Predominant membrane localization is an essential feature of the bacterial signal recognition particle receptor
© Mircheva et al. 2009
Received: 24 September 2009
Accepted: 13 November 2009
Published: 13 November 2009
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© Mircheva et al. 2009
Received: 24 September 2009
Accepted: 13 November 2009
Published: 13 November 2009
The signal recognition particle (SRP) receptor plays a vital role in co-translational protein targeting, because it connects the soluble SRP-ribosome-nascent chain complex (SRP-RNCs) to the membrane bound Sec translocon. The eukaryotic SRP receptor (SR) is a heterodimeric protein complex, consisting of two unrelated GTPases. The SRβ subunit is an integral membrane protein, which tethers the SRP-interacting SRα subunit permanently to the endoplasmic reticulum membrane. The prokaryotic SR lacks the SRβ subunit and consists of only the SRα homologue FtsY. Strikingly, although FtsY requires membrane contact for functionality, cell fractionation studies have localized FtsY predominantly to the cytosolic fraction of Escherichia coli. So far, the exact function of the soluble SR in E. coli is unknown, but it has been suggested that, in contrast to eukaryotes, the prokaryotic SR might bind SRP-RNCs already in the cytosol and only then initiates membrane targeting.
In the current study we have determined the contribution of soluble FtsY to co-translational targeting in vitro and have re-analysed the localization of FtsY in vivo by fluorescence microscopy. Our data show that FtsY can bind to SRP-ribosome nascent chains (RNCs) in the absence of membranes. However, these soluble FtsY-SRP-RNC complexes are not efficiently targeted to the membrane. In contrast, we observed effective targeting of SRP-RNCs to membrane-bond FtsY. These data show that soluble FtsY does not contribute significantly to cotranslational targeting in E. coli. In agreement with this observation, our in vivo analyses of FtsY localization in bacterial cells by fluorescence microscopy revealed that the vast majority of FtsY was localized to the inner membrane and that soluble FtsY constituted only a negligible species in vivo.
The exact function of the SRP receptor (SR) in bacteria has so far been enigmatic. Our data show that the bacterial SR is almost exclusively membrane-bound in vivo, indicating that the presence of a soluble SR is probably an artefact of cell fractionation. Thus, co-translational targeting in bacteria does not involve the formation of a soluble SR-signal recognition particle (SRP)-ribosome nascent chain (RNC) intermediate but requires membrane contact of FtsY for efficient SRP-RNC recruitment.
The signal recognition particle (SRP) dependent targeting constitutes a universally conserved protein targeting pathway that ensures the co-translational delivery of substrates to the membrane-bound Sec translocon . Co-translational targeting is achieved because SRP recognizes its cargo early in translation [2, 3]. Subsequently, the SRP-ribosome nascent chain complex (SRP-RNC) is targeted to the membrane-bound SRP receptor (SR) [4, 5], which in eukaryotes is composed of two GTPase subunits. SRα is tethered to the ER membrane via the membrane integral SRβ subunit and is responsible for binding the SRP-RNC. However, SRβ is not only required for the anchoring of SRα to the membrane, it is also involved in coordinating the transfer of the RNC to the Sec translocon [6, 7].
Despite its conservation, the SRP-dependent targeting in bacteria such as Escherichia coli deviates from the eukaryotic pathway because, here, SRP delivers almost exclusively inner membrane proteins, while secretory proteins are targeted by the post-translational SecA/SecB pathway . In addition, the bacterial SR consists of only the SRα homologue FtsY, but lacks a membrane-integral SRβ subunit. However, FtsY can bind to the E. coli membrane via two lipid-binding helices, one located at the N-terminus of FtsY and a second at the interface between the non-essential A-domain and the essential N-domain [8, 9]. Deleting both lipid-binding helices prevents targeting [9–11], which supports data showing that only membrane-bound FtsY is able to induce efficient dissociation of SRP from the RNC . FtsY also contacts the Sec translocon directly [10, 13, 14], suggesting that in bacteria a single polypeptide is sufficient for the binding of SRP-RNCs to the membrane and for coordinating their transfer to the Sec translocon.
Despite the importance of the FtsY-membrane interaction, in cell fractionation studies about 60% of FtsY were found in the cytosolic cell fraction and only 40% at the membrane . However, the function of the soluble FtsY is still largely enigmatic. Despite its inability to induce SRP release from the RNCs, in vitro data have shown that soluble FtsY is able to associate with SRP in the absence of membranes [16–20] and that the presence of RNCs strongly accelerates the FtsY-SRP complex formation in solution . These data are consistent with a model in which FtsY binds to SRP-RNCs already in the cytosol and then targets the SRP-RNC complex to the membrane . Nevertheless, the formation of a soluble FtsY-SRP-RNC complex is probably not a prerequisite for cotranslational targeting in bacteria, because FtsY derivatives which are permanently membrane-tethered via a transmembrane domain are functional in vivo .
In the current study we have analysed the contribution of soluble FtsY to cotranslational targeting in vitro and found that, although FtsY can bind to SRP-RNCs in solution, these soluble FtsY-SRP-RNC complexes were not efficiently targeted to the membrane. Furthermore, we re-examined the localization of FtsY in vivo by fluorescence microscopy and found it almost exclusively located at the cytoplasmic membrane.
The presence of a predominantly soluble SRP receptor in bacteria has led to the hypothesis that FtsY binds to SRP-RNCs already in the cytosol and then targets the SRP-RNCs to the membrane . Several studies have shown that FtsY is able to interact with SRP or SRP-RNCs in solution, that is, in the absence of membranes [16–21]. However, whether FtsY-SRP-RNC complexes which were assembled in the absence of membranes are efficiently targeted to the membrane, has not so far been analysed.
By adding purified FtsY and the RNCs to FtsY-depleted INV, we were unable to distinguish between targeting that involves the formation of soluble FtsY-SRP-RNC complexes and targeting that is achieved because FtsY binds to the membrane first and only then accepts the SRP-RNCs. We therefore incubated FtsY-depleted IY28 INV with purified FtsY and re-isolated these reconstituted INV by centrifugation before adding the MtlA-189 RNCs. Flotation gradient analyses revealed significant targeting of MtlA-189 RNCs to the reconstituted IY 28 INV (Figure 2B).
Western blotting confirmed that FtsY was almost undetectable in FtsY-depleted INV (Figure 2C) and revealed that the FtsY content of the reconstituted IY28 INV was comparable to that of wild-type INV (Figure 2C). Antibodies against the membrane protein YidC were used as a control in order to ensure that comparable amounts of protein were loaded (Figure 2C). As the in vitro transcription/translation system used in these experiments does not contain soluble FtsY (, Figure 2D), these data demonstrate that the formation of a soluble FtsY-SRP-RNC complex is obviously not essential for efficient targeting.
The targeting of the SRP-MtlA-189 RNC complexes and the FtsY-SRP-MtlA-189 RNC complexes was then analysed using flotation gradient analyses. Efficient targeting of SRP-MtlA-189 RNCs was observed only when membrane-bound FtsY was present - for example, in the presence of wild-type INV or FtsY-reconstituted IY28 INV - but not with FtsY-depleted IY28 INV (Figure 3B). Strikingly, we did not observe efficient targeting of soluble FtsY-SRP-MtlA-189 RNCs complexes to FtsY-depleted IY28 INV (Figure 3B). Although a complex formation between FtsY and SRP-RNCs is possible in solution, this early interaction obviously does not permit the subsequent membrane targeting. It is important to emphasize that the addition of GMP-PNP does not prevent targeting, because GTP hydrolysis is not required for the insertion of the signal peptide into the translocon but rather for the dissociation of the SRP-SR complex .
The in vitro data demonstrated that soluble FtsY does not contribute significantly to co-translational targeting and so it is possible that soluble FtsY is involved in processes other than SRP-dependent targeting. This could also explain the vast excess of FtsY over SRP (10.000 molecules FtsY versus 100 molecules Ffh/E. coli cell) . Alternatively, because FtsY is only peripherally attached to the membrane [8, 11], it is also conceivable that during cell breakage a significant fraction of FtsY is detached from the membrane. We therefore analysed the distribution of FtsY in E. coli by non-invasive fluorescence microscopy using an FtsY derivative with a C-terminally fused GFP-(green fluorescent protein) tag. The functionality of this construct was confirmed by testing its ability to suppress the growth defect of IY28 cells. These cells, carrying only the arabinose-inducible endogenous ftsY gene, are unable to grow on fructose-containing plates (Figure 4B). However, expressing plasmid-borne copies of wild-type FtsY, or of the FtsY-GFP construct, in trans restored growth completely (Figure 4B). As a control, we also fused GFP to the C-terminus of the FtsY mutants FtsY(B3) and FtsY(NG+1). Both FtsY derivatives carry mutations/deletions in the lipid-binding domains of FtsY and show reduced membrane binding [9, 28]. As a result, they are only partially active and were unable to completely restore the growth of IY28 on fructose media, despite their higher expression level in comparison to endogenous FtsY (Figure 4C)
In E. coli and other proteobacteria, membrane localization of FtsY is mainly achieved via two cooperating lipid binding domains; in Gram positive bacteria and archaea, FtsY contains either a true transmembrane helix or a single, but extended, lipid-binding helix [29–31]. We therefore analysed the localization of FtsY also in the Gram positive bacterium Bacillus subtilis by creating a C-terminal YFP (yellow fluorescent protein) fusion. B. subtilis cells expressing only the FtsY-YFP fusion from the original gene locus were viable, indicating that FtsY-YFP was a functional substitute of the essential endogenous FtsY . Unlike E. coli FtsY, B. subtilis FtsY formed defined foci along the lateral cell membrane (Figure 5C, indicated by white triangle), and occasionally at the cell poles (in 20% of the cells showing defined signals). We did not detect FtsY foci in about 25% of all cells, probably because they were too faint. Fluorescence within the cytosol was similar to background fluorescence in cells lacking any YFP fusion, showing that, despite the differences in the mode of membrane binding between E. coli FtsY and B. subtilis FtsY, the latter is also highly enriched at the cytoplasmic membrane (Figure 5C).
So far, the function of soluble FtsY in E. coli and other prokaryotes has been mysterious, and our data now demonstrate that soluble FtsY represents only a minor species in vivo. The high amount of soluble FtsY observed after cell fractionation is most likely to be an artefact of cell breakage. Thus, the exclusive membrane localization of FtsY/SRα appears to be an evolutionary conserved feature, although the exact mechanisms of tethering FtsY/SRα to the membrane are different. In eukaryotes, it is mainly achieved via the protein-protein contact to SRβ, while in prokaryotes, protein-lipid contact is dominating [8, 9, 11]. These differences in the mode of membrane binding also explain why only the SRP- and GTP-interacting NG domains of FtsY/SRα are highly conserved, while the low conserved N-terminal domains are adapted to their particular mode of membrane binding.
The predominant membrane localization of FtsY in bacteria also mitigates an otherwise crucial obstacle to the bacterial SRP cycle: if SRP and FtsY interacted efficiently with each other in the cytosol, they would probably undergo futile cycles of GTP hydrolysis. To prevent this, FtsY-SRP complex formation or stability should respond to cargo loading. Kinetic studies have demonstrated that the formation of the SRP-SR complex is slow in the absence of RNCs [4, 21, 32, 33]. However, even in the presence of cargo, significant GTP hydrolysis and complex dissociation is observed in the solution . Thus, to prevent futile GTP hydrolysis, the GTPase cycle should also respond to the presence of membranes. A recent study has shown that mutating the lipid binding domain in chloroplast FtsY results in the loss of membrane-induced GTPase stimulation and higher rates of GTP hydrolysis in solution ; a similar link between GTP hydrolysis and membrane binding has also been proposed in E. coli .
Biochemical data have shown that FtsY binds preferentially to negatively charged phospholipids [8, 11, 35] and at least transiently to the SecY translocon [10, 13, 14]. Due the limited number of SecYEG translocons (300-500/E. coli cell, ), the exclusive membrane localization of FtsY suggests that in vivo FtsY is mainly bound to phospholipids. However, this probably excludes phospholipids as major player in regulating co-translational protein targeting in bacteria. Instead, the FtsY-translocon contact might be the key element in controlling the GTPase cycle and the insertion of the substrate into the translocation channel. In eukaryotes, the GTPase domain of the SRβ subunit appears to be crucial for the coordination of RNC binding with the subsequent transfer to the Sec translocon [4, 6, 7, 36]. As FtsY can directly interact with the SecYEG translocon [10, 13, 14], the SRP receptor in prokaryotes can probably mediate both functions: binding of the SRP-RNCs and coordinating their transfer to the Sec translocon.
So far, the kinetic analyses of the bacterial SRP cycle have only been performed in the absence of membranes and, in some cases, with N-terminal truncated FtsY derivatives lacking at least the first lipid-binding domain [20, 21, 37, 38]. Although these studies have provided a wealth of important information about the SRP cycle, it is essential to determine the impact of membranes and the Sec translocon on the kinetics of the SRP cycle in future studies. Finally, our data also show that, although FtsY can bind to SRP-RNCs, in solution it fails to efficiently target these SRP-RNCs to the membrane. It seems likely that the interaction of FtsY with SRP-RNCs in solution interferes with the subsequent binding of FtsY to lipids or SecY, although this needs to be confirmed. Nevertheless, considering that soluble FtsY obviously represents only a minor species in E. coli, its low targeting activity should not impose any problems for the cell.
The prokaryotic SRP receptor lacks a membrane-integral SRβ subunit and has been mainly localized to the cytosolic cell fraction after cell breakage. This predominant cytosolic localization has been taken as an indication that, in bacteria, the SRP receptor interacts with the SRP-RNCs already in the cytosol and then targets them to the membrane. Our in vivo data now show that, despite the lack of a SRβ subunit, FtsY is almost exclusively membrane bound in bacteria and that targeting of SRP-RNCs is only possible when FtsY is membrane-bound. Thus, the exclusive membrane localization of FtsY/SRα appears to be an evolutionary conserved feature, although the exact mechanisms of tethering FtsY/SRα to the membrane are different between prokaryotes and eukaryotes.
The following E. coli strains were used: Bl21, MRE 600 , TY0  and IY28 (obtained from Eitan Bibi). The conditional FtsY-depletion strain IY28 was routinely grown on LB medium supplemented with 0.4% arabinose. For FtsY-depletion, IY28 was grown overnight on media supplemented with 0.2% arabinose. After harvesting the cells by centrifugation, cells were washed twice with media lacking arabinose and used to inoculate cultures containing either 0.2% arabinose to induce FtsY expression or 0.2% fructose for FtsY depletion. Growth was monitored by measuring the optical density at 600 nm. For in vitro protein synthesis the following plasmids were used: pKSM717-MtlA (MtlA) , pTP37 (FtsY)  and pET19b-Ffh . For FtsY-GFP fusions, FtsY was PCR amplified using pTP37 as template and ligated into pTrc99a using NcoI and BamHI restriction, resulting in plasmid pTrc99a-FtsY. pTrc99a-FtsY was then digested with HindIII and the100 bp HindIII fragment (containing the C-terminal His Tag and the stop codon of FtsY) was replaced by a 754 bp long polymerase chain reaction (PCR) product containing the GFP. This PCR product was generated by using the plasmid pCA24NCycY-GFP (National Bioresource Project Japan) and the primer FtsY-GFPfw (5'-GAAACAGTCAAGCTTC-GCGGCC-3') and FtsY-GFPrev (5'-CCTGCAGCCA-AGCTTAATTAGCT-3'). The construction of the FtY(B3) and FtsY NG+1 GFP fusions followed the same strategy, with the exception that the first PCR was performed with pSAFtsY(NG+1)  or pTP37-FtsYB3  as templates.
In order to generate an FtsY-YFP fusion in B. subtilis, the last 500 bp of the ftsY gene were amplified by PCR and were cloned into plasmid pSG1164y  using ApaI and EcoRI restriction sites. B. subtilis PY79 was transformed with the resulting plasmid, selecting for chloramphenicol resistance, leading to an integration of the plasmid into the chromosome at the ftsY locus. All chemicals and growth media components were obtained from Roth (Karlsruhe, Germany) unless otherwise stated.
For cell fractionation, E. coli cells were grown in INV medium at 37°C up to an OD600 of 1.2. After harvesting, the cells were resuspended in buffer A (50 mM triethanolamine acetate, pH 7.5, 0.25 M sucrose, 1 mM EDTA, 1 mM DTT, 5 ml/1 g cells) and broken by three passages through a French Pressure Cell at 8000 psi in the presence of phenylmethylsulfonyl fluoride (1 mM) and Complete-EDTA-free protease inhibitor (Roche, Mannheim, Germany). Unbroken cells and large cell debris were removed by centrifugation for 30 min at 5000 rpm in a SS34 rotor (Kendro-Sorvall, Langenselbold, Germany). The supernatant was then subjected to an ultracentrifugation step to separate the membrane fraction from the soluble fraction. The standard protocol included a centrifugation at 45,000 rpm in a Ti50.2 rotor (Beckman-Coulter, Krefeld, Germany) for 2.5 h at 4°C. The membrane pellet was resuspended in INV buffer (buffer A without EDTA).
The in vitro synthesis of RNCs and flotation gradient analyses of membrane-bound RNCs were performed (as described in [24–26]). For flotation gradients, 1 μl of INV (50 μg protein) were incubated with a 50 μl in vitro reaction mixture. For sedimentation assays, 50 μl RNCs were pelleted through a sucrose cushion (100 μl, 40 mM triethanolamine acetate, pH 7.5; 70 mM potassium acetate; 10 mM magnesium acetate, 1 mM DTT and 580 mM sucrose) for 60 min at 90,000 rpm in a Beckmann 100.2 rotor. In vitro synthesized FtsY and Ffh were purified via Talon metal affinity resin (as described in ) before incubation with RNCs. SRP was reconstituted by incubating purified Ffh and purified 4.5S RNA in a 1:2 ratio for 15 min at 25°C . For reconstituting SRP with in vitro synthesized Ffh, 35S-labelled Ffh was incubated with 1 μg of 4.5S RNA as described above and then purified via Talon metal affinity resin. FtsY, Ffh and 4.5S RNA were purified (as described in [24, 42]). Immune precipitation was performed in fivefold scaled-up reactions using polyclonal rabbit antibodies against FtsY and Ffh, covalently linked to protein A-sepharose matrix . Radioactively labelled proteins were separated on 13% SDS-polyacrylamide gels and visualized using a phosphorimager. The radioactive material was quantified using the Imagequant software (GE Healthcare, Munich, Germany).
In order to investigate GFP-tagged proteins, bacterial cells were immobilized on a microscope slide with low melting agarose. For immune fluorescence, E. coli cells were grown to exponential phase (OD600~0.8 to 1.2) in LB medium supplemented with the appropriate antibiotics and 0.4% arabinose. Five hundred microlitres of culture were fixed with 100 μl 16% paraformaldehyde in phosphate buffered saline (PBS, 10 mM Na2HPO4/NaH2PO4, 150 mM NaCl, 3 mM KCl, pH 7.4) with 0.125% glutardialdehyde for 15 min at room temperature and afterwards for an additional 30 min on ice. Following three washing steps with PBS, cells were resuspended in 500 μl GTE buffer (50 mM glucose, 10 mM EDTA, 20 mM Tris pH 7.5). Lysozyme was added to a final concentration of 2 μg/ml and an appropriate amount of the cell suspension was directly applied to the wells of an eight-well microscope slide (Thermo Scientific, Braunschweig, Germany) coated with Poly-L-Lysine (Sigma Aldrich, Steinheim; Germany). After 5 min of incubation, the excess cells were removed using a vacuum pump and the wells were washed once with PBS. The samples were then blocked with 2% bovine serum albumine in PBS for 15 min at room temperature. Primary antibodies (rabbit-raised polyclonal anti-FtsY or anti-SecY anti-serum) in 2% BSA/PBS were added directly afterwards and incubated over night at 4°C. The dilution yielding the best results was determined by titration for each antibody independently. The next-day samples were washed 10 times with PBS and, subsequently, an Alexa Fluor 555 coupled goat anti-rabbit antibody (Invitrogen; Karlsruhe, Germany) was added at a final concentration of 4 μg/ml in 2% BSA/PBS. After incubation for 90 min in the dark at room temperature and washing with PBS, the samples were dried, an appropriate amount of SlowFade Gold (Invitrogen, Karlsruhe, Germany) was applied and the slide was covered with microscope cover slips. Stained proteins were visualized using an Olympus BX-51 fluorescence microscope at a 100× magnification with a numerical aperture of 1.4 and a Cy3 fluorescence filter set. Images were acquired with a charge-coupled device camera (F-View, Olympus, Hamburg, Germany). Z-stacks were captured on a Zeiss Axioimager Microscope with an objective piezo. A three dimensional deconvolution was performed using Autodeblur X software.
green fluorescent protein
guanosine 5'(β,-γ imido) triphosphate
inner membrane vesicles
polyacrylamide gel electrophoresis
phosphate buffered saline
polymerase chain reaction
signal recognition particle receptor
signal recognition particle
yellow fluorescent protein
We thank Eitan Bibi for providing E. coli strain IY28, the National BioResource Project E. coli (NIG, Japan) for pCA24NCycY-GFP and Felix Dempwolff for capturing the Z-series. This work was supported by a fellowship from the Deutschen Akademischen Austauschdienst (DAAD) to MM and by grants from the Deutsche Forschungsgemeinschaft (DFG Forschergruppe 929 to PG and HGK and DFG Forschergruppe 967 to HGK).
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