Requirement of the SecB chaperone for export of a non-secretory polypeptide in Escherichia coli

The Active Protein-conducting Channel of Escherichia coli Contains an Apolar Patch

Protein translocation across the cytoplasmic membrane of Escherichia coli is mediated by translocase, a complex of a protein-conducting channel, SecYEG, and a peripheral motor domain, SecA. SecYEG has been proposed to constitute an aqueous path for proteins to pass the membrane in an unfolded state. To probe the solvation state of the active channel, the polarity sensitive fluorophore N-((2-(iodoacetoxy)ethyl)-N-methyl) amino-7-nitrobenz-2-oxa-1,3-diazole was introduced at specific positions in the C-terminal region of the secretory protein proOmpA. Fluorescence measurements with defined proOmpA-DHFR translocation intermediates indicate mostly a water-exposed environment with a hydrophobic region in the center of the channel.

SecA supports a constant rate of preprotein translocation

In Escherichia coli, secretory proteins (preproteins) are translocated across the cytoplasmic membrane by the Sec system composed of a protein-conducting channel, SecYEG, and an ATP-dependent motor protein, SecA. After binding of the preprotein to SecYEG-bound SecA, cycles of ATP binding and hydrolysis by SecA are thought to drive the stepwise translocation of the preprotein across the membrane. To address how the length of a preprotein substrate affects the SecA-driven translocation process, we constructed derivatives of the precursor of the outer membrane protein A (proOmpA) with 2, 4, 6, and 8 in-tandem repeats of the periplasmic domain. With increasing polypeptide length, an increasing delay in the time before full-length translocation was observed, but the translocation rate expressed as amino acid translocation per minute remained constant. These data indicate that in the ATP-dependent reaction, SecA drives a constant rate of preprotein translocation consistent with a stepping mechanism of translocation.

Protein traffic in bacteria: multiple routes from the ribosome to and across the membrane

Bacteria use several routes to target their exported proteins to the plasma membrane. The majority are exported through pores formed by SecY and SecE. Two different molecular machineries are used to target proteins to the SecYE translocon. Translocated proteins, synthesized as precursors with cleavable signal sequences, require cytoplasmic chaperones, such as SecB, to remain competent for posttranslational transport. In concert with SecB, SecA targets the precursors to SecY and energizes their translocation by its ATPase activity. The latter function involves a partial insertion of SecA itself into the SecYE translocon, a process that is strongly assisted by a couple of membrane proteins, SecG, SecD, SecF, YajC, and the proton gradient across the membrane. Integral membrane proteins, however, are specifically recognized by a direct interaction between their noncleaved signal anchor sequences and the bacterial signal recognition particle (SRP) consisting of Ffh and 4.5S RNA. Recognition occurs during synthesis at the ribosome and leads to a cotranslational targeting to SecYE that is mediated by FtsY and the hydrolysis of GTP. No other Sec protein is required for integration unless the membrane protein also contains long translocated domains that engage the SecA machinery. Discrimination between SecA/SecB- and SRP-dependent targeting involves the specificity of SRP for hydrophobic signal anchor sequences and the exclusion of SRP from nascent chains of translocated proteins by trigger factor, a ribosome-associated chaperone. The SecYE pore accepts only unfolded proteins. In contrast, a class of redox factor-containing proteins leaves the cell only as completely folded proteins. They are distinguished by a twin arginine motif of their signal sequences that by an unknown mechanism targets them to specific pores. A few membrane proteins insert spontaneously into the bacterial plasma membrane without the need for targeting factors and SecYE. Insertion depends only on hydrophobic interactions between their transmembrane segments and the lipid bilayer and on the transmembrane potential. Finally, outer membrane proteins of Gram-negative bacteria after having crossed the plasma membrane are released into the periplasm, where they undergo distinct folding events until they insert as trimers into the outer membrane. These folding processes require distinct molecular chaperones of the periplasm, such as Skp, SurA, and PpiD.

Eukaryotic precursor proteins are processed by Escherichia coli outer membrane protein OmpP

A new specific endopeptidase that cleaves eukaryotic precursor proteins has been found in Escherichia coli K but not in E. coli B strains. After purification, protein sequencing and Western blotting, the endopeptidase was shown to be identical with E. coli outer membrane protein OmpP [Kaufmann, A., Stierhof, Y.-D. & Henning, U. (1994) J. Bacteriol. 176, 359-367]. Further characterization of enzymatic properties of the new peptidase was performed. Comparison of the cleavage specificities of the newly found endopeptidase and that of rat mitochondrial processing peptidase (MPP) showed that patterns of proteolytic cleavage on the investigated precursor proteins by both enzymes are similar. By using three mitochondrial precursor proteins, the specificity assigned to OmpP previously, a cleavage position between two basic amino-acid residues, was extended to a three amino-acid recognition sequence. Positions +1 to +3 of this extended recognition site consist of an amino-acid residue with a small aliphatic side chain such as alanine or serine, a large hydrophobic residue such as leucine or valine followed by an arginine residue. Additionally, structural motifs of the substrate seem to be required for OmpP cleavage.

Protein targeting to the bacterial cytoplasmic membrane

Proteins that perform their activity within the cytoplasmic membrane or outside this cell boundary must be targeted to the translocation site prior to their insertion and/or translocation. In bacteria, several targeting routes are known; the SecB- and the signal recognition particle-dependent pathways are the best characterized. Recently, evidence for the existence of a third major route, the twin-Arg pathway, was gathered. Proteins that use either one of these three different pathways possess special features that enable their specific interaction with the components of the targeting routes. Such targeting information is often contained in an N-terminal extension, the signal sequence, but can also be found within the mature domain of the targeted protein. Once the nascent chain starts to emerge from the ribosome, competition for the protein between different targeting factors begins. After recognition and binding, the targeting factor delivers the protein to the translocation sites at the cytoplasmic membrane. Only by means of a specific interaction between the targeting component and its receptor is the cargo released for further processing and translocation. This mechanism ensures the high-fidelity targeting of premembrane and membrane proteins to the translocation site.

Preprotein transfer to the Escherichia coli translocase requires the co-operative binding of SecB and the signal sequence to SecA

In Escherichia coli, precursor proteins are targeted to the membrane-bound translocase by the cytosolic chaperone SecB. SecB binds to the extreme carboxy-terminus of the SecA ATPase translocase subunit, and this interaction is promoted by preproteins. The mutant SecB proteins, L75Q and E77K, which interfere with preprotein translocation in vivo, are unable to stimulate in vitro translocation. Both mutants bind proOmpA but fail to support the SecA-dependent membrane binding of proOmpA because of a marked reduction in their binding affinities for SecA. The stimulatory effect of preproteins on the interaction between SecB and SecA exclusively involves the signal sequence domain of the preprotein, as it can be mimicked by a synthetic signal peptide and is not observed with a mutant preprotein (delta8proOmpA) bearing a non-functional signal sequence. Delta8proOmpA is not translocated across wild-type membranes, but the translocation defect is suppressed in inner membrane vesicles derived from a prIA4 strain. SecB reduces the translocation of delta8proOmpA into these vesicles and almost completely prevents translocation when, in addition, the SecB binding site on SecA is removed. These data demonstrate that efficient targeting of preproteins by SecB requires both a functional signal sequence and a SecB binding domain on SecA. It is concluded that the SecB-SecA interaction is needed to dissociate the mature preprotein domain from SecB and that binding of the signal sequence domain to SecA is required to ensure efficient transfer of the preprotein to the translocase.

Requirements for the translocation of elongation-arrested, ribosome-associated OmpA across the plasma membrane of Escherichia coli

An oligodeoxynucleotide-dependent method to generate nascent polypeptide chains was adopted for use in a cell-free translation system prepared from Escherichia coli. In this way, NH2-terminal pOmpA fragments of distinct sizes were synthesized. Because most of these pOmpA fragments could be covalently linked to puromycin, precipitated with cetyltrimethylammonium bromide, and were enriched by sedimentation, they represent a population of elongation-arrested, ribosome-associated nascent chains. Translocation of these nascent pOmpA chains into inside-out membrane vesicles of E. coli required SecA and (depending on size) SecB. Whereas their translocation was strictly dependent on the H+-motive force of the vesicles, no indication for the involvement of the bacterial signal recognition particle was obtained. SecA and SecB, although required for translocation, did not mediate binding of the ribosome-associated pOmpA to membrane vesicles. However, SecA and SecB cotranslationally associated with nascent pOmpA, since they could be co-isolated with the ribosome-associated nascent chains and as such catalyzed translocation subsequent to the release of the ribosome. These results indicate that in E. coli, SecA also functionally interacts with preproteins before they are targeted to the translocase of the plasma membrane.

Folding of barnase in the presence of the molecular chaperone SecB

SecB is a molecular chaperone dedicated to interact exclusively with proteins destined for translocation across membranes. We find that SecB interacts with barnase during its folding in a similar manner to its interaction with GroEL. On mixing acid-denatured barnase with SecB in a stopped-flow spectrofluorimeter under conditions that favour refolding, we observe a series of fluorescence changes, corresponding to the binding of the denatured protein and the subsequent refolding of multiply and singly bound forms. The different phases were assigned using a combination of kinetics and mutant proteins. The refolding of barnase when bound to SecB is strongly retarded but never blocked. Multiply bound barnase is less tightly bound and refolds with a higher rate constant than singly bound barnase. Up to 4 mol of denatured barnase bind to 1 mol of tetrameric SecB.

A new periplasmic protein of Escherichia coli which is synthesized in spheroplasts but not in intact cells

The gene spy from Escherichia coli has been cloned and sequenced. It encodes a precursor of a so far unknown 139-residue, rather basic periplasmic protein. It was not detectable immunologically in intact cells but was produced abundantly in spheroplasts. It could be a stress protein specific for spheroplasting.

Characterization of the helper proteins for the assembly of tail fibers of coliphages T4 and lambda

Assembly of tail fibers of coliphage T4 requires the action of helper proteins. In the absence of one of these, protein 38 (p38), p37, constituting the distal part of the long tail fiber, fails to oligomerize. In the absence of the other, p57, p34 (another component of the long tail fiber), p37, and p12 (the subunit of the short tail fiber) remain unassembled. p38 can be replaced by the Tfa (tail fiber assembly) protein (pTfa) of phage lambda, which has the advantage of remaining soluble even when produced in massive amounts. The mechanisms of action of the helpers are unknown. As a first step towards elucidation of these mechanisms, p57 and pTfa have been purified to homogeneity and have been crystallized. The identity of gene 57 (g57), not known with certainty previously, has been established. The 79-residue protein p57 represents a very exotic polypeptide. It is oligomeric and acidic (an excess of nine negative charges). It does not contain Phe, Trp, Tyr, His, Pro, and Cys. Only 25 N-terminal residues were still able to complement a g57 amber mutant, although with a reduced efficiency. In cells overproducing the protein, it assumed a quasi-crystalline structure in the form of highly ordered fibers. They traversed the cells longitudinally (and thus blocked cell division) with a diameter approaching that of the cell and with a hexagonal appearance. The 194-residue pTfa is also acidic (an excess of 13 negative charges) and is likely to be dimeric.

Chaperone SecB: conformational changes demonstrated by circular dichroism

The chaperone SecB, which is involved in protein export in Escherichia coli, is shown by circular dichroism measurements to contain a high content of beta-pleated sheets. Prediction of the secondary structure of SecB is in good agreement with the observed content of beta-sheet. In accordance with the previous studies in which changes in conformation were assessed indirectly [Randall (1992), Science 257, 241-245], here we show that the conformation of SecB changes with the concentration of salt in the milieu and also when SecB interacts with a peptide ligand.

Diffusion-limited interaction between unfolded polypeptides and the Escherichia coli chaperone SecB

SecB is a chaperone dedicated to protein translocation in Escherichia coli. SecB binds to a subset of precursor proteins, and targets them in a translocation-competent state to the SecA subunit of the translocase. The nature and kinetics of the interaction of SecB with polypeptides were studied by spectroscopic techniques using the reduced form of bovine pancreatic trypsin inhibitor (BPTI) as a model substrate. Binding of SecB to BPTI resulted in an increase in the fluorescence of the surface-exposed tryptophan residue 36 of SecB. SecB reversibly binds BPTI in stoichiometric amounts. Labeling of BPTI with the fluorophore acrylodan allowed the analysis of the binding reaction at nanomolar concentrations. High-affinity binding (KD of 5.4 nM) of labeled BPTI to SecB resulted in a blue shift of the acrylodan emission maximum and an increase in the fluorescence quantum yield, suggesting that BPTI binds in an apolar environment. Stopped-flow acquisition of rate constants of complex formation between SecB and BPTI yielded a second-order binding rate constant of 5 x 10(9) M-1 s-1, and a dissociation rate constant of 48 s-1. These data demonstrate that in vitro, the association of SecB with polypeptide substrates is limited by the rate of collision. In vivo, SecB binding is selective, and predominantly occurs with nascent polypeptides. Since these chains are not expected to fold into stable structures, SecB association may be governed by "more or less" specific interactions and be limited by the rate of chain elongation rather than the rate of folding.

Determination of the binding frame within a physiological ligand for the chaperone SecB

The hallmark of the class of proteins called chaperones is the amazing ability to bind tightly to a wide array of polypeptide ligands that have no consensus in sequence; chaperones recognize non-native structure. As a step in the elucidation of the molecular mechanism of such remarkable binding, we have characterized complexes between the bacterial chaperone SecB and a series of ligands related to maltose-binding protein. SecB interacts at multiple sites on its polypeptide ligand. The entire binding region covers approximately half of the primary sequence of maltose-binding protein and comprises contiguous sites positioned around the center of the sequence.

Membrane topology and assembly of the outer membrane protein OmpA of Escherichia coli K12

The 325-residue outer membrane protein OmpA of Escherichia coli has been proposed to consist of a membrane-embedded moiety (residues 1 to about 170) and a C-terminal periplasmic region. The former is thought to comprise eight transmembrane segments in the form of antiparallel beta-strands, forming an amphiphilic beta-barrel, connected by exposed turns. Several questions concerning this model were addressed. Thus no experimental evidence had been presented for the turns at the inner leaflet of the membrane and it was not known whether or not the periplasmic part of the polypeptide plays a role in the process of membrane incorporation. Oligonucleotides encoding trypsin cleavage sites were inserted at the predicted turn sites of the ompA gene and it was shown that the encoded proteins indeed become accessible to trypsin at the modified sites. Together with previous results, these data also show that the turns on both sides of the membrane do not possess specifically topogenic information. In two cases one of the two expected tryptic fragments was lost and could be detected at low concentration in only one case. Therefore, bilateral proteolytic digestion of outer membranes can cause loss of beta-strands and does not necessarily produce a reliable picture of protein topology. When ompA genes were constructed coding for proteins ending at residue 228 or 274, the membrane assembly of these proteins was shown to be partially defective with about 20% of the proteins not being assembled. No such defect was observed when, following the introduction of a premature stop codon, a truncated protein was produced ending with residue 171.(ABSTRACT TRUNCATED AT 250 WORDS)

New outer membrane-associated protease of Escherichia coli K-12

The gene for a new outer membrane-associated protease, designated OmpP, of Escherichia coli has been cloned and sequenced. The gene encodes a 315-residue precursor protein possessing a 23-residue signal sequence. Including conservative substitutions and omitting the signal peptides, OmpP is 87% identical to the outer membrane protease OmpT. OmpP possessed the same enzymatic activity as OmpT. Immuno-electron microscopy demonstrated the exposure of the protein at the cell surface. Digestion of intact cells with proteinase K removed 155 N-terminal residues of OmpP, while the C-terminal half remained protected. It is possible that much of this N-terminal part is cell surface exposed and carries the enzymatic activity. Synthesis of OmpP was found to be thermoregulated, as is the expression of ompT (i.e., there is a low rate of synthesis at low temperatures) and, in addition, was found to be controlled by the cyclic AMP system.

SecA protein: autoregulated ATPase catalysing preprotein insertion and translocation across the Escherichia coli inner membrane

Recent insight into the biochemical mechanisms of protein translocation in Escherichia coli indicates that SecA ATPase is required both for the initial binding of preproteins to the inner membrane as well as subsequent translocation across this structure. SecA appears to promote these events by direct recognition of the preprotein or preprotein-SecB complex, binding to inner-membrane anionic phospholipids, insertion into the membrane bilayer and association with the preprotein translocator, SecY/SecE. ATP binding appears to control the affinity of SecA for the various components of the system and ATP hydrolysis promotes cycling between its different biochemical states. As a component likely to catalyse a rate-determining step in protein secretion, SecA synthesis is co-ordinated with the activity of the protein export pathway. This form of negative regulation appears to rely on SecA protein binding to its mRNA and repressing translation if conditions of rapid protein secretion prevail within the cell. A precise biochemical scheme for SecA-dependent catalysis of protein export and the details of secA regulation appear to be close at hand. The evolutionary conservation of SecA protein among eubacteria as well as the general requirement for translocation ATPases in other protein secretion systems argues for a mechanistic commonality of all prokaryotic protein export pathways.

Lysis protein T of bacteriophage T4

Lysis protein T of phage T4 is required to allow the phage's lysozyme to reach the murein layer of the cell envelope and cause lysis. Using fusions of the cloned gene t with that of the Escherichia coli alkaline phosphatase or a fragment of the gene for the outer membrane protein OmpA, it was possible to identify T as an integral protein of the plasma membrane. The protein was present in the membrane as a homooligomer and was active at very low cellular concentrations. Expression of the cloned gene t was lethal without causing gross leakiness of the membrane. The functional equivalent of T in phage lambda is protein S. An amber mutant of gene S can be complemented by gene t, although neither protein R of lambda (the functional equivalent of T4 lysozyme) nor S possess any sequence similarity with their T4 counterparts. The murein-degrading enzymes (including that of phage P22) have in common a relatively small size (molecular masses of ca. 18,000) and a rather basic nature not exhibited by other E. coli cystosolic proteins. The results suggest that T acts as a pore that is specific for this type of enzyme.

In-vitro studies on the folding characteristics of the Escherichia coli precursor protein prePhoE. Evidence that SecB prevents the precursor from aggregating by forming a functional complex

We characterised the behaviour of the purified precursor protein prePhoE upon dilution from 8 M urea by CD, fluorescence spectroscopy and gel-filtration techniques. It is demonstrated that prePhoE rapidly adopts beta structure, folds and aggregates upon dilution to urea concentrations below 3 M. These processes are paralleled by a loss of translocation competence. Furthermore the interaction of prePhoE with SecB was investigated. SecB is shown to have a very high content of beta structure, therefore we propose that precursor recognition by SecB is mediated through beta-beta interaction. It is shown that SecB has little effect on the adoption of secondary structure and tertiary folding upon dilution of the precursor from urea. However, SecB prevents the precursor from aggregating by forming a functional and stable complex.