Membrane insertion of the Escherichia coli MalF protein in cells with impaired secretion machinery

Signal recognition particle-dependent inner membrane targeting of the PulG Pseudopilin component of a type II secretion system

The pseudopilin PulG is an essential component of the pullulanase-specific type II secretion system from Klebsiella oxytoca. PulG is the major subunit of a short, thin-filament pseudopilus, which presumably elongates and retracts in the periplasm, acting as a dynamic piston to promote pullulanase secretion. It has a signal sequence-like N-terminal segment that, according to studies with green and red fluorescent protein chimeras, anchors unassembled PulG in the inner membrane. We analyzed the early steps of PulG inner membrane targeting and insertion in Escherichia coli derivatives defective in different protein targeting and export factors. The beta-galactosidase activity in strains producing a PulG-LacZ hybrid protein increased substantially when the dsbA, dsbB, or all sec genes tested except secB were compromised by mutations. To facilitate analysis of native PulG membrane insertion, a leader peptidase cleavage site was engineered downstream from the N-terminal transmembrane segment (PrePulG*). Unprocessed PrePulG* was detected in strains carrying mutations in secA, secY, secE, and secD genes, including some novel alleles of secY and secD. Furthermore, depletion of the Ffh component of the signal recognition particle (SRP) completely abolished PrePulG* processing, without affecting the Sec-dependent export of periplasmic MalE and RbsB proteins. Thus, PulG is cotranslationally targeted to the inner membrane Sec translocase by SRP.

Membrane integration of E. coli model membrane proteins

The molecular events of membrane translocation and insertion have been investigated using a number of different model proteins. Each of these proteins has specific features that allow interaction with the membrane components which ensure that the proteins reach their specific local destination and final conformation. This review will give an overview on the best-characterized proteins studied in the bacterial system and emphasize the distinct aspects of the pathways.

Membrane topology of PssT, the transmembrane protein component of the type I exopolysaccharide transport system in Rhizobium leguminosarum bv. trifolii strain TA1

The pssT gene was identified as the fourth gene located upstream of the pssNOP gene cluster possibly involved in the biosynthesis, polymerization, and transport of exopolysaccharide (EPS) in Rhizobium leguminosarum bv. trifolii strain TA1. The hydropathy profile and homology searches indicated that PssT belongs to the polysaccharide-specific transport family of proteins, a component of the type I system of the polysaccharide transport. The predicted membrane topology of the PssT protein was examined with a series of PssT-PhoA fusion proteins and a complementary set of PssT-LacZ fusions. The results generally support a predicted topological model for PssT consisting of 12 transmembrane segments, with amino and carboxyl termini located in the cytoplasm. A mutant lacking the C-terminal part of PssT produced increased amounts of total EPS with an altered distribution of high- and low-molecular-weight forms in comparison to the wild-type RtTA1 strain. The PssT mutant produced an increased number of nitrogen fixing nodules on clover.

The sensor protein KdpD inserts into the Escherichia coli membrane independent of the Sec translocase and YidC

KdpD is a sensor kinase protein in the inner membrane of Escherichia coli containing four transmembrane regions. The periplasmic loops connecting the transmembrane regions are intriguingly short and protease mapping allowed us to only follow the translocation of the second periplasmic loop. The results show that neither the Sec translocase nor the YidC protein are required for membrane insertion of the second loop of KdpD. To study the translocation of the first periplasmic loop a short HA epitope tag was genetically introduced into this region. The results show that also the first loop was translocated independently of YidC and the Sec translocase. We conclude that KdpD resembles a new class of membrane proteins that insert into the membrane without enzymatic assistance by the known translocases. When the second periplasmic loop was extended by an epitope tag to 27 amino acid residues, the membrane insertion of this loop of KdpD depended on SecE and YidC. To test whether the two periplasmic regions are translocated independently of each other, the KdpD protein was split between helix 2 and 3 into two approximately equal-sized fragments. Both constructed fragments, which contained KdpD-N (residues 1-448 of KdpD) and the KdpD-C (residues 444-894 of KdpD), readily inserted into the membrane. Similar to the epitope-tagged KdpD protein, only KdpD-C depended on the presence of the Sec translocase and YidC. This confirms that the four transmembrane helices of KdpD are inserted pairwise, each translocation event involving two transmembrane helices and a periplasmic loop.

Genetic screen yields mutations in genes encoding all known components of the Escherichia coli signal recognition particle pathway

We describe the further utilization of a genetic screen that identifies mutations defective in the assembly of proteins into the Escherichia coli cytoplasmic membrane. The screen yielded mutations in each of the known genes encoding components of the E. coli signal recognition particle pathway: ffh, ffs, and ftsY, which encode Ffh, 4.5S RNA, and FtsY, respectively. In addition, the screen yielded mutations in secM, which is involved in regulating levels of the SecA component of the bacterium's protein export pathway. We used a sensitive assay involving biotinylation to show that all of the mutations caused defects in the membrane insertions of three topologically distinct membrane proteins, AcrB, MalF, and FtsQ. Among the mutations that resulted in membrane protein insertion defects, only the secM mutations also showed defects in the translocation of proteins into the E. coli periplasm. Genetic evidence suggests that the S382T alteration of Ffh affects the interaction between Ffh and 4.5S RNA.

Topogenesis of membrane proteins: determinants and dynamics

For targeting and integration of proteins into the mammalian endoplasmic reticulum, two types of signals can be distinguished: those that translocate their C-terminal sequence (cleavable signals and signal-anchors) and those that translocate their N-terminus (reverse signal-anchors). In addition to the well established effect of flanking charges, also the length and hydrophobicity of the apolar core of the signal as well as protein folding and glycosylation contribute to orienting the signal in the translocon. In multi-spanning membrane proteins, topogenic determinants are distributed throughout the sequence and may even compete with each other. During topogenesis, segments of up to 60 residues may move back and forth through the translocon, emphasizing unexpected dynamic aspects of topogenesis.

A mutant hunt for defects in membrane protein assembly yields mutations affecting the bacterial signal recognition particle and Sec machinery

We describe an Escherichia coli genetic screen that yields mutations affecting two different cellular processes: disulfide bond formation and membrane protein assembly. The mutants defective in disulfide bond formation include additional classes of dsbA and dsbB mutations. The membrane protein assembly defective mutants contain a mutation in the secA operon and three mutations in the ffs gene, which encodes 4.5S RNA. These latter mutations are the only ones to be isolated in a gene encoding a component of the bacterial signal recognition particle by screening in vivo for defects in membrane protein insertion. A sensitive method for examining membrane protein localization shows that the ffs and secA locus mutations affect membrane assembly of the polytopic membrane protein, MalF. The ffs mutations also affect the membrane insertion of the FtsQ and the AcrB proteins. Although both the ffs and the secA locus mutations interfere with membrane protein assembly, only the latter also reduces export of a protein containing a cleavable signal sequence.

In vitro studies with purified components reveal signal recognition particle (SRP) and SecA/SecB as constituents of two independent protein-targeting pathways of Escherichia coli

The molecular requirements for the translocation of secretory proteins across, and the integration of membrane proteins into, the plasma membrane of Escherichia coli were compared. This was achieved in a novel cell-free system from E. coli which, by extensive subfractionation, was simultaneously rendered deficient in SecA/SecB and the signal recognition particle (SRP) components, Ffh (P48), 4. 5S RNA, and FtsY. The integration of two membrane proteins into inside-out plasma membrane vesicles of E. coli required all three SRP components and could not be driven by SecA, SecB, and DeltamicroH+. In contrast, these were the only components required for the translocation of secretory proteins into membrane vesicles, a process in which the SRP components were completely inactive. Our results, while confirming previous in vivo studies, provide the first in vitro evidence for the dependence of the integration of polytopic inner membrane proteins on SRP in E. coli. Furthermore, they suggest that SRP and SecA/SecB have different substrate specificities resulting in two separate targeting mechanisms for membrane and secretory proteins in E. coli. Both targeting pathways intersect at the translocation pore because they are equally affected by a blocked translocation channel.

An artificial transmembrane segment directs SecA, SecB, and electrochemical potential-dependent translocation of a long amino-terminal tail

Many integral membrane proteins contain an amino-terminal segment, often referred to as an N-tail, that is translocated across a membrane. In many cases, translocation of the N-tail is initiated by a cleavable, amino-terminal signal peptide. For N-tail proteins lacking a signal peptide, translocation is initiated by a transmembrane segment that is carboxyl to the translocated segment. The mechanism of membrane translocation of these segments, although poorly understood, has been reported to be independent of the protein secretion machinery. In contrast, here we describe alkaline phosphatase mutants containing artificial transmembrane segments that demonstrate that translocation of a long N-tail across the membrane is dependent upon SecA, SecB, and the electrochemical potential in the absence of a signal peptide. The corresponding mutants containing signal peptides also use the secretion machinery but are less sensitive to inhibition of its components. We present evidence that inhibition of SecA by sodium azide is incomplete even at high concentrations of inhibitor, which suggests why SecA-dependent translocation may not have been detected in other systems. Furthermore, by varying the charge around the transmembrane segment, we find that in the absence of a signal peptide, the orientation of the membrane-bound alkaline phosphatase is dictated by the positive inside rule. However, the presence of a signal peptide is an overriding factor in membrane orientation and renders all mutants in an Nout-Cin orientation.

Translocation, folding, and stability of the HflKC complex with signal anchor topogenic sequences

HflK and HflC are plasma membrane proteins of Escherichia coli, each having a large C-terminal domain exposed to the periplasmic space and an N-terminally located transmembrane segment, which should act as a signal anchor sequence for their biogenesis. They form a complex, HflKC. We studied in vivo processes of biogenesis of this pair of membrane proteins. Translocation of the C-terminal domains across the membrane, as assessed by their accessibility to externally added protease, was completed within 1 min after the synthesis in wild-type cells as well as in the secB mutant cells or in the FtsY-depleted cells. In contrast, translocation of these domains was retarded markedly when sodium azide was added to inhibit SecA ATPase and blocked almost completely in secY- or secD-defective mutant cells. Thus, although targeting of these membrane proteins depends neither on the SecB chaperone nor on the SRP pathway, their translocation occurs exclusively via the Sec translocase complex. Translocated HflK molecules were then folded into a partially protease-resistant conformation, taking a few minutes, and this folding was induced upon association with HflC. Singly expressed HflK and HflC were unstable in vivo and periplasmic proteases DegP and Prc were involved in the degradation of the HflK subunit. We characterized several hflA alleles isolated in early studies; they alter the HflK or the HflC sequence and destabilize the HflKC complex.

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

Spontaneous, pH-dependent membrane insertion of a transbilayer alpha-helix

A question of fundamental importance concerning the biosynthesis of integral membrane proteins is whether transmembrane secondary structure can insert spontaneously into a lipid bilayer. It has proven to be difficult to address this issue experimentally because of the poor solubility in aqueous solution of peptides and proteins containing these extremely hydrophobic sequences. We have identified a system in which the kinetics and thermodynamics of alpha-helix insertion into lipid bilayers can be studied systematically and quantitatively using simple spectroscopic assays. Specifically, we have discovered that a 36-residue polypeptide containing the sequence of the C-helix of the integral membrane protein bacteriorhodopsin exhibits significant solubility in aqueous buffers free of both detergents and denaturants. This helix contains two aspartic acid residues in the membrane-spanning region. At neutral pH, the peptide associates with lipid bilayers in a nonhelical and presumably peripheral conformation. With a pKa of 6.0, the peptide inserts into the bilayer as a transbilayer alpha-helix. The insertion reaction proceeds rapidly at room temperature and is fully reversible.

Protein targeting and translocation; a comparative survey

The last few years has seen enormous progress in understanding of protein targeting and translocation across biological membranes. Many of the key molecules involved have been identified, isolated, and the corresponding genes cloned, opening up the way for detailed analysis of the structure and function of these molecular machines. It has become clear that the protein translocation machinery of the endoplasmic reticulum is very closely related to that of bacteria, and probably represents an ancient solution to the problem of how to get a protein across a membrane. One of the thylakoid translocation systems looks as if it will also be very similar, and probably represents a pathway inherited from the ancestral endosymbiont. It is interesting that, so far, there is a perfect correlation between thylakoid proteins which are present in photosynthetic prokaryotes and those which use the sec pathway in chloroplasts; conversely, OE16 and 23 which use the delta pH pathway are not found in cyanobacteria. To date, no Sec-related proteins have been found in mitochondria, although these organelles also arose as a result of endosymbiotic events. However, virtually nothing is known about the insertion of mitochondrially encoded proteins into the inner membrane. Is the inner membrane machinery which translocates cytoplasmically synthesized proteins capable of operating in reverse to export proteins from the matrix, or is there a separate system? Alternatively, do membrane proteins encoded by mitochondrial DNA insert independently of accessory proteins? Unlike nuclear-encoded proteins, proteins encoded by mtDNA are not faced with a choice of membrane and, in principle, could simply partition into the inner membrane. The ancestors of mitochondria almost certainly had a Sec system; has this been lost along with many of the proteins once encoded in the endosymbiont genome, or is there still such a system waiting to be discovered? The answer to this question may also shed light on the controversy concerning the sorting of the inter-membrane space proteins cytochrome c1 and cytochrome b2, as the conservative-sorting hypothesis would predict re-export of matrix intermediates via an ancestral (possibly Sec-type) pathway. Whereas the ER and bacterial systems clearly share homologous proteins, the protein import machineries of mitochondria and chloroplasts appear to be analogous rather than homologous. In both cases, import occurs through contact sites and there are separate translocation complexes in each membrane, however, with the exception of some of the chaperone molecules, the individual protein components do not appear to be related. Their similarities may be a case of convergent rather than divergent evolution, and may reflect what appear to be common requirements for translocation, namely unfolding, a receptor, a pore complex and refolding. There are also important differences. Translocation across the mitochondrial inner membrane is absolutely dependent upon delta psi, but no GTP requirement has been identified. In chloroplasts the reverse is the case. The roles of delta psi and GTP, respectively, remain uncertain, but it is tempting to speculate that they may play a role in regulating the import process, perhaps by controlling the assembly of a functional translocation complex. In the case of peroxisomes, much still remains to be learned. Many genes involved in peroxisome biogenesis have been identified but, in most cases, the biochemical function remains to be elucidated. In this respect, understanding of peroxisome biogenesis is at a similar stage to that of the ER 10 years ago. The coming together of genetic and biochemical approaches, as with the other organelles, should provide many of the answers.

Biotinylation in vivo as a sensitive indicator of protein secretion and membrane protein insertion

Escherichia coli biotin ligase is a cytoplasmic protein which specifically biotinylates the biotin-accepting domains from a variety of organisms. This in vivo biotinylation can be used as a sensitive signal to study protein secretion and membrane protein insertion. When the biotin-accepting domain from the 1.3S subunit of Propionibacterium shermanii transcarboxylase (PSBT) is translationally fused to the periplasmic proteins alkaline phosphatase and maltose-binding protein, there is little or no biotinylation of PSBT in wild-type E. coli. Inhibition of SecA with sodium azide and mutations in SecB, SecD, and SecF, all of which slow down protein secretion, result in biotinylation of PSBT. When PSBT is fused to the E. coli inner membrane protein MalF, it acts as a topological marker: fusions to cytoplasmic domains of MalF are biotinylated, and fusions to periplasmic domains are generally not biotinylated. If SecA is inhibited by sodium azide or if the SecE in the cell is depleted, then the insertion of the MalF second periplasmic domain is slowed down enough that PSBT fusions in this part of the protein become biotinylated. Compared with other protein fusions that have been used to study protein translocation, PSBT fusions have the advantage that they can be used to study the rate of the insertion process.

Insertion of the polytopic membrane protein MalF is dependent on the bacterial secretion machinery

We examined the dependence of protein export and membrane protein insertion on SecE and SecA, two components of the secretion (Sec) apparatus of Escherichia coli. The magnitude of the secretion defect observed for signal sequence-containing proteins in cells depleted of SecE is larger and more general than that in many temperature- or cold-sensitive Sec mutants. In addition, we show that the proper insertion of the polytopic MalF protein (synthesized without a signal sequence) into the cytoplasmic membrane is also SecE-dependent. In contrast to an earlier study (McGovern, K., and Beckwith, J. (1991) J. Biol. Chem. 266, 20870-20876), the membrane insertion of MalF also is inhibited by treatment of cells with sodium azide, a potent inhibitor of SecA. Therefore, our data strongly suggest that the cytoplasmic membrane insertion of MalF is dependent on the same cellular machinery as is involved in the export of signal sequence-containing proteins. We propose that the mechanism of export from the cytoplasm is related for both signal sequence-containing and cytoplasmic membrane proteins, but hydrophobic membrane proteins such as MalF may have a higher affinity for the Sec apparatus.

The functional integration of a polytopic membrane protein of Escherichia coli is dependent on the bacterial signal-recognition particle

In eukaryotes, the cotranslational targeting of proteins to the endoplasmic reticular membrane is initially mediated by the signal-recognition particle (SRP), a ribonucleoprotein complex consisting of the 7SL RNA and six protein subunits. Since the discovery of sequence homology between (a) the Escherichia coli 4.5S RNA (Ffs) and 7SL RNA, and (b) the E. coli P48 (Ffh) and SRP 54-kDa subunit, more evidence has been obtained that E. coli also possesses an SRP-type pathway that acts in the translocation of secreted proteins. Such a pathway could possibly be involved in the cotranslational integration of hydrophobic membrane proteins that cannot be effectively targeted post-translationally due to folding and aggregation. In this study, we report that disruption of the E. coli SRP complex with a dominant lethal 4.5S RNA mutant in vivo prevents functional membrane integration of the E. coli lactose permease (LacY). Likewise, depletion of the P48 (Ffh) protein also results in a decrease in the amount of functional LacY inserted into the E. coli plasma membrane. In direct contrast, inhibition of SecA function does not affect LacY integration. These results suggest a major function of the bacterial SRP in the targeting and subsequent integration of hydrophobic membrane proteins as opposed to SecA mediating the post-translational targeting of secretory proteins.

SecA-dependence of the translocation of a large periplasmic loop in the Escherichia coli MalF inner membrane protein is a function of sequence context

We have analysed the translocation of a large periplasmic loop in the Escherichia coli MalF inner membrane protein when placed in different sequence contexts and under conditions when the function of the SecA protein is inhibited. The results show that the degree of SecA-dependence varies with sequence context: while translocation of the large loop in its normal context is only minimally affected by SecA inhibition, translocation is much more sensitive to SecA inhibition when the loop is placed in the context of other inner membrane proteins. Conversely, when the large MalF loop is replaced by segments from other proteins, translocation of those segments is again very sensitive to SecA inhibition. Thus, SecA-dependence is not an all-or-none phenomenon and is not only a simple function of, e.g. the length of a translocated segment or the hydrophobicity of the flanking transmembrane segments.

Synthetic competition between cytoplasmic folding and translocation of a soluble membrane protein domain

In wild-type strains of Escherichia coli, alkaline phosphatase (AP), either when present as a soluble protein or when fused to a membrane protein, is only active after translocation to the periplasm. In thioredoxin reductase (trxB) mutants, however, cytoplasmically localized AP can form disulphide bonds and can reach an active conformation. Once it has folded in the cytoplasm, it can no longer be translocated. On the other hand, when AP is fused to periplasmic domains of a membrane protein, translocation can be more rapid than folding. Thus, expressing hybrids of AP and integral membrane proteins in a trxB mutant generates competition between folding of AP in the cytoplasm and its translocation to the periplasm. The cellular localization of AP can be monitored in phosphoserine phosphatase (serB) mutants causing auxotrophy for L-serine. Cytoplasmically but not periplasmically localized AP can compensate for the lack of SerB, leading to growth on indicator plates. As expected, when AP was fused to cytoplasmic domains of membrane proteins, serB-mediated auxotrophy was abolished. Surprisingly, AP fusions to periplasmic domains exhibited a non-uniform response pattern. Fusions that translocate AP rapidly did not complement the SerB defect, while those that export AP only slowly could do so. The usefulness of these strains for studying a variety of aspects related to membrane protein biogenesis is discussed.

Proteolytic cleavage and cell wall anchoring at the LPXTG motif of surface proteins in gram-positive bacteria

Many surface proteins are thought to be anchored to the cell wall of Gram-positive bacteria via their C-terminus. Cell wall anchoring requires a specific sorting signal, normally located at the predicted C-terminus of surface proteins. Here we show that when placed into the middle of a polypeptide chain, the sorting signal causes the specific cleavage of the precursor as well as the cell wall anchoring of its N-terminal fragment, while the C-terminal fragment remains within the cytoplasm. N-terminal sequencing of the C-terminal cleavage fragment suggests that the cleavage site is located between threonine (T) and glycine (G) of the LPXTG motif, the signature sequence of cell wall sorting signals. All surface proteins harbouring an LPXTG sequence motif may therefore be cleaved and anchored by a universal mechanism. We also propose a novel hypothesis for the cell wall linkage of surface proteins in Gram-positive bacteria.

Requirements for translocation of periplasmic domains in polytopic membrane proteins

Periplasmic domains of cytoplasmic membrane proteins require export signals for proper translocation. These signals were studied by using a MalF-alkaline phosphatase fusion in a genetic selection that allowed the isolation of mislocalization mutants. In the original construct, alkaline phosphatase is fused to the second periplasmic domain of the membrane protein, and its activity is thus confined exclusively to the periplasm. Mutants that no longer translocated alkaline phosphatase were selected by complementation of a serB mutation. A total of 11 deletions in the amino terminus were isolated, all of which spanned at least the third transmembrane segment. This domain immediately precedes the periplasmic domain to which alkaline phosphatase was fused. Our results obtained in vivo support the model that amino-terminal membrane-spanning segments are required for translocation of large periplasmic domains. In addition, we found that the inability to export the alkaline phosphatase domain could be suppressed by a mutation, prlA4, in the secretion apparatus.

Membrane insertion defects caused by positive charges in the early mature region of protein pIII of filamentous phage fd can be corrected by prlA suppressors

The filamentous phage coat protein pIII has been used to display a variety of peptides and proteins to allow easy screening for desirable binding properties. We have examined the biological constraints that restrict the expression of short peptides located in the early mature region of pIII, adjacent to the signal sequence cleavage site. Many functionally defective pIII fusion proteins contained several positively charged amino acids in this region. These residues appear to inhibit proper insertion of pIII into the Escherichia coli inner membrane, blocking the assembly and extrusion of phage particles. Suppressor mutations in the prlA (secY) component of the protein export apparatus dramatically alleviate the phage growth defect caused by the positively charged residues. We conclude that insertion of pIII fusion proteins into the inner membrane can occur by a sec gene-dependent mechanism. The suppressor strains should be useful for increasing the diversity of peptides displayed on pIII in phage libraries.

Sec-independent protein insertion into the inner E. coli membrane. A phenomenon in search of an explanation

Translocation of proteins through the inner membrane of E. coli is normally catalyzed by the so-called sec-machinery. Yet, many integral inner membrane proteins appear not to require a fully functional sec-machinery for proper insertion, in spite of the fact that sometimes quite sizable domains have to be translocated to the periplasmic side. This review will focus on recent studies of sec-independent translocation events in an attempt to pin-point the main differences between sec-dependent and sec-independent translocation.

Sorting of protein A to the staphylococcal cell wall

The cell wall of gram-positive bacteria can be thought of as representing a unique cell compartment, which contains anchored surface proteins that require specific sorting signals. Some biologically important products are anchored in this way, including protein A and fibronectin binding protein of Staphylococcus aureus and streptococcal M protein. Studies of staphylococcal protein A and Escherichia coli alkaline phosphatase show that the signal both necessary and sufficient for cell wall anchoring consists of an LPXTGX motif, a C-terminal hydrophobic domain, and a charged tail. These sequence elements are conserved in many surface proteins from different gram-positive bacteria. We propose the existence of a hitherto undescribed sorting mechanism that positions proteins on the surface of gram-positive bacteria.