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PubMed1994

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.

ATP-Binding Cassette Transporters↗
PubMed1997

Defective export in Escherichia coli caused by DsbA'-PhoA hybrid proteins whose DsbA' domain cannot fold into a conformation resistant to periplasmic proteases.

The disulfide bond-forming factor DsbA and the alkaline phosphatase are stable in the Escherichia coli periplasmic space and can be overproduced without significant perturbation of the cell's physiology. By contrast, DsbA'-PhoA hybrid proteins resulting from TnphoA insertions into different regions of a plasmid-borne dsbA gene could become toxic (lethal) to bacteria. Toxicity was concomitant with an impairment of some step of the export mechanism and depended on at least three parameters, i.e., (i) the rate of expression of the hybrid protein, (ii) the ability of the amino-terminal DsbA' domain of the hybrid protein to fold into a protease-resistant conformation in the periplasmic space, and (iii) the activity of the DegP periplasmic protease. Even under viable conditions of low expression, DsbA' folding-deficient hybrid proteins accumulated more than the folding-proficient ones in the insoluble material and this was aggravated in a strain lacking the DegP protease. When production was more elevated, the folding-deficient hybrid proteins became lethal, but only in strains lacking the DegP activity, while the folding-proficient ones were not. Under conditions of very high production by degP+ or degP strains, both types of hybrid proteins accumulated as insoluble preproteins. Meanwhile, the export machinery was dramatically handicapped and the cells lost viability. However, the folding-deficient hybrid proteins had a higher killing efficiency than the folding-proficient ones. Free DsbA'-truncated polypeptides, although not toxic, were processed more slowly when they could not fold into a protease-resistant form in the periplasmic space. This provides indications in E. coli for a direct or indirect influence of the folding of a protein in the periplasmic environment on export efficiency.

Alkaline Phosphatase↗
PubMed1998

Isolation of a periplasmic molecular chaperone-like protein of Rhodobacter sphaeroides f. sp. denitrificans that is homologous to the dipeptide transport protein DppA of Escherichia coli.

A periplasmic protein has been found to prevent aggregation of the acid-unfolded dimethyl sulfoxide reductase (DMSOR), the periplasmic terminal reductase of dimethyl sulfoxide respiration in the phototroph Rhodobacter sphaeroides f. sp. denitrificans, in a manner similar to that of the Escherichia coli chaperonin GroEL (Matsuzaki et al., Plant Cell Physiol. 37:333-339, 1996). The protein was isolated from the periplasm of the phototroph. It had a molecular mass of 58 kDa and had no subunits. The sequence of 14 amino-terminal residues of the protein was completely identical to that of the periplasmic dipeptide transport protein (DppA) of E. coli. The 58-kDa protein prevented aggregation to a degree comparable to that of GroEL on the basis of monomer protein. The 58-kDa protein also decreased aggregation of guanidine hydrochloride-denatured rhodanese, a mitochondrial matrix protein, during its refolding upon dilution. The 58-kDa protein is a kind of molecular chaperone and could be involved in maintaining unfolded DMSOR, after secretion of the latter into the periplasm, in a competent form for its correct folding.

Amino Acid Sequence↗
PubMed2001

Periplasmic transit and disulfide bond formation of the autotransported Shigella protein IcsA.

The Shigella outer membrane protein IcsA belongs to the family of type V secreted (autotransported) virulence factors. Members of this family mediate their own translocation across the bacterial outer membrane: the carboxy-terminal beta domain forms a beta barrel channel in the outer membrane through which the amino-terminal alpha domain passes. IcsA, which is localized at one pole of the bacterium, mediates actin assembly by Shigella, which is essential for bacterial intracellular movement and intercellular dissemination. Here, we characterize the transit of IcsA across the periplasm during its secretion. We show that an insertion in the dsbB gene, whose gene product mediates disulfide bond formation of many periplasmic intermediates, does not affect the surface expression or unipolar targeting of IcsA. However, IcsA forms one disulfide bond in the periplasm in a DsbA/DsbB-dependent fashion. Furthermore, cellular fractionation studies reveal that IcsA has a transient soluble periplasmic intermediate. Our data also suggest that IcsA is folded in a proteinase K-resistant state in the periplasm. From these data, we propose a novel model for the secretion of IcsA that may be applicable to other autotransported proteins.

Bacterial Proteins↗
PubMed2005

A periplasmic drug-binding site of the AcrB multidrug efflux pump: a crystallographic and site-directed mutagenesis study.

The Escherichia coli AcrB multidrug efflux pump is a membrane protein that recognizes many structurally dissimilar toxic compounds. We previously reported the X-ray structures of four AcrB-ligand complexes in which the ligands were bound to the wall of the extremely large central cavity in the transmembrane domain of the pump. Genetic studies, however, suggested that discrimination between the substrates occurs mainly in the periplasmic domain rather than the transmembrane domain of the pump. We here describe the crystal structures of the AcrB mutant in which Asn109 was replaced by Ala, with five structurally diverse ligands, ethidium, rhodamine 6G, ciprofloxacin, nafcillin, and Phe-Arg-beta-naphthylamide. The ligands bind not only to the wall of central cavity but also to a new periplasmic site within the deep external depression formed by the C-terminal periplasmic loop. This depression also includes residues identified earlier as being important in the specificity. We show here that conversion into alanine of the Phe664, Phe666, or Glu673 residue in the periplasmic binding site produced significant decreases in the MIC of most agents in the N109A background. Furthermore, decreased MICs were also observed when these residues were mutated in the wild-type AcrB background, although the effects were more modest. The MIC data were also confirmed by assays of ethidium influx rates in intact cells, and our results suggest that the periplasmic binding site plays a role in the physiological process of drug efflux.

Alanine↗
PubMed2001

The emerging periplasm-localized subclass of AroQ chorismate mutases, exemplified by those from Salmonella typhimurium and Pseudomonas aeruginosa.

BACKGROUND: Chorismate mutases of the AroQ homology class are widespread in the Bacteria and the Archaea. Many of these exist as domains that are fused with other aromatic-pathway catalytic domains. Among the monofunctional AroQ proteins, that from Erwinia herbicola was previously shown to have a cleavable signal peptide and located in the periplasmic compartment. Whether or not this might be unique to E. herbicola was unknown. RESULTS: The gene coding for the AroQ protein was cloned from Salmonella typhimurium, and the AroQ protein purified from both S. typhimurium and Pseudomonas aeruginosa was shown to have a periplasmic location. The periplasmic chorismate mutases (denoted *AroQ) are shown to be a distinct subclass of AroQ, being about twice the size of cytoplasmic AroQ proteins. The increased size is due to a carboxy-terminal extension of unknown function. In addition, a so-far novel aromatic aminotransferase was shown to be present in the periplasm of P. aeruginosa. CONCLUSIONS: Our analysis has detected a number of additional *aroQ genes. The joint presence of *AroQ, cyclohexadienyl dehydratase and aromatic aminotransferase in the periplasmic compartment of P. aeruginosa comprises a complete chorismate-to-phenylalanine pathway and accounts for the "hidden overflow pathway" to phenylalanine described previously.

Amino Acid Sequence↗
PubMed1994

Two cysteines in each periplasmic domain of the membrane protein DsbB are required for its function in protein disulfide bond formation.

DsbB is a protein component of the pathway that leads to disulfide bond formation in periplasmic proteins of Escherichia coli. Previous studies have led to the hypothesis that DsbB oxidizes the periplasmic protein DsbA, which in turn oxidizes the cysteines in other periplasmic proteins to make disulfide bonds. Gene fusion approaches were used to show that (i) DsbB is a membrane protein which spans the membrane four times and (ii) both the N- and C-termini of the protein are in the cytoplasm. Mutational analysis shows that of the six cysteines in DsbB, four are necessary for proper DsbB function in vivo. Each of the periplasmic domains of the protein has two essential cysteines. The two cysteines in the first periplasmic domain are in a Cys-X-Y-Cys configuration that is characteristic of the active site of other proteins involved in disulfide bond formation, including DsbA and protein disulfide isomerase.

Alkaline Phosphatase↗
PubMed1993

Periplasmic aminopeptidases in Acinetobacter calcoaceticus and Pseudomonas aeruginosa.

The greater part of the intracellular aminopeptidases in Pseudomonas aeruginosa and Acinetobacter calcoaceticus is soluble. The localization of aminopeptidases in the cells was examined using the osmotic shock method with some modifications. When the cells of A. calcoaceticus and P. aeruginosa of the logarithmic phase were subjected to an osmotic shock, all aminopeptidases investigated were mainly localized in the sucrose supernatants and in the periplasm. Acid phosphatase as marker enzyme for periplasm showed a similar distribution between the fractions as the aminopeptidases. The periplasmic aminopeptidases of both microorganisms were separated by FPLC on Superose 12 and their molecular masses were determined. The results obtained show that at least four different aminopeptidases occur in the periplasm, a leucyl aminopeptidase (LAP, cleaving Leu-NH-NH2, 400 kDa), a glutamyl aminopeptidase (GAP, 200 kDa), an alanyl aminopeptidase (AAP, 80 kDa) and a prolyl aminopeptidase (PAP, 65 kDa). The results are in agreement for both species. Our results show clearly that aminopeptidases of these typical members of Gram-negative bacteria are mainly periplasmic like degrading enzymes (alkaline and acid phosphatases, 5'-nucleotidase, cyclic phosphodiesterase), detoxifying enzymes and binding proteins for amino acids and sugars.

Acinetobacter calcoaceticus↗
PubMed1991

Isolation and characterization of extragenic suppressor mutants of the tolA-876 periplasmic-leaky allele in Escherichia coli K-12.

tolA mutants of Escherichia coli K-12 release periplasmic proteins into the extracellular medium; they are sensitive to growth inhibitors such as cholic acid and tolerant to group A colicins and filamentous bacteriophage. Suppressor mutants of the tolA-876 allele were isolated by selecting for cholic acid resistant clones that did not release periplasmic ribonuclease I. One class of tolA suppressor strains carried mutations in the staA gene (for suppressor of tolA) located a 41 min. tolA-876 staA strains partially recovered a wild-type phenotype: they exported alkaline phosphatase and beta-lactamase into the periplasm and only released very low amounts of periplasmic proteins; moreover, they were sensitive to E1 and A colicins and more resistant than tolA-876 staA+ strains to various growth inhibitors. Furthermore, tolA-876 staA-2 and tolA+staA-2 mutants were 10- to 2700-times more resistant than staA+ strains to bacteriophages TuIa, TuIb and T4, and TuII whose receptors are major outer membrane proteins OmpF, OmpC and OmpA, respectively. SDS-PAGE analysis suggested that cell envelopes of staA or staA+ strains contained similar amounts of these proteins but characterization of strains carrying ompF (or C or A)-phoA gene fusions showed that mutation stA-2 reduced ompF gene expression by a factor of two. Analysis of double mutants strains carrying mutation staA-2 and a tolA, tolB, excC or excD periplasmic-leaky mutation showed that staA suppression was allele specific which suggested that proteins TolA and StaA might directly interact.

Alkaline Phosphatase↗
PubMed1994

Periplasmic location of Brucella abortus Cu/Zn superoxide dismutase.

Two types of superoxide dismutase (SOD) have been found in Brucella abortus, a cytosolic Mn-SOD and a Cu/Zn-SOD of unknown location. We sought to determine the subcellular location of Cu/Zn-SOD in B. abortus ST 19. We report a modified spheroplasting procedure for the release of periplasmic contents from B. abortus cells using a dipolar ionic detergent, Zwittergent 316. This detergent, used in place of EDTA, destabilizes the outer membrane sufficiently to allow penetration of lysozyme and the subsequent selective release of periplasmic proteins by osmotic shock. Cytoplasmic cross-contamination of periplasmic fractions was assessed by assaying for malate dehydrogenase activity. Cyanide-sensitive and cyanide-insensitive SOD activity was measured by both the xanthine oxidase-cytochrome c method and a hematoxylin assay. Results suggest that B. abortus Cu/Zn-SOD activity is periplasmic. This zwittergent-lysozyme extraction procedure may be applicable to the separation, isolation and characterization of many other periplasmic proteins of B. abortus and other Gram-negative organisms especially when cytosolic contamination is undesirable.

Brucella abortus↗
PubMed2004

Periplasmic competition for zinc uptake between the metallochaperone ZnuA and Cu,Zn superoxide dismutase.

We have investigated the availability of zinc in the periplasmic space of Escherichia coli using a mutant Cu,Zn superoxide dismutase whose dimerization is triggered by zinc binding. This mutant enzyme accumulates in the monomeric form when wild type cells are grown in minimal medium, but assembles in the dimeric form when it is produced in the same medium by a mutant strain lacking the periplasmic zinc metallochaperone ZnuA. These results indicate that periplasmic zinc-containing proteins compete for metal binding when bacteria grow in environments where this element is present in traces. The effective ZnuA ability to sequester the available zinc ions from the periplasm suggests that zinc-containing cytoplasmic proteins are more important for bacterial viability than the periplasmic ones.

ATP-Binding Cassette Transporters↗
PubMed1995

The Escherichia coli K88 periplasmic chaperone FaeE forms a heterotrimeric complex with the minor fimbrial component FaeH and with the minor fimbrial component FaeI.

K88ab fimbriae are long polymeric protein structures mainly composed of FaeG proteins. The Escherichia coli K88 periplasmic chaperone FaeE is a homodimer and forms a heterotrimeric complex with the K88 major fimbrial component FaeG in the periplasm. In this study the direct interaction of FaeE and the minor K88 fimbrial subunits FaeH and FaeI were investigated. The faeH gene and the faeI gene were subcloned in a pINIIIA1-derivative vector containing the faeE gene. SDS-PAGE using normal and gradient gels and immunoblotting revealed that the subcloned genes were expressed in the periplasm. Analyses of periplasmic fractions by native gel electrophoresis and isoelectric focusing (IEF) showed that FaeE and FaeH, as well as FaeE and FaeI formed protein complexes. These complexes were isolated and purified by FPLC or IEF and native gel electrophoresis. The stoichiometry of the proteins in these complexes was studied by automated Edman degradation and gel image analysis. The results showed that FaeE and FaeH, and FaeE and FaeI formed heterotrimeric E2H and E2I complexes, respectively. In addition to the E2H complex, cells expressing FaeE and FaeH accumulated unbound FaeH in their periplasm. In contrast to the E2G complex, the purified E2H complex was not stable and was partly dissociated in the experimental conditions used, suggesting that the interaction between FaeE and FaeH is not as strong as the interaction of FaeE and FaeG.

Amino Acid Sequence↗
PubMed1992

Kinetic properties of enzyme populations in vivo: alkaline phosphatase of the Escherichia coli periplasm.

Studies were conducted to determine the role that diffusion may play in the in vivo kinetics of the Escherichia coli periplasmic enzyme, alkaline phosphatase (AP, encoded by the gene pho A). Passive diffusion of solutes, from solution into the periplasm, is thought to occur mainly through porins in the outer membrane. The outer membrane therefore serves as a diffusion barrier separating a population of periplasmic enzymes from bulk substrate. E. coli strains containing a plasmid with the pho A gene linked to the lac promoter were used in this study in order to vary the amount of enzyme per cell. Alkaline phosphatase assays were conducted with intact cells, and the substrate concentration at half-maximum velocity (normally the Km for the enzyme) was determined as a function of enzyme concentration per cell. The results showed that diffusion of substrate to the enzyme caused as much as a 1000-fold change in this parameter, compared to that of purified enzyme. This suggested that diffusion was the rate-limiting step of the enzymatic reaction in these cells. In agreement with this type of reaction, Eadie-Hofstee and Lineweaver-Burk plots were not linear. At their extremes, these plots represented two types of kinetics. At high substrate concentration, equilibrium of substrate between bulk solution and the periplasm was achieved, and the kinetic properties conformed to Michaelis-Menten. At low substrate concentrations, there were a large number of free (unbound) enzymes, and each substrate molecule that entered the periplasm, through the diffusion barrier, resulted in product formation.(ABSTRACT TRUNCATED AT 250 WORDS)

Alkaline Phosphatase↗
PubMed1996

Accurate kinetic modeling of alkaline phosphatase in the Escherichia coli periplasm: implications for enzyme properties and substrate diffusion.

Alkaline phosphatase in the periplasm of Escherichia coli presents many of the complex factors that may influence enzymes in vivo. These include an environment that contains a high enzyme concentration, is densely populated with other macromolecules, and is separated from other compartments by a partial diffusion barrier. A previous study provided a partial description of this situation and developed a model that utilized kinetic behavior to estimate the permeability of the outer membrane [Martinez, M. B., et al., (1992) Biochemistry 31, 11500]. This study extends that description to provide a complete model for the enzyme at all substrate levels. Some of the parameters needed for complete modeling include the following: outer membrane permeability to the substrate and product, catalytic efficiency of the enzyme, number of enzymes per cell, and effects of the reaction product (an inhibitor) on the enzyme. The theoretical model fit the data quite well over a wide range of values for each of these parameters. The best fit of theory with experimental data required that the rate constant for product escape from the periplasm was 4-fold greater than that for substrate entry. This correlated with the relative sizes of the substrate and product. The excellent fit of theory and results suggested that alkaline phosphatase and its substrate were unaffected by the solution conditions in the periplasm. That is, the catalytic parameters (kcat and KM), determined for the enzyme in dilute solution, appeared to be unchanged by the conditions in the periplasm. The major factor that altered the kinetic behavior was the combined effect of the permeability barrier and the dense population of enzyme molecules in the periplasm. Given the large impact of these parameters on reaction properties, the excellent fit of theory and results was striking. Overall, this study demonstrated that enzyme action in the complex biological environment can be accurately modeled, if all factors that influence enzyme behavior are known.

Alkaline Phosphatase↗
PubMed1996

Role of the periplasmic domain of the Escherichia coli NarX sensor-transmitter protein in nitrate-dependent signal transduction and gene regulation.

The narX, narQ and narL genes of Escherichia coli encode a nitrate-responsive two-component regulatory system that controls the expression of many anaerobic electron-transport- and fermentation-related genes. When nitrate is present, the NarX and NarQ sensor-transmitter proteins function to activate the response-regulator protein, NarL, which in turn binds to its DNA-recognition sites to modulate gene expression. The sensor-transmitter proteins are anchored in the cytoplasmic membrane by two transmembrane domains that are separated by a periplasmic region of approximately 115 amino acids. In this study we report the isolation and characterization of narX* (star) mutants that constitutively activate nitrate reductase (narGHJI) gene expression and repress fumarate reductase (frdABCD) gene expression when no nitrate is provided for the cell. An additional narX mutant was identified that has lost its ability to respond to environmental signals. Each narX defect was caused by a single amino acid substitution within a conserved 17 amino acid sequence, called the 'P-box', in the periplasmic exposed region of the NarX protein. As a result, DNA binding is then 'locked-on' or 'locked-off' to give the observed pattern of gene expression. Diploid analysis of these narX mutants showed that a NarX P-box mutant which conferred a 'locked-on' phenotype was trans dominant over wild-type NarX. Both were also trans dominant over the NarX P-box mutant which conferred a 'locked-off' phenotype. Certain narX P-box mutations, when combined with a narX 'linker' region mutation, were recessive to the NarX linker mutation. Finally, a truncated form of the NarX protein that lacked the periplasmic and membrane regions also showed a 'locked-on' phenotype in vivo. Thus, the periplasmic and membrane domains are essential for signal transduction to NarL. From these findings, we propose that nitrate is detected in the periplasmic space of the cell, and that a signal-transduction event through the cytoplasmic membrane into the interior of the cell modulates the NarX-dependent phosphorylation/dephosphorylation of NarL.

Amino Acid Sequence↗
PubMed2000

Transfer of electrons across the cytoplasmic membrane by DsbD, a membrane protein involved in thiol-disulphide exchange and protein folding in the bacterial periplasm.

Reduction of non-native protein disulphides in the periplasm of Escherichia coli is catalysed by three enzymes, DsbC, DsbG and DsbE, each of which harbours a catalytic Cys-X-X-Cys dithiol motif. This dithiol motif requires continuous reduction for activity. Genetic evidence suggests that the source of periplasmic reducing power resides within the cytoplasm, provided by thioredoxin (trxA) and thioredoxin reductase (trxB). Cytoplasmic electrons donated by thioredoxin are thought to be transferred into the periplasm via the DsbD membrane protein. To understand the molecular nature of electron transfer, we have analysed the membrane topology of DsbD. DsbD is exported by an N-terminal signal peptide. The N- and C-terminal domains are positioned in the periplasmic space, connected by eight transmembrane segments. Electron transfer was shown to require five cysteine sulphydryl of DsbD. Trans complementation of mutant DsbD molecules revealed intermolecular electron transfer. We discuss a model whereby the membrane-embedded disulphides of DsbD accept electrons from cytoplasmic thioredoxin and transfer them to the C-terminal periplasmic dithiol motif of DsbD.

Amino Acid Sequence↗
PubMed1986

Secretion of beta-lactamase into the periplasm of Escherichia coli: evidence for a distinct release step associated with a conformational change.

The secretion of beta-lactamase (EC 3.5.2.6) into the periplasm of Escherichia coli has been followed by pulse-chase labeling at 15 degrees C. Though the periplasmic fraction contains only the mature form of the enzyme, the spheroplast fraction contains the completed precursor and a hitherto undocumented processed form. When whole spheroplasts are treated with trypsin, the processed form in this fraction is completely digested. This is in contrast to the native mature enzyme localized in the periplasm, which is trypsin resistant. The beta-lactamase is evidently processed after translocation to a trypsin-sensitive form that is transiently bound to the periplasmic face of the inner membrane. The release of this processed form into the periplasm occurs concomitantly with a conformational change that results in the soluble, catalytically active, trypsin-resistant structure.

Cell Compartmentation↗
PubMed1987

Cloning, characterization, and sequencing of the genes encoding the large and small subunits of the periplasmic [NiFe]hydrogenase of Desulfovibrio gigas.

The structural genes for the large and small subunits of Desulfovibrio gigas periplasmic [NiFe]hydrogenase were identified and isolated by immunological and oligonucleotide screening. The gene for the small subunit codes for a 266-amino-acid, 28,724-dalton polypeptide which is separated by 63 nucleotides from the large subunit gene that codes for a 560-amino-acid, 61,707-dalton polypeptide. A putative signal peptide precedes the small subunit coding region, which may direct transport of the enzyme into the periplasmic compartment. Comparison of the amino acid sequence of this enzyme with those of two other classes of hydrogenase found in Desulfovibrio revealed that the D. gigas periplasmic hydrogenase has some homologies to the periplasmic [NiFeSe]hydrogenase of D. baculatus but none to the periplasmic [Fe]hydrogenase of D. vulgaris. The genes for the large and small subunits of the D. gigas hydrogenase hybridize strongly to genomic DNAs from several species of Desulfovibrio, indicating molecular similarity of the [NiFe]hydrogenase among sulfate reducers.

Amino Acid Sequence↗