Escherichia coli takes up ferric citrate through the outer membrane by active transport mediated by the FecA receptor protein and the TonB-ExbB-ExbD energy-transducing device. The TonB-ExbB-ExbD complex (
2,
18,
23) transfers the energy required for active transport across the outer membrane (
2). Ferric citrate or iron is subsequently released from FecA and binds to FecB in the periplasm. Iron is then transported across the cytoplasmic membrane by an ATP-binding cassette transport system consisting of the FecC, -D, and -E proteins (
3,
10,
19,
24,
30). Ferric citrate binding to FecA induces transcription of the
fecABCDE transport genes, but does not affect transcription of the
fecIR regulatory genes (
15,
16). Induction can be uncoupled from transport by point mutations in
fecAthat lead to constitutive induction of transcription and the inability to transport ferric citrate (
9). Furthermore, the deletion of residues 14 to 68 of mature FecA removes the induction function; however, transport activity is fully retained (
10). A further vital component for the response to ferric citrate is FecR. FecR is an integral cytoplasmic membrane protein of 317 residues; the N terminus has been localized to the cytoplasm and the C terminus has been localized to the periplasm. A hydrophobic sequence from residues 85 to 100 probably forms the single transmembrane segment (
28). The location of FecR in the three subcellular compartments (the periplasm, the cytoplasmic membrane, and the cytoplasm) suggests a structural and functional role in the signaling cascade of the
fec system. C- terminally truncated FecR derivatives display a constitutive phenotype and a FecR N-terminal fragment of only 59 amino acids (aa) is able to induce
fectransport gene transcription independently of ferric citrate (
15). These data led us to propose that the information of ferric citrate binding to FecA is transmitted across the outer membrane by FecA and across the cytoplasmic membrane by FecR. FecR subsequently activates FecI, which binds the RNA polymerase core enzyme and directs it to the
fecA promoter to initiate transcription of the
fecA, -
B, -
C, -
D, and -
E genes. Therefore, signal transduction could involve a series of conformational changes; starting with the binding of ferric citrate to FecA, a signal is then transmitted through the N terminus of FecA to the C terminus of FecR and then across the cytoplasmic membrane to the N terminus of FecR, which interacts with FecI. To support the model of such a signal cascade, we searched for a physical interaction between the proposed Fec signal-transducing proteins. Using N-terminally and C-terminally His-tagged FecR bound to Ni-nitrilotriacetic acid (NTA) agarose columns, we have shown that there is a specific interaction between isolated FecR and isolated FecA and FecI proteins. An alternative approach was undertaken using an in vivo system based on the ability of the Lex repressor to bind to an altered operator placed upstream of
lacZ (
5). Using this system, we demonstrated heterodimer formation of the N terminus of FecA with the C terminus of FecR and of the N terminus of FecR with FecI. The in vitro and in vivo data demonstrate an interaction of the FecAIR proteins and their subdomains as predicted by the proposed model.
DISCUSSION
The chromosomally encoded FecR regulatory protein is contained in cells in such low amounts that it cannot be detected after radiolabeling and SDS-PAGE or by Western blotting. It has to be overexpressed, and then it precipitates as inclusion bodies (
15,
29). Although FecR-(His)
6 and (His)
10-FecR were more hydrophilic than FecR, they also formed inclusion bodies which were barely contaminated with other proteins, as revealed by SDS-PAGE. The inclusion bodies were not soluble in buffers and buffers supplemented with detergents that usually do not denature proteins, such as octylglucoside, Triton X-100, Tween 20, CHAPS {3-[(3-cholamidopropyl)-dimethylammonio]-1-propanesulfonate}, and Nonidet P-40; for this reason these detergents are frequently used to solubilize cytoplasmic membrane proteins. Very likely, the small portion of active FecR-(His)
6 and (His)
10-FecR that was inserted in the cytoplasmic membrane was solubilized, but the amounts were not sufficient for detection by staining after SDS-PAGE and for performing in vitro binding studies. Urea (6 M) had to be used to solubilize the inclusion bodies. This procedure almost certainly denatured FecR-(His)
6 and (His)
10-FecR, and it is not known to what extent FecR-(His)
6 and (His)
10-FecR renatured during the dialysis to remove urea. However, retention of FecA and lack of retention of FecAΔ47-101 on the Ni-NTA agarose column and retention of FecI by FecR-(His)
6 but not by (His)
10-FecR demonstrate binding specificity which suggests correctly folded FecR derivatives are present. In addition, since not only the His-tagged complete proteins and the His-tagged proteolytic fragments but also the untagged fragments were retained by the Ni-NTA column, the untagged fragments were probably bound to the His-tagged fragments. A well-known example of the preservation and restoration of an active protein after the cleavage of a peptide bond is α-complementation of β-galactosidase. FecR is also cleaved by an unknown protease to the same two major products as are the His-tagged FecR derivatives. The requirement for cleavage of FecR for induction of the
fec system was studied with a number of FecR mutants (
29). Of eight FecR mutants which were inactive or which transcribed
fecA-lacZconstitutively, seven were no longer cleaved. This clearly showed that there is no correlation between cleavage and phenotype, and since the mutations were scattered over the entire polypeptide, specific proteolytic processing can be ruled out for FecR activity (
29).
The interaction and binding of the FecA N-terminal, but not the C-terminal, region to (His)
10-FecR was shown by control experiments which demonstrated that FecA47, lacking residues 14 to 68, did not bind to (His)
10-FecR, which clearly shows the specificity for the N terminus of FecA. Furthermore, the specificity of binding to the N terminus of FecR was demonstrated by experiments in which FecA did not bind to FecR-(His)
6. The histidine residues at the C terminus of FecR-(His)
6 apparently prevented binding of FecA. This lack of binding could be due to steric reasons such that the His tag masks the binding site on FecR or that fixation of FecR-(His)
6 on Ni-NTA agarose hinders access to the C-terminal portion of FecR or the partially charged His residues repulse FecA. Since FecR-(His)
6 displayed 60% in vivo activity in ferric citrate-dependent regulation of
fecA-lacZtranscription, and since this activity should be much lower if binding of FecA to FecR-(His)
6 is impaired, it is more likely that fixation of FecR-(His)
6 to Ni-NTA agarose is the cause for the lack of FecA–FecR-(His)
6 interaction. For the in vivo relevance of the demonstrated interaction between FecA and FecR-(His)
6, one has to take into account that the in vitro interactions were not influenced by the addition of ferric citrate (data not shown). This was not unexpected, since transcription initiation in vivo requires not only binding of ferric citrate to FecA but also the electrochemical potential of the cytoplasmic membrane mediated by the Ton system (
10). Since the in vitro conditions do not reflect the in vivo situation, these experiments do not reveal whether FecA binds permanently to FecR in vivo. However, the in vitro data clearly demonstrate that the N terminus of FecA and the C terminus of FecR are required for FecA-FecR interaction, which supports the previous in vivo data (
10).
Active FecI was solubilized from inclusion bodies with a detergent, as was demonstrated previously (
1). Solubilized FecI was shown to direct the RNA polymerase core enzyme to the promoter upstream of the
fecA gene, as revealed by bandshift experiments and by in vitro runoff transcription assays (
1). Here, FecR-(His)
6 but not (His)
10-FecR retained FecI on Ni-NTA-agarose; this result supports our previous data, which localized the N terminus of FecR in the cytoplasm and which demonstrated constitutive transcription of the
fec transport genes by cytoplasmic N-terminal fragments of FecR (
15,
28). The reasons for the failure of (His)
10-FecR to bind FecI may be the same as those proposed for the failure of FecA to bind to FecR-(His)
6. The relative levels of binding of FecA to (His)
10-FecR compared to that seen for FecI binding to FecR-(His)
6 may be explained by possible differences in the affinity of FecA compared to FecI for FecR. Alternatively, the binding sites on FecR-(His)
6 for FecI are more accessible than those for FecA for binding to (His)
10-FecR.
The approximately 60% activity of FecR-(His)
6 and (His)
10-FecR in ferric citrate-dependent induction of
fecA transcription indicates that a fraction of the His-tagged FecR derivatives is properly inserted in the cytoplasmic membrane, receives the signal from FecA, transmits the signal across the cytoplasmic membrane, and activates FecI. Using SDS-PAGE and immunoblotting (see Fig.
1C) of the His-tagged FecR proteins cloned into high-copy-number plasmids and overexpressed, we found no indication that a fraction of the proteins lost the His tags and for this reason were active. The assays carried out to determine if the His-tagged FecR proteins are active were done using low-copy-number plasmids, which should significantly reduce the possibility that there is active FecR without a His tag. We cannot, however, rule out the possibility that very small amounts (below our levels of detection) of the His-tagged FecR proteins have lost their tag. Attempts to maintain FecR in solution by creating a hybrid protein with thioredoxin, which has been shown to work in a number of cases (
12), did not prevent the formation of inclusion bodies for FecR (data not shown). The hybrid protein containing thioredoxin fused to the N-terminus of FecR displayed regulatory activities, similar to (His)
10-FecR. Upon the addition of ferric citrate to the growth medium, β-galactosidase activity of a
fecA-lacZpromoter fusion increased from 9 to 250 U, which amounts to 77% of the β-galactosidase activity obtained by induction with wild-type
fecR (data not shown). This high level of activity is not surprising, since we know from our in vivo experiments with the bacterial two-hybrid Lex-based system that the first 9 aa of FecR are dispensable for activity and may serve as a linker between FecR and thioredoxin, thus leaving the cytoplasmic activity domain unaffected to interact with FecI.
The regions of FecA and FecR chosen to examine the interaction with the two-hybrid system were localized to the periplasm according to our previous studies. Moreover, the FecA N-proximal region constitutes a domain whose sole function appears to be important for the induction of
fec transport gene transcription but not for transport itself. This has been shown by deletion studies in which residues 14 to 68 of the mature FecA protein were removed; this resulted in an induction-inactive but transport-competent FecA derivative. The structure of the N-terminal region of FecA is quite distinct from those of other TonB-dependent transporters. The TonB box required for transport and induction is located at residues 81 to 84 in FecA, since the FecA N terminus represents an extension when compared to the other TonB-dependent transporters in the outer membrane of
E. coliK-12 in which the TonB box is close to the N terminus (
10). The extension of FecA is not part of the globular domain that closes the channel of the β barrel in the crystal structure of FhuA (
6,
13) and FepA (
4), if one assumes an overall structure of FecA that is similar to FhuA and FepA. Rather, the long N terminus of FecA would be contained in the periplasm like the N terminus of FhuA and FepA which are not seen in the crystal structure, probably because they are flexible and assume no fixed structure. The strong allosteric changes in the periplasmically exposed region of the globular domain of FhuA upon ferrichrome binding may occur similarly in FecA upon ferric citrate binding. However, FecA in contrast to FhuA employs the structural transition to initiate a signaling cascade that finally initiates transcription of the
fec transport genes. The C-proximal region of FecR and the N-proximal region of FecR used for studying interactions with FecA and FecI also form domains that are separated by the FecR transmembrane region (residues 85 to 100). We therefore employed three domains in the two-hybrid system which display some structural independence but receive signals from the surface-exposed ferric citrate binding site of FecA and transmit signals through the C-proximal region of FecR to the N-terminus of FecR and from there to FecI.
The use of the in vivo LexA-based repression system to look at the interaction of FecA with FecR and FecR with FecI clearly shows that these interactions do take place in vivo and supports the data obtained from the in vitro column binding assays. The LexA system has been successfully used to define very small regions of protein interaction, for example between the Jun and Fos zipper motifs (
5). We have been able to show that the first 79 aa of the mature FecA polypeptide interact with the proposed periplasmic domain of FecR, consisting of aa 101 to 317. It has not been possible to reduce this region in FecR and still maintain FecR activity. FecA may interact with FecR over a large region, or FecA may interact with the N and C termini of the 101- to 317-aa region of FecR. It is also feasible that the active conformation of the periplasmic segment of FecR is impaired by the deletions.
Interaction of the cytoplasmic region of FecR with FecI has been reduced to a region between aa 9 and 58. In contrast, it has not been possible to determine the precise region of FecI that interacts with FecR, since both deletion derivatives were unable to form heterodimers. The interaction may take place over large or multiple domains of FecI, or the conformation of FecI may be disturbed by the deletions. We have some initial data based on phage display library biopanning which indicate that the FecR interactions take place over the entire FecI protein. FecI belongs to the family of ECF (extracytoplasmic function) sigma factors, which contain a number of functional domains. The deleted segments represent all of regions 2 and 4.2 of FecI. Initial data show that FecI deletion mutants, which have region 3 removed, are still able to interact with FecR. This would indicate, first, that deletions in FecI do not necessarily lead to instability and, second, that it is likely that there are sites within regions 2 and 4.2 which interact with FecR. The lack of interaction between the various deletion constructs indicates that the interaction of the various components of the Fec system is dependent on secondary structure conservation, and thus many deletions are likely to disrupt the structural framework. Alternatively, the deletions we have constructed in FecR and FecI are unstable, and attempts to show the stability of all of the LexA fusions used were unfortunately unsuccessful. It was not possible to show the presence of these fusion proteins either by Coomassie blue staining in the soluble or insoluble fraction or by immunoblotting with either FecA or FecR antiserum. This would indicate that these proteins are expressed at very low levels or, alternatively, that our antisera do not recognize those regions fused to LexA1–87. This is unlikely in the case of FecR, where large regions of FecR are fused to LexA; however, in the case of FecA, this is a possible explanation since only about 10% of the total length of the protein was fused to LexA.
Both the in vitro and in vivo data show interactions between the N terminus of FecA and the periplasmic domain of FecR and between the cytoplasmic domains of FecR and FecI. However, these interactions occurred in the absence of the ferric citrate inducer. We therefore conclude that the signal transduction from FecA to FecR and then to FecI is not due simply to the interaction itself but possibly to changes in interaction upon binding of ferric citrate to FecA. Alternatively, the Fec proteins may show an interaction pattern similar to that seen in the aspartate receptor in the chemotaxis sensory signaling cascade. In this system, there is a stable complex consisting of the aspartate receptor, CheW, and CheA. The binding of aspartate does not change the association constant of these proteins; in fact, binding causes only a very small change in the aspartate receptor itself. It is now assumed that this change is a piston-like motion of approximately 1 Å of the α-helical transmembrane domains of the receptor. This motion is transmitted from the periplasmic to the cytoplasmic side of the membrane and it is assumed to be perceived by the methylation and phosphorylation enzymes (
17). This system exemplifies that protein-protein interactions are able to occur in these systems in the absence of an inducer molecule.