12E). Furthermore, chloroplasts isolated from a viable tic56-3 pale green mutant had a notable protein import defect (figs. S14 and S15).

Fig. 3

Characterization of tic100 and tic56 Arabidopsis knockout mutants. (A) Schematic representation of the genes encoding Tic100 and Tic56. Triangles, T-DNA insertions; solid boxes, exons; thin lines, introns; shaded boxes, untranslated regions. (B) Visible phenotypes of various tic and toc mutants (16, 1922, 27) grown on sucrose-containing media for 3 weeks. Scale bars, 5 mm. (C) Total proteins were extracted from 3-week-old wild-type Arabidopsis and from homozygous albino tic100-1, tic56-1, and tic20-I mutants; 24 μg of total protein was subjected to SDS-PAGE and immunoblotting. Hsp93 and Hsp70, stromal molecular chaperones; LHCP, light-harvesting chlorophyll-binding protein; OE33, 33-kD protein of the oxygen-evolving complex of photosystem II. (D) Double and single knockouts were identified in the progeny derived from a +/tic20-I +/tic100-1 heterozygous plant (left) and from a +/tic20-I +/tic56-1 heterozygous plant (right). Scale bars, 1 cm.

Like the tic20-I mutant (20), no photosynthetic proteins accumulated in the albino seedlings of the tic100-1 and tic56-1 mutants, although some housekeeping proteins did accumulate (Fig. 3C). This residual import ability in the tic20-I mutant can be attributed to partial compensation by the elevated expression of the minor, partially redundant homolog Tic20-IV (Fig. 3C) (20), because a tic20-I tic20-IV double-knockout mutant exhibits more severe embryo lethality (20, 21). The tic20-I tic56-1 and tic20-I tic100-1 double-knockout mutants showed phenotypes similar to those of the single-knockout mutants, tic20-I, tic56-1, or tic100-1, indicating that neither Tic56 nor Tic100 contributes to the compensation provided by Tic20-IV (Fig. 3D and fig. S12). By contrast, neither a tic20-IV tic56-1 nor a tic20-IV tic100-1 double-knockout mutant could be identified, which suggests that such double-knockout mutants are also embryo-lethal. Hence, there seems to be a residual import pathway for some housekeeping proteins in which Tic20-IV but neither Tic20-I, Tic56, nor Tic100 is involved (Fig. 3C), and impairment of both pathways causes embryo lethality (20).

The chloroplast gene initially called ycf1 was reported to be an essential gene in tobacco (11) and in Chlamydomonas (12). Thus, one can anticipate that Tic214 is an essential Arabidopsis protein. Overall, like Tic20-I, both Tic100 and Tic56 (and most likely Tic214) are indispensable components of the 1-MD TIC complex required for photosynthetic protein import, and are therefore essential for plant viability.

When reconstituted into planar lipid bilayers, the purified 1-MD TIC complexes showed ion channel activity (Fig. 4 and fig. S16). In most cases, three identical channels appeared to be simultaneously incorporated into the bilayer as a unit (fig. S16C). This also suggests a trimeric assembly of Tic214, Tic100, Tic56, and Tic20-I to form the 1-MD complex. The single-channel current-voltage (I-V) curve (Fig. 4B) indicates weak rectification, because current was slightly larger at negative voltages than at positive voltages. The average slope conductance at 0 mV was 266 ± 18 pS (N = 10), a value comparable to those obtained with other protein translocons (2325). Channel gating had a weak dependence on the membrane voltage, as spike-like short closures were frequently observed at negative high voltages (Fig. 4A). Because they always showed rectifying and voltage-dependent gating properties, we concluded that TIC channels incorporated into planar bilayers had the same orientation (fig. S16B).

Fig. 4

Reconstituted 1-MD TIC complexes form preprotein-sensitive channels in planar bilayer membranes. (A) Representative current fluctuations in reconstituted 1-MD TIC complexes at different membrane voltages. Solid line labeled C indicates zero current. The distance between dashed lines corresponds to a unitary step. (B) The single-channel current-voltage (I-V) relationship. Data are means ± SD (N = 8 to 19). (C) Representative current recordings in the absence (control) and presence of 0.1 μM pS-protA in the intermembrane space side at the indicated membrane voltage. (D) Representative current recordings in the absence (control) and presence of 1 μM mS-protA in the intermembrane space side at the indicated membrane voltage.

In the presence of 0.1 μM preprotein (pS-protA) in the physiological intermembrane space side of the membrane (fig. S16B), TIC channels were blocked at positive voltage but open at negative voltage (Fig. 4C). At high positive voltages, the open probability decreased with an increase in preprotein concentration (fig. S16D). In contrast, TIC currents were only slightly affected, even by a high concentration (1 μM) of mature protein (mS-protA) lacking a transit peptide (Fig. 4D and fig. S16D). When preproteins were added to the opposite (stromal) side of the membrane, TIC channels were not blocked either at positive or negative voltage (fig. S16E). Thus, the TIC complex forms membrane channels, where preproteins specifically interact with and plug the channel pore.

Although homologs of Tic20 have been identified in cyanobacteria and are well conserved among virtually all plastid-containing lineages (21), phylogenetic analysis (fig. S17) revealed no direct homologs for Tic214, Tic100, or Tic56 in extant cyanobacteria, Glaucophyta, or Rhodophyta, indicating that this TIC transport system evolved largely after the initial endosymbiotic event. Thus, the chloroplast inner membrane protein translocon that we describe here has changed markedly during evolution through modifications of both nuclear and chloroplast genomes.

Supplementary Materials

Materials and Methods

Figs. S1 to S17

Table S1

References (2848)

References and Notes

  1. Acknowledgments: We thank K. Iwasaki, N. Miyazaki, S. Thompson, T. Takao, C. Awada, H. Mori, and J. Mima for helpful suggestions and valuable discussions; P. Jarvis, D. Schnell, and I. Nishimura for vectors; the Arabidopsis Biological Resource Center, Institut National de la Recherche Agronomique, and Cold Spring Harbor Laboratory for the T-DNA lines; and RIKEN Bioresource Center for the full-length cDNAs. Supported by grants-in-aid for scientific research from the Ministry of Education, Culture, Sports, Science and Technology, Japan (20059022, 22020024, 24117511, and 24657073, M.N.; 21107518 and 22370059, T.I.; 23770190 and 23113519, M.H.) and by a Japan Society for the Promotion of Science postdoctoral fellowship for foreign researchers (J.B.). S.K., J.B., Y.H., M.O., M.I., M.T., and M.N. performed biochemical and genetic analyses; M.H. and T.I. performed electrophysiological analyses; M.N. conceived and supervised the whole project and wrote the paper.
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