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J. Biol. Chem., Vol. 279, Issue 12, 11259-11263, March 19, 2004
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From the Genetic Engineering Laboratory, Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Calcutta 700032, India
Received for publication, December 11, 2003 , and in revised form, January 7, 2004.
| ABSTRACT |
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| INTRODUCTION |
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Using in vitro systems, it was shown that tRNA import in yeast, Leishmania and Trypanosoma mitochondria is ATP-dependent (710) and requires ATP hydrolysis (11). ATP could have a direct role in inducing conformational changes leading to opening of import channels. Alternatively, the mitochondrial F1-F0-ATPase, or some other ATPase dedicated to import, could generate a proton gradient that actually drives import. A role of protons was indicated by the inhibitory effect of protonophores (11), which dissipate proton gradients, but whether protons are sufficient to induce import remains an open question. Finally, it is unclear whether proton gradient generation and tRNA translocation are separate or coupled processes and whether tRNA itself plays an active role in proton translocation.
We have recently reported the isolation of a multiprotein complex (the RNA import complex or RIC)1 that is sufficient to induce import of tRNAs into artificial phospholipid vesicles (12). This reconstituted system retains all the properties of import in intact mitoplasts, including ATP dependence and sensitivity to respiratory uncouplers and inhibitors (12). Two tRNA-binding proteins were identified within this complex by photo-cross-linking and immunochemistry, a 45-kDa protein that binds tRNATyr directly and another 21-kDa protein that binds tRNAIle only in the presence of tRNATyr, suggesting allosteric changes within RIC leading to modulation of tRNA affinities (1214). In the present study, we have used the RIC-reconstituted liposome system to study the bioenergetic transactions leading to import.
| MATERIALS AND METHODS |
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Preparation of ProteoliposomesEmpty liposomes were prepared (12) by suspending phosphatidyl choline (250 µg) in 50 mM HEPES-KOH, pH 7.5, 10 mM MgAc2, 2 mM DTT, 10% glycerol, 0.25% deoxycholate and dialyzing the suspension against 5 mM HEPES-KOH, pH 7.5, 5 mM MgAc2, 20 mM KCl for 18 h at 4 °C. Aggregated material was removed by centrifugation at 2300 x g and the supernatant, containing mainly unilamellar vesicles, was used. For reconstitution, liposomes (25 µg) and RIC (100 ng) were incubated in the same buffer without deoxycholate for 1 h before import or ATPase assays.
Import Substrates32P-Labeled tRNATyr(GUA) or tRNAGln(CUG) was prepared by T7 RNA polymerase transcription as described previously (15).
Import AssaysProteoliposomes (equivalent to 100 ng of RIC) were incubated with 100 fmol of substrate RNA in 20 µl of import buffer (10 mM Tris-HCl, pH 7.5, 10 mM MgCl2, 1 mM DTT, and 4 mM ATP) at 37 °C for 15 min, then RNases A and T1 were added at final concentrations of 2.5 µg/ml and 50 units/ml, respectively, and RNase digestion continued at 37 °C for 15 min. The proteoliposomes were then washed with 3 ml of liposome washing buffer (5 mM HEPES-KOH, pH 7.5, 2 mM DTT, 5 mM EDTA) and the vesicles recovered by centrifugation at 120,000 x g for 30 min at 4 °C. RNA was isolated from the liposomes as described previously (12, 16).
ATPase AssayRIC (10 ng) or proteoliposomes reconstituted with 10 ng of RIC (25 µg of phopholipid) was incubated in a 5-µl reaction with 1 mM [
-32P]ATP (specific activity 2000 cpm/pmol) in 10 mM Tris-HCl, pH 8.0, 10 mM MgAc2, and 2 mM DTT, in the presence or absence of low specific activity (5000 cpm/pmol) tRNA (5 nM) as indicated. Inhibitors were preincubated with RIC or proteoliposomes on ice for 15 min prior to addition of the assay mix. After incubation at 37 °C for 10 min, 1 µl of each reaction was mixed with 1 µl of 1% SDS, deoxycholate, or Triton X-100 and spotted on prewashed polyethyleneimine (PEI) cellulose thin layer chromatography (TLC) plates (Sigma), essentially as described previously (17). The plates were developed by sequential runs in 0.1 M acetic acid and 1 M LiCl and autoradiographed. Radioactive spots were quantified by liquid scintillation counting or densitometry. Apparent Km values were estimated from rate curves as the concentration of ATP or tRNATyr for half-maximal activity (pmol of ATP hydrolyzed per min). To determine the site of ATP hydrolysis, proteoliposomes were washed with isotonic sucrose-Tris-EDTA (STE; Ref. 8) and separated from free, i.e. external ATP by centrifugal ultrafiltration with a Microcon 30 ultrafilter (Amicon) at 16,000 x g, and resuspended in 10 µl of STE for TLC.
Rhodamine 123 Uptake AssayRIC-proteoliposomes (10 µg of lipid and 3 ng of RIC) were incubated with 0.05% rhodamine 123 in 10 µl of import buffer with 4 mM ATP for 15 min at 37 °C. Wherever indicated, liposomes were preincubated with inhibitors at 4 °C for 15 min. The proteoliposome suspension was mixed with an equal volume of STE containing 20% glycerol and observed under a Leica DMIRB inverted confocal microscope with laser excitation at 488 nm and emission at 540668 nm. Images at x1000 magnification were analyzed and quantified by the Leica SP2 confocal software. The mean fluorescence intensity per particle was calculated as the product fav x nf, where fav = average intensity of fluorescence in stained particles, and nf = fraction of particles staining above background.
| RESULTS |
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-32P]ATP and radiolabeled Pi separated by thin layer chromatography. At high concentrations of RIC, a nonspecific ATPase activity was observed (data not shown). However, at low RIC concentrations, ATP hydrolysis was stimulated
16-fold by the import substrate tRNATyr (Fig. 1A). In contrast, tRNAGln(CUG), which is not imported in vivo or in vitro, had only a 4-fold effect (Fig. 1A); total Escherichia coli tRNA had no effect (data not shown). The preference of ATPase stimulatory activity for an importable tRNA indicates the relevance of this ATPase to import. From rate curves (Fig. 1C), the apparent
for ATP hydrolysis was 0.98 nM, which is close to the value of 1.16 nM for RIC-mediated import (12). Similarly,
for the ATPase was 1.32 mM, compared with 1.35 mM for import (12).
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Import both in vitro (11, 12) and in transfected cells (14) has been shown to be sensitive to oligomycin, a specific inhibitor of the mitochondrial F1-F0-ATPase. Oligomycin apparently exerts its effect by reducing the permeability of the F0 portion of the enzyme to protons (18). The ATPase activity of RIC was resistant to oligomycin, both in the free (Fig. 1D) and membrane-bound (Fig. 1E) forms. Thus, the oligomycin-sensitive step in import must be after the initial ATP hydrolysis step.
ATP Hydrolysis Inside the LiposometRNA-stimulated ATP hydrolysis by membrane-bound RIC could occur on either side of the liposome membrane. The site of hydrolysis was determined in two ways. First, we had previously observed that import in intact mitochondria (11) or mitoplasts2 is sensitive to carboxyatractyloside, a specific inhibitor of the adenine nucleotide translocator (ANT) on the inner membrane, suggesting the requirement of transport of ATP into the matrix. In the RIC-liposome system, tRNA uptake was similarly sensitive to carboxyatractyloside (Fig. 3C). In the same system, ATP hydrolysis was also inhibited by the drug, but the ATPase activity of the free RIC was unaffected (Fig. 1, F and G). These results are consistent with the presence of ANT, or an ANT-like carrier, in the complex and further indicate that upon insertion of RIC into the membrane the ATPase active site is exposed to the inner compartment.
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-32P]ATP and separated from free ATP by ultrafiltration. When the liposomes were directly run on TLC plates, most of the radioactivity was concentrated near the origin, with little or no free Pi near the solvent front (Fig. 1H, lane 2). However, Pi was released upon treatment of the liposomes with Triton X-100 (Fig. 1H, lane 1). In a control experiment, free RIC was similarly incubated with ATP and ultrafiltered; neither ATP nor Pi was detected in the retentate (Fig. 1H), excluding the possibility of RIC itself binding or protecting significant amounts of these molecules. This experiment confirms the uptake and hydrolysis of ATP within the proteoliposome. RIC- and tRNA-dependent Generation of Membrane PotentialThe lipophilic cationic dye rhodamine 123 is taken up into respiring mitochondria of living cells in a membrane potential-dependent manner (19). We have previously observed uptake of rhodamine 123 into isolated Leishmania mitochondria in presence of ATP (11). The availability of the RIC-liposome system allowed the development of a microscopic assay of membrane potential generation by rhodamine 123 uptake.
Control or RIC-reconstituted liposomes were incubated with tRNA and ATP and uptake of rhodamine 123 monitored by confocal fluorescence microscopy. About 80% of the vesicles became labeled in the complete system (Fig. 2). Uptake was dependent on the presence of RIC, ATP, and tRNATyr. ATP could not be substituted by the non-hydrolyzable analogue AMPPCP, showing a requirement for ATP hydrolysis. tRNATyr could not be replaced by the non-importable tRNAGln(CUG). Moreover, uptake was inhibited by the protonophore uncoupler m-chlorocarbonylcyanide phenylhydrazone (CCCP), which dissipates trans-membrane proton gradients; this implies that the membrane potential is generated by RIC-mediated pumping of protons. Uptake was also completely sensitive to oligomycin, a proton channel blocker. Inhibition of ATP transport by carboxyatractyloside abolished uptake of rhodamine 123, implying the requirement of ATP hydrolysis within the vesicles. These results indicate the generation of a membrane potential (negative inside) by a proton pump activity of RIC.
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) of the protonmotive force, whereas nigericin, which exchanges H+ for K+, disrupts the chemical component (
pH) without affecting 
. Thus, these experiments indicate the requirement of both components for RIC-mediated import. An interesting difference between ATP-dependent and proton-dependent import was observed with respect to their responses to oligomycin. Whereas ATP-dependent import was sensitive to oligomycin (Fig. 3B), proton-dependent import was resistant (Fig. 3E). This indicates that, in the energy-transduction pathway, the oligomycin-sensitive step occurs between ATP hydrolysis and proton-driven translocation, i.e. at the step of proton extrusion with concomitant generation of a membrane potential (see above).
| DISCUSSION |
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; 6) the tRNA is transported through the import pore. Excess external protons (
pH) are required at this step. The protons may act to neutralize the negative charges on the RNA phosphate groups or line the pore to allow "electrophoretic" translocation of the RNA.
The RNA-stimulated ATPase (which we designate as R-ATPase) appears to be functionally related to, but distinct from, the mitochondrial respiratory F-ATPase and the vacuolar V-ATPase (for a comparison of the latter two enzymes, see Ref. 20). In all three cases ATP hydrolysis is coupled to proton translocation across the membrane. Moreover, proton movement occurs away from the compartment in which ATP hydrolysis is occurring, and both F- and R-ATPases, in their membrane-bound form, pump protons in an oligomycin-sensitive manner. There are also structural similarities; spherical particles resembling the knobs of the F1 sector of F-ATPase have been observed with purified RIC preparations (12). Additionally, our recent peptide sequencing studies3 reveal the occurrence of an RIC subunit with homology to the
-subunit of F-ATPase, which is also present in V-ATPase (20). Thus the F-, V-, and R-ATPases may belong to a superfamily of multiprotein complexes dedicated to different intracellular functions.
One interesting aspect of the RIC is the ease with which it induces tRNA translocation across membranes; simple addition to, or preincubation with membrane vesicles, whether liposomes (12) or mitoplasts or intact mitochondria (unpublished data), is sufficient, and exhaustive reconstitution by dialysis, as is common with respiratory complexes (21), is unnecessary. This suggests a facile insertion of the complex into membranes. Moreover, membrane insertion of the complex may be non-random. This is indicated by the fact that in the reconstituted liposome, ATP hydrolysis occurs internally, and the R-ATPase activity is totally sensitive to carboxyatractyloside (Fig. 1), whereas the soluble ATPase is resistant, implying that most or all of the ATPase active sites are internal to the membrane; random insertion would be expected to yield about 50% carboxyatractyloside-resistant ATPase activity. The mechanism of facile, non-random insertion is unknown; one possibility is insertion via a lipid anchor of the type found in Leishmania and Trypanosoma surface glycoproteins (22).
It is curious that the mitochondrial inner membrane contains a mechanism for generating a membrane potential that is independent of respiratory chain-mediated electron transport; indeed, we have observed that with intact mitochondria or mitoplasts, respiratory substrates such as succinate, citrate, etc. are unable to replace ATP as an energy source for import.4 Thus the question arises as to whether the tRNA-dependent proton gradient generated by RIC is dedicated to import or whether it can be utilized under certain conditions to catalyze other inner membrane transport processes. The present study reveals the presence of several entities within the RIC that appear to be related to known mitochondrial components involved in ATP synthesis and transport: an oligomycin-sensitive ATPase, proton channels, and an ATP carrier. It will be important to identify the corresponding proteins to establish the relationship between tRNA import and oxidative phosphorylation.
| FOOTNOTES |
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Received a Fellowship from the Council of Scientific and Industrial Research. ![]()
To whom correspondence should be addressed. Tel.: 91-33-2473-3491 (ext. 136); Fax: 91-33-2473-5197; E-mail: sadhya{at}iicb.res.in.
1 The abbreviations used are: RIC, RNA import complex; DTT, dithiothreitol; PEI, polyethyleneimine; TLC, thin layer chromatography; STE, sucrose-Tris-EDTA; ANT, adenine nucleotide translocator; AMPPCP, adenosine 5'-(
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-methylene)triphosphate; CCCP, m-chlorocarbonylcyanide phenylhydrazone. ![]()
2 S. N. Bhattacharyya and S. Adhya, unpublished data. ![]()
3 S. N. Bhattacharyya, S. Chatterjee, S. Goswami, and S. Adhya, unpublished data. ![]()
4 S. N. Bhattacharyya, S. Mukherjee, and S. Adhya, unpublished data. ![]()
| ACKNOWLEDGMENTS |
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| REFERENCES |
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