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© The Rockefeller University Press,
0021-9525/2002/11/403 $5.00
The Journal of Cell Biology, Volume 159, Number 3, 403-410
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Accumulation of endoplasmic membranes and novel membrane-bound ribosomesignal recognition particle receptor complexes in Escherichia coli
Address correspondence to Eitan Bibi, Dept. of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel. Tel./Fax: 972-8-934-3464. E-mail: bcbibi{at}wicc.weizmann.ac.il
| Abstract |
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In Escherichia coli, ribosomes must interact with translocons on the membrane for the proper integration of newly synthesized membrane proteins, cotranslationally. Previous in vivo studies indicated that unlike the E. coli signal recognition particle (SRP), the SRP receptor FtsY is required for membrane targeting of ribosomes. Accordingly, a putative SRP-independent, FtsY-mediated ribosomal targeting pathway has been suggested (Herskovits, A.A., E.S. Bochkareva, and E. Bibi. 2000. Mol. Microbiol. 38:927939). However, the nature of the early contact of ribosomes with the membrane, and the involvement of FtsY in this interaction are unknown. Here we show that in cells depleted of the SRP protein, Ffh or the translocon component SecE, the ribosomal targeting pathway is blocked downstream and unprecedented, membrane-bound FtsYribosomal complexes are captured. Concurrently, under these conditions, novel, ribosome-loaded intracellular membrane structures are formed. We propose that in the absence of a functional SRP or translocon, ribosomes remain jammed at their primary membrane docking site, whereas FtsY-dependent ribosomal targeting to the membrane continues. The accumulation of FtsY-ribosome complexes induces the formation of intracellular membranes needed for their quantitative accommodation. Our results with E. coli, in conjunction with recent observations made with the yeast Saccharomyces cerevisiae, raise the possibility that the SRP receptormediated formation of intracellular membrane networks is governed by evolutionarily conserved principles.
Key Words: E. coli; signal recognition particle; ribosome; protein targeting; membrane proteins
| Introduction |
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-subunit of the eukaryotic SRP-receptor, SR
) (Bernstein et al., 1989; Romisch et al., 1989). The Ffh protein is important for proper assembly of integral membrane proteins (Macfarlane and Muller, 1995; de Gier et al., 1996; Ulbrandt et al., 1997), and FtsY is required for their expression (Seluanov and Bibi, 1997; unpublished data). Interestingly, only FtsY was shown to be essential for membrane targeting of ribosomes in vivo (Herskovits and Bibi, 2000), suggesting an alternative SRP-independent, FtsY-mediated targeting of ribosomes to the cytoplasmic membrane in E. coli (Herskovits et al., 2000). After targeting to the cytoplasmic membrane, ribosomes are transferred to the SecYEG site (the E. coli translocon) (Fig. 1, f) (Valent et al., 1998; Prinz et al., 2000a) or other translocation sites (Cristobal et al., 1999), but the molecular details of their initial interaction(s) with the membrane have remained unclear. Possibly, these interactions are transient and therefore attempts to isolate the relevant complexes in E. coli (other than the ribosometranslocon complex) have thus far been unsuccessful. We reasoned that by blocking essential targeting steps downstream, the putative transient ribosome-membrane contact(s) might be stabilized and prolonged. Our results show that under conditions of efficient depletion of the translocon or the SRP, membrane-bound ribosomal complexes containing FtsY are indeed accumulated, in accordance with the proposed role of FtsY in membrane targeting of ribosomes (Herskovits et al., 2000). Moreover, in both cases, novel endoplasmic membrane networks are synthesized possibly in response to the increase in the number of membrane-bound ribosomes. We propose that the FtsY-ribosome complexes represent primary membrane-docking sites for ribosomes in E. coli.
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| Results and discussion |
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FtsY forms a membrane-bound complex with the ribosome in the absence of Ffh
Next, we examined the interaction between FtsY and membrane-bound ribosomes in depleted and nondepleted cells using coimmunoprecipitation assays. Briefly, membranes purified from Ffh- and SecE-depleted cells were solubilized by digitonin, and the solubilized material was immunoprecipitated with immobilized, affinity-purified anti-FtsY antibodies, or anti-GroEL antibodies as a control. Samples containing equal amounts of immunoprecipitated FtsY (unpublished data) were subjected to Western blotting with antibodies to FtsY, L15, and Ffh. As shown in Fig. 1 d, anti-FtsY beads always precipitated in addition to FtsY also the ribosomal protein L15, indicating that FtsY interacts with membrane-bound ribosomes. In nondepleted samples, Ffh was also precipitated, as might be expected if some posttargeting intermediates exist (Murphy et al., 1997; Song et al., 2000; Fig. 1 f). However, a significantly lower amount of Ffh was coprecipitated with equal amounts of FtsY from the SecE-depleted samples, suggesting that some of the complexes do not contain Ffh. This was further confirmed by using saturating amounts of anti-FtsY beads (unpublished data). Furthermore, the surprising possibility that FtsY and ribosomes form complexes in the absence of SRP (Fig. 1 f) is strongly supported by the results obtained with Ffh-depleted samples, where in the absence of detectable amounts of Ffh, ribosomal proteins coprecipitated efficiently with the anti-FtsY beads (Fig. 1 d). In control experiments, the ability of anti-FtsY antibodies to immunoprecipitate ribosomes in the absence of FtsY was tested. Extracts of FtsY-depleted or nondepleted cells were ultracentrifuged, and the total ribosomal pellets (membrane and cytosolic ribosomes) were solubilized by digitonin. The solubilized material was subjected to immunoprecipitation with anti-FtsY beads. The results clearly show that despite the large amount of ribosomes, the anti-FtsY beads precipitated ribosomes only in the presence of FtsY (Fig. 1 e). Finally, in reverse coimmunoprecipitation experiments, we tested the ability of anti-ribosomal protein antibodies to precipitate FtsY from membranes of Ffh-depleted cells. For this purpose, a hybrid L1-YFP was constructed (Fig 5 a), and coimmunoprecipitation with anti-GFP beads showed that antibodies to the hybrid ribosomal protein efficiently precipitated other ribosomal proteins such as L27, and also FtsY, from solubilized Ffh-depleted membranes (Fig. 1 e). To our knowledge, this is the first demonstration of an interaction between the SRP receptor and membrane-bound ribosomes, in the absence of SRP. This complex may therefore represent the initial ribosome docking site on the E. coli membrane.
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58% of all ribosomes are membrane-bound (Randall and Hardy, 1977; Herskovits and Bibi, 2000). Therefore, the accumulation of membrane-bound ribosomes in cells depleted of Ffh or SecE raised the question as to how the cytoplasmic membrane can accommodate such an increased amount of ribosomes. In order to investigate this issue, the morphology of Ffh- and SecE-depleted cells was examined by transmission EM (TEM). Although TEM sections from nondepleted cells (Fig. 2, a) or FtsY-depleted cells (Fig. 2 b) look similar, sections of Ffh- or SecE-depleted cells revealed tightly packed intracellular membrane structures (Fig. 2, c and e). At a higher magnification, the bilayers of these membranes (Fig. 2, d and f) are clearly apparent, as well as the ribosomes (Fig. 2, c, d, and f, arrowheads) that surround the membrane structures.
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In summary, we have described the identification of unprecedented membrane-bound complexes, which contain ribosomes and FtsY, but not Ffh. Such ribosomeFtsY complexes presumably accumulate when the final steps of ribosomal targeting to the translocon are blocked, and therefore may represent an early ribosome-docking step during the biosynthesis of membrane proteins. These results lend further support to our previous proposal that in addition to the suggested SRP-dependent pathway for membrane targeting of ribosomes in E. coli, an alternative, Ffh-independent pathway exist, in which FtsY plays a central role (Herskovits and Bibi, 2000; Herskovits et al., 2000, 2001). The later pathway implies that FtsY mediates constant supply of essential membrane bound ribosomes. According to this model, the transfer of these ribosomes to the translocon requires recognition of newly translated hydrophobic nascent peptides by SRP. This scenario implies that the SRP can also function downstream of FtsY during the biosynthesis of SRP substrates (Fig. 1 f). This model is currently being examined by additional studies of putative steps along the pathway of membrane protein biogenesis in E. coli. Future studies will also determine whether the interaction between the receptor and the ribosome is direct or mediated by additional components, such as a functional analogue of the ß-subunit of the mammalian SRP-receptor (Fig. 1 f; Bacher et al., 1999; Fulga et al., 2001).
Finally, the accumulation of membrane-bound ribosomeFtsY complexes is intriguingly linked to the production of novel endoplasmic membrane networks, suggesting that these two consequences of Ffh- or SecE-depletion are related. In this regard, it has been shown recently that in the yeast Sacharomyces cerevisiae, the ER morphology is disrupted by conditional mutations in SP101 and SP102, encoding the respective
- and ß-subunits of the SRP receptor (Prinz et al., 2000c). Accordingly, it was suggested that the role of the SRP receptor in maintaining the ER structure is related to its known function in targeting ribosomes to the ER membrane. Thus, our results in E. coli bring about a possibility that the principles of ribosome targeting and intracellular membrane network formation are evolutionarily conserved.
| Materials and methods |
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Cell fractionation
Membranes were purified as described previously (Herskovits and Bibi, 2000) with some modifications. Usually, a 10 liter-cultures was harvested, and washed in buffer R (25 mM K-Hepes, pH 7.6, 150 mM KOAc, 10 mM Mg(OAc)2, 1 mM PMSF) supplemented with 0.25 M sucrose and 20 µg/ml RNAse-free DNase. After French Press treatment (four times at 8000 psi), and removal of cell debris, membranes were collected by ultracentrifugation (1.5 h, 53,000 rpm) and resuspended in buffer R. The membranes were further purified by flotation in a step-wise sucrose gradient (8 h, 39,000 rpm, 4°C) using SW41 rotor (Beckman Coulter). The isolated membranes were washed in buffer R supplemented with 0.25 M sucrose, and aliquots of 2 mg membrane proteins were frozen in liquid nitrogen and stored at -80°C.
Membrane solubilization, density gradient separation, and immunoprecipitation
1 mg/ml of membrane proteins was solubilized in buffer R containing 3% digitonin (Calbiochem), and 1 mM dithiotreithol. After a 40-min incubation at room temperature and 2 h at 10°C the mixture was separated in 10 ml of 520% sucrose gradients prepared in buffer R containing 0.1% digitonin, by ultracentrifugation (1.5 h, 39,000 rpm, 4°C) using SW41 rotor (Beckman Coulter). The migration of ribosomes in the gradients was followed by measuring the absorbance of RNA at O.D.260. Fractions were then precipitated in 10% TCA, separated by SDS-PAGE and analyzed by Western blotting with antibodies to ribosomal proteins. Immunoprecipitation of the solubilized membranes was performed using 4 Fast Flow protein A-Sepharose beads (Amersham Biosciences) covalently coated with purified anti-FtsY antibodies, anti-GFP antibodies (BAbCO) or anti-GroEL antibodies as a control. For cross-linking we used dimethyl pimalidate (Packman and Perhan, 1982). Initially, nonsolubilized material was removed from the digitonin-solubilized membranes (see previous section) by centrifugation through a 20% sucrose cushion (10 min, 67,000 rpm, 4°C) using a TLA100.3 rotor (Beckman Coulter). Samples were incubated with 40 µl of anti-FtsY, anti-GFP or anti-GroEL beads as a control, washed thoroughly and eluted in SDS sample buffer.
Transmission EM
Nondepleted or depleted cells were drawn into cellulose capillary tubes and frozen in a Bal-Tec HPM010 high-pressure freezing machine (Hohenberg et al., 1994). Cells were subsequently freeze-substituted in a Leica AFS device in anhydrous acetone containing 0.1% osmium tetroxide for 3 d at -90°C and then warmed up to 0°C over 24 h. Samples were embedded in Epon; 6080-nm sections, stained with uranyl acetate and lead citrate and examined in an FEI Tecnai T12 electron microscope operating at 120 kV.
Membrane staining and confocal microscopy
For staining, cells were incubated with 2.5 µg/ml DiOC6 (3,3'-dihexyloxacarbocyanine iodide) or 0.5 µM Mito Tracker Deep Red 633 (Molecular Probes) for 5 and 15 min, respectively, on ice. The cells were washed three times with 10 mM potassium phosphate buffer, pH 7.4, 0.14 M NaCl, fixed in 0.25% glutaraldehyde for 10 min and washed again. The stained cells were observed using the FV500 laser scanning confocal microscope and the Fluoview software (Olympus). The following filters were used (excitationemission): for DiOC6 and L1-YFP fluorescence, 488525 nm; Mito Tracker Deep Red 633, 633665 nm.
In vivo lipid radiolabeling
E. coli WAM113 cells were grown in LB broth with and without arabinose for 5 h at 37°C. After 1 h, 1 µCi/ml of [2-14C]-acetate and 10 µCi/ml of L-[3-3H]-serine (Amersham Biosciences) were added to the cultures. At various time points samples were withdrawn and subjected to phospholipids extraction (Folch et al., 1957) and total protein determination. Lipids were extracted as follow: cells (1 ml samples) were washed three times in LB and transferred to a tube containing 3 ml chloroform/methanol (2:1). After 2 h incubation at room temperature, the mixture was diluted by addition of 1 ml of water, mixed and centrifuged for 5 min at 1,400 rpm. After removal of the water-methanol phase, the chloroform phase was washed twice by 2 ml of water/methanol (1:1) and centrifuged for 5 min at 1,400 rpm. Finally, ethanol (0.5 ml) was added to the chloroform phase and the samples were dried under nitrogen. For determination of the incorporated radioactivity, the dried pellets were resuspended in 2 ml of benzene:methanol (1:1) and 0.5 ml samples were transferred to scintillation vials containing scintillation fluid Ultima Gold (Sigma-Aldrich).
Ribosome labeling
For the construction of L1-YFP, the chromosomal gene for L1, rplA was amplified by PCR and cloned upstream to the YFP encoding gene using the pEYFP plasmid (CLONTECH Laboratories, Inc.). E. coli WAM113 expressing the L1-YFP hybrid were grown with or without arabinose, and subjected to confocal microscopy.
| Footnotes |
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| Acknowledgments |
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This work was supported by the Israel Science Foundation founded by the Israel Academy of Sciences and Humanities, and in part by the German-Israeli Foundation for Scientific Research and Development.
Submitted: 29 April 2002
Revised: 3 October 2002
Accepted: 3 October 2002
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