Precursor forms of penicillin-binding proteins 5 and 6 of E. coli cytoplasmic membrane

Not just an antibiotic target: Exploring the role of type I signal peptidase in bacterial virulence

The looming antibiotic crisis has prompted the development of new strategies towards fighting infection. Traditional antibiotics target bacterial processes essential for viability, whereas proposed antivirulence approaches rely on the inhibition of factors that are required only for the initiation and propagation of infection within a host. Although antivirulence compounds have yet to prove their efficacy in the clinic, bacterial signal peptidase I (SPase) represents an attractive target in that SPase inhibitors exhibit broad-spectrum antibiotic activity, but even at sub-MIC doses also impair the secretion of essential virulence factors. The potential consequences of SPase inhibition on bacterial virulence have not been thoroughly examined, and are explored within this review. In addition, we review growing evidence that SPase has relevant biological functions outside of mediating secretion, and discuss how the inhibition of these functions may be clinically significant.

Peptidoglycan hydrolases of Escherichia coli

The review summarizes the abundant information on the 35 identified peptidoglycan (PG) hydrolases of Escherichia coli classified into 12 distinct families, including mainly glycosidases, peptidases, and amidases. An attempt is also made to critically assess their functions in PG maturation, turnover, elongation, septation, and recycling as well as in cell autolysis. There is at least one hydrolytic activity for each bond linking PG components, and most hydrolase genes were identified. Few hydrolases appear to be individually essential. The crystal structures and reaction mechanisms of certain hydrolases having defined functions were investigated. However, our knowledge of the biochemical properties of most hydrolases still remains fragmentary, and that of their cellular functions remains elusive. Owing to redundancy, PG hydrolases far outnumber the enzymes of PG biosynthesis. The presence of the two sets of enzymes acting on the PG bonds raises the question of their functional correlations. It is difficult to understand why E. coli keeps such a large set of PG hydrolases. The subtle differences in substrate specificities between the isoenzymes of each family certainly reflect a variety of as-yet-unidentified physiological functions. Their study will be a far more difficult challenge than that of the steps of the PG biosynthesis pathway.

Investigation of the mechanism of the cell wall DD-carboxypeptidase reaction of penicillin-binding protein 5 of Escherichia coli by quantum mechanics/molecular mechanics calculations

Penicillin-binding protein 5 (PBP 5) of Escherichia coli hydrolyzes the terminal D-Ala-D-Ala peptide bond of the stem peptides of the cell wall peptidoglycan. The mechanism of PBP 5 catalysis of amide bond hydrolysis is initial acylation of an active site serine by the peptide substrate, followed by hydrolytic deacylation of this acyl-enzyme intermediate to complete the turnover. The microscopic events of both the acylation and deacylation half-reactions have not been studied. This absence is addressed here by the use of explicit-solvent molecular dynamics simulations and ONIOM quantum mechanics/molecular mechanics (QM/MM) calculations. The potential-energy surface for the acylation reaction, based on MP2/6-31+G(d) calculations, reveals that Lys47 acts as the general base for proton abstraction from Ser44 in the serine acylation step. A discrete potential-energy minimum for the tetrahedral species is not found. The absence of such a minimum implies a conformational change in the transition state, concomitant with serine addition to the amide carbonyl, so as to enable the nitrogen atom of the scissile bond to accept the proton that is necessary for progression to the acyl-enzyme intermediate. Molecular dynamics simulations indicate that transiently protonated Lys47 is the proton donor in tetrahedral intermediate collapse to the acyl-enzyme species. Two pathways for this proton transfer are observed. One is the direct migration of a proton from Lys47. The second pathway is proton transfer via an intermediary water molecule. Although the energy barriers for the two pathways are similar, more conformers sample the latter pathway. The same water molecule that mediates the Lys47 proton transfer to the nitrogen of the departing D-Ala is well positioned, with respect to the Lys47 amine, to act as the hydrolytic water in the deacylation step. Deacylation occurs with the formation of a tetrahedral intermediate over a 24 kcal x mol(-1) barrier. This barrier is approximately 2 kcal x mol(-1) greater than the barrier (22 kcal x mol(-1)) for the formation of the tetrahedral species in acylation. The potential-energy surface for the collapse of the deacylation tetrahedral species gives a 24 kcal x mol(-1) higher energy species for the product, signifying that the complex would readily reorganize and pave the way for the expulsion of the product of the reaction from the active site and the regeneration of the catalyst. These computational data dovetail with the knowledge on the reaction from experimental approaches.

An investigation into the lipid interactions of peptides corresponding to the C-terminal anchoring domains of Escherichia coli penicillin-binding proteins 4, 5 and 6

The Escherichia coli low molecular mass penicillin-binding proteins PBP4, PBP5 and PBP6 are DD-peptidases involved in murein biosynthesis. It has been suggested that these proteins may be anchored to the periplasmic face of the inner membrane via their C termini. Here, peptide homologues (P4, P5 and P6) of the PBP4, PBP5 and PBP5 C-terminal regions have been used to investigate potential protein-lipid interactions involved in this anchoring mechanism. Surface pressure changes observed for the interactions of P5 and P6 with a range of monolayers indicated that the peptides are membrane interactive and that the interactions proceeded via predominantly hydrophobic forces with only minor requirements for anionic lipid. In contrast, P4 interactions with monolayers appeared to proceed via predominantly electrostatic forces with a major requirement for anionic lipid. The lipid interactions of all three peptides were generally enhanced by low pH and for P5 and P6 were in the range of 10-15 mN m-1 whereas for P4 interactions they were in the range of 3-7 mN m-1. CD analysis implied the presence of alpha-helical structure in P5 and P6 and molecular area determinations implied that P4 may also possess helical architecture in the presence of dioleoylphosphatidylglycerol monolayers. Overall, our results support the view that C-terminal amphiphilic alpha-helices are involved in the membrane anchoring of PBP5 and PBP6 and suggest that a similar mechanism could contribute to PBP4-membrane anchoring. Furthermore, we have speculated that the presence of cationic residues in the hydrophilic face of these alpha-helices may help facilitate membrane interaction.

Alpha-helical conformation in the C-terminal anchoring domains of E. coli penicillin-binding proteins 4, 5 and 6

The E. coli low molecular mass penicillin-binding proteins (PBP's) are penicillin sensitive, enzymes involved in the terminal stages of peptidoglycan biosynthesesis. These PBP's are believed to anchor to the periplasmic face of the inner membrane via C-terminal amphiphilic alpha-helices but to date the only support for this hypothesis has been obtained from theoretical analysis. In this paper, the conformational behaviour of synthetic peptides corresponding to these C-terminal anchoring domains was studied as a function of solvent, pH, sodium dodecyl sulphate micelles and phospholipid (DOPC, DOPG) vesicles using circular dichroism (CD) spectroscopy. The CD data showed that in 2,2,2-trifluoroethanol or sodium dodecylsulphate, all three peptides have the capacity to form an alpha-helical conformation but in aqueous solution or in the presence of phospholipid vesicles only those peptides corresponding to the PBP5 and PBP6 C-termini were observed to do so. A pH dependent loss of alpha-helical conformation in the peptide corresponding to the PBP5 C-terminus was found to correlate with the susceptibility of PBP5 to membrane extraction. This correlation would agree with the hypothesis that an alpha-helical conformation is required for membrane interaction of the PBP5 C-terminal region.

dacD, an Escherichia coli gene encoding a novel penicillin-binding protein (PBP6b) with DD-carboxypeptidase activity

In the course of a study of genes located at min 44 of the Escherichia coli genome, we identified an open reading frame with the capacity to encode a 43-kDa polypeptide whose predicted amino acid sequence is strikingly similar to those of the well-known DD-carboxipeptidases penicillin-binding proteins PBP5 and PBP6. The gene product was shown to bind [3H]benzylpenicillin and to have DD-carboxypeptidase activity on pentapeptide muropeptides in vivo. Therefore, we called the protein PBP6b and the gene dacD. As with other E. coli DD-carboxypeptidases, PBP6b is not essential for cell growth. A quadruple dacA dacB dacC dacD mutant was constructed and shown to grow as well as its isogenic wild-type strain, indicating that the loss of any known PBP-associated DD-carboxypeptidase activity is not deleterious for E. coli. We also identified the homologous gene of dacD in Salmonella typhimurium as one of the components of the previously described phsBCDEF gene cluster.

Multiple mechanisms of membrane anchoring of Escherichia coli penicillin-binding proteins

The major penicillin-binding proteins (PBPs) of Escherichia coli play vital roles in cell wall biosynthesis and are located in the inner membrane. The high M(r) PBPs 1A, 1B, 2 and 3 are essential bifunctional transglycosylases/transpeptidases which are thought to be type II integral inner membrane proteins with their C-terminal enzymatic domains projecting into the periplasm. The low M(r) PBP4 is a DD-carboxypeptidase/endopeptidase, whereas PBPs 5 and 6 are DD-carboxypeptidases. All three low M(r) PBPs act in the modification of peptidoglycan to allow expansion of the sacculus and are thought to be periplasmic proteins attached with varying affinities to the inner membrane via C-terminal amphiphilic alpha-helices. It is possible that the PBPs and other inner membrane proteins form a peptidoglycan synthesizing complex to coordinate their activities.

Cleavable signal peptides are rarely found in bacterial cytoplasmic membrane proteins (review)

Most proteins destined for secretion are synthesized with amino-terminal extensions, known as signal peptides, which play a vital role in their translocation across the membrane bordering the cytoplasm. Following translocation across the eukaryotic endoplasmic reticulum (ER) membrane or the bacterial cytoplasmic membrane, signal peptides are proteolytically removed from the preproteins. The process of membrane protein assembly can be likened to that of protein export in that it involves the translocation of portions of proteins across membranes. Moreover, the topological similarities between eukaryotic ER and plasma membrane proteins and bacterial cytoplasmic membrane proteins suggest that the mechanisms of membrane protein assembly may, like those of protein export, share fundamental similarities in eukaryotic and bacterial cells. However, whilst many of the ER and plasma membrane proteins of higher eukaryotes are synthesized with cleavable signal peptides, the same is true of only very few bacterial cytoplasmic membrane proteins. This fact is not widely appreciated, probably because certain exceptional (signal peptide-containing) bacterial membrane proteins, such as the major coat protein of bacteriophage M13, have been the subject of extensive investigations. In this review we highlight this anomaly and discuss it within the general context of membrane protein topology.

Possible role of Escherichia coli penicillin-binding protein 6 in stabilization of stationary-phase peptidoglycan

Plasmids for high-level expression of penicillin-binding protein 6 (PBP6) were constructed, giving rise to overproduction of PBP6 under the control of the lambda pR promoter in either the periplasmic or the cytoplasmic space. In contrast to penicillin-binding protein 5 (PBP5), the presence of high amounts of PBP6 in the periplasm as well as in the cytoplasm did not result in growth as spherical cells or in lysis. Deletion of the C-terminal membrane anchor of PBP6 resulted in a soluble form of the protein (PBP6s350). Electron micrographs of thin sections of cells overexpressing both native membrane-bound and soluble PBP6 in the periplasm revealed a polar retraction of the cytoplasmic membrane. Cytoplasmic overexpression of native PBP6 gave rise to the formation of membrane vesicles, whereas the soluble PBP6 formed inclusion bodies in the cytoplasm. Both the membrane-bound and the soluble forms of PBP6 were purified to homogeneity by using the immobilized dye Procion rubine MX-B. Purified preparations of PBP6 and PBP6s350 formed a 14[C]penicillin-protein complex at a 1:1 stoichiometry. The half-lives of the complexes were 8.5 and 6 min, respectively. In contrast to PBP5, no DD-carboxypeptidase activity could be detected for PBP6 by using bisacetyl-L-Lys-D-Ala-D-Ala and several other substrates. These findings led us to conclude that PBP6 has a biological function clearly distinct from that of PBP5 and to suggest a role for PBP6 in the stabilization of the peptidoglycan during stationary phase.

A new mercury-penicillin V derivative as a probe for ultrastructural localization of penicillin-binding proteins in Escherichia coli

The precise ultrastructural localization of penicillin-binding protein (PBP)-antibiotic complexes in Escherichia coli JM101, JM101 (pBS96), and JM101(pPH116) was investigated by high-resolution electron microscopy. We used mercury-penicillin V (Hg-pen V) as a heavy-metal-labeled, electron-dense probe for accurately localizing PBPs in situ in single bacterial cells grown to exponential growth phase. Biochemical data derived from susceptibility tests and bacteriolysis experiments revealed no significant differences between Hg-pen V and the parent compound, penicillin V, or between strains. Both antibiotics revealed differences in the binding affinities for PBPs of all strains. Deacylation rates for PBPs were slow despite the relatively low binding affinities of antibiotics. Cells bound most of the Hg-pen V added to cultures, and the antibiotic-PBP complex could readily be seen by electron microscopy of unstained whole mounts as distinct, randomly situated electron-dense particles. Fifty to 60% of the antibiotic was retained by cells during processing for conventional embedding so that thin sections could also be examined. These revealed similar electron-dense particles located predominantly on the plasma membrane and less frequently in the cytoplasm. Particles positioned on the plasma membranes were occasionally shown to protrude into the periplasmic space, thereby reflecting the high resolution of the Hg-pen V probe. Moreover, some particles were observed free in the periplasm, suggesting, for the first time, that a proportion of PBPs may not be restricted to the plasma membrane but may be tightly associated with the peptidoglycan for higher efficiency of peptidoglycan assembly. All controls were devoid of the electron-dense particles. The presence of electron-dense particles in cells of the wild-type JM101, demonstrated that our probe could identify PBPs in naturally occurring strains without inducing PBP overproduction.

Cloning, mapping, and characterization of the Escherichia coli prc gene, which is involved in C-terminal processing of penicillin-binding protein 3

The prc gene, which is involved in cleavage of the C-terminal peptide from the precursor form of penicillin-binding protein 3 (PBP 3) of Escherichia coli, was cloned and mapped at 40.4 min on the chromosome. The gene product was identified as a protein of about 80 kDa in maxicell and in vitro systems. Fractionation of the maxicells producing the product suggested that the product was associated with the periplasmic side of the cytoplasmic membrane. This was consistent with the notion that the C-terminal processing of PBP 3 probably occurs outside the cytoplasmic membrane: the processing was found to be dependent on the secY and secA functions, indicating that the prc product or PBP 3 or both share the translocation machinery with other extracytoplasmic proteins. DNA sequencing analysis of the prc gene region identified an open reading frame, with two possible translational starts 6 bp apart from each other, that could code for a product with a calculated molecular weight of 76,667 or 76,432. The prc mutant was sensitive to thermal and osmotic stresses. Southern analysis of the chromosomal DNA of the mutant unexpectedly revealed that the mutation was a deletion of the entire prc gene and thus that the prc gene is conditionally dispensable. The mutation resulted in greatly reduced heat shock response at low osmolarity and in leakage of periplasmic proteins.

Cloning and expression of the ponB gene, encoding penicillin-binding protein 1B of Escherichia coli, in heterologous systems

A fragment from the ponB region of the Escherichia coli chromosome comprising the promoterless sequence encoding penicillin-binding protein 1B (PBP 1B) has been cloned in a broad-host-range expression vector under the control of the kanamycin resistance gene promoter present in the vector. The hybrid plasmid (pJP3) was used to transform appropriate strains of Salmonella typhimurium, Pseudomonas putida, and Pseudomonas aeruginosa. In all instances, the coding sequence was expressed in the heterologous hosts, yielding a product with electrophoretic mobility, protease accessibility, membrane location, and beta-lactam-binding properties identical to those of native PBP 1B in E. coli. These results indicated that PBP 1B of E. coli is compatible with the cytoplasmic membrane environment of unrelated bacterial species and support the idea that interspecific transfer of mutated alleles of genes coding for PBPs could potentially be an efficient spreading mechanism for intrinsic resistance to beta-lactams.

Sequence of the peh gene of Erwinia carotovora: homology between Erwinia and plant enzymes

Polygalacturonase (Peh) and other pectolytic enzymes play a crucial role in the maceration of vegetables by soft rot Erwinia spp. We have sequenced the peh gene of Erwinia carotovora subsp. carotovora, and identified its product as a precursor of molecular weight 42,639, and a mature protein of molecular weight 42,200. A putative KdgR-binding site was identified in the region 5' to the peh gene. The Peh protein showed significant homology with Peh from tomato. In addition, we have found homologies between pectin methylesterase and pectate lyase from Erwinia and their counterparts in tomato. These homologies are described, and their significance discussed.

Extracellular and periplasmic isoenzymes of pectate lyase from Erwinia carotovora subspecies carotovora belong to different gene families

Pectate lyase (Pel) plays a crucial role in the maceration of vegetables by soft rot Erwinia spp. We have characterized the four Pel isoenzymes of Erwinia carotovora subspecies carotovora strain SCRI193. In this paper we concentrate on two isoenzymes which have different locations in SCRI193: PLb is periplasmic and PLc is extracellular. Comparison of the gene products and nucleotide sequences of pelB and pelC allowed us to assign them to different gene families. In addition, we have identified a number of conserved amino acid residues that are common to all extracellular Pel isoenzymes.

Membrane topology of penicillin-binding protein 3 of Escherichia coli

The beta-lactamase fusion vector, pJBS633, has been used to analyse the organization of penicillin-binding protein 3 (PBP3) in the cytoplasmic membrane of Escherichia coli. The fusion junctions in 84 in-frame fusions of the coding region of mature TEM beta-lactamase to random positions within the PBP3 gene were determined. Fusions of beta-lactamase to 61 different positions in PBP3 were obtained. Fusions to positions within the first 31 residues of PBP3 resulted in enzymatically active fusion proteins which could not protect single cells of E. coli from killing by ampicillin, indicating that the beta-lactamase moieties of these fusion proteins were not translocated to the periplasm. However, all fusions that contained greater than or equal to 36 residues of PBP3 provided single cells of E. coli with substantial levels of resistance to ampicillin, indicating that the beta-lactamase moieties of these fusion proteins were translocated to the periplasm. PBP3 therefore appeared to have a simple membrane topology with residues 36 to the carboxy-terminus exposed on the periplasmic side of the cytoplasmic membrane. This topology was confirmed by showing that PBP3 was protected from proteolytic digestion at the cytoplasmic side of the inner membrane but was completely digested by proteolytic attack from the periplasmic side. PBP3 was only inserted in the cytoplasmic membrane at its amino terminus since replacement of its putative lipoprotein signal peptide with a normal signal peptide resulted in a water-soluble, periplasmic form of the enzyme. The periplasmic form of PBP3 retained its penicillin-binding activity and appeared to be truly water-soluble since it fractionated, in the absence of detergents, with the expected molecular weight on Sephadex G-100 and was not retarded by hydrophobic interaction chromatography on Phenyl-Superose.

A water-soluble form of penicillin-binding protein 2 of Escherichia coli constructed by site-directed mutagenesis

Penicillin-binding protein (PBP) 2 of Escherichia coli is located in the cytoplasmic membrane. The N-terminal hydrophobic segment (31 amino acids, residues 15-45) of PBP2 was removed by a deletion in the PBP2 gene by site-directed mutagenesis, resulting in the production of a water-soluble form of PBP2 (called PBP2*). PBP2* retained the penicillin-binding activity, was localized in the cytoplasm and was overproduced under the control of the lpp-lac promoter. this indicates that the removed hydrophobic segment is an uncleaved signal sequence required for translocation of PBP2 across the cytoplasmic membrane, and also suggests that the segment anchors the protein to the membrane.

Use of a beta-lactamase fusion vector to investigate the organization of penicillin-binding protein 1B in the cytoplasmic membrane of Escherichia coli

The coding region for the mature form of TEM beta-lactamase was fused to random positions within the coding region of the penicillin-binding protein 1B (PBP 1B) gene and the nucleotide sequences across the fusion junctions of 100 in-frame fusions were determined. All fusion proteins that contained at least the NH2-terminal 94 residues of PBP 1B provided individual cells of E. coli with substantial levels of ampicillin resistance, suggesting that the beta-lactamase moiety had been translocated to the periplasm. Fusion proteins that contained less than or equal to 63 residues of PBP 1B possessed beta-lactamase activity, but could not protect single cells of E. coli from ampicillin, indicating that the beta-lactamase moiety of these fusion proteins remained in the cytoplasm. The beta-lactamase fusion approach suggested a model for the organization of PBP 1B in which the protein is embedded in the cytoplasmic membrane by a single hydrophobic transmembrane segment (residues 64-87), with a short NH2-terminal domain (residues 1-63), and the remainder of the polypeptide (residues 88-844) exposed on the periplasmic side of the cytoplasmic membrane. The proposed model for the organization of PBP 1B was supported by experiments which showed that the protein was completely digested by proteinase K added from the periplasmic side of the cytoplasmic membrane but was only slightly reduced in size by protease attack from the cytoplasmic side of the membrane.

Nucleotide sequence of the pbpA gene and characteristics of the deduced amino acid sequence of penicillin-binding protein 2 of Escherichia coli K12

We have determined the nucleotide sequence of the pbpA gene encoding penicillin-binding protein (PBP) 2 of Escherichia coli. The coding region for PBP 2 was 1899 base pairs in length and was preceded by a possible promoter sequence and two open reading frames. The primary structure of PBP 2, deduced from the nucleotide sequence, comprised 633 amino acid residues. The relative molecular mass was calculated to be 70867. The deduced sequence agreed with the NH2-terminal sequence of PBP 2 purified from membranes, suggesting that PBP 2 has no signal peptide. The hydropathy profile suggested that the NH2-terminal hydrophobic region (a stretch of 25 non-ionic amino acids) may anchor PBP 2 in the cytoplasmic membrane as an ectoprotein. There were nine homologous segments in the amino acid sequence of PBP 2 when compared with PBP 3 of E. coli. The active-site serine residue of PBP 2 was predicted to be Ser-330. Around this putative active-site serine residue was found the conserved sequence of Ser-Xaa-Xaa-Lys, which has been identified in all of the other E. coli PBPs so far studied (PBPs 1A, 1B, 3, 5 and 6) and class A and class C beta-lactamases. In the higher-molecular-mass PBPs 1A, 1B, 2 and 3, Ser-Xaa-Xaa-Lys-Pro was conserved. In the putative peptidoglycan transpeptidase domain there were six amino acid residues, which are common only in the PBPs of higher molecular mass.

Intermediates in the assembly of the TonA polypeptide into the outer membrane of Escherichia coli K12

The tonA gene of Escherichia coli K12 was cloned into a multicopy plasmid, leading to substantial overproduction of the corresponding 78,000 Mr polypeptide in the outer membrane. The approximate size of the tonA gene and its direction of transcription were established by Tn1000 mutagenesis. A family of tonA deletions was constructed in vitro by Bal31 exonuclease digestion, followed by splicing of an "oligo stop" sequence to each 3' terminus in order to ensure prompt termination of translation of the truncated polypeptides in vivo. All these polypeptides proved to be extremely unstable in exponentially growing cultures but were relatively stable in maxicells. Under these conditions the truncated polypeptides, unlike wild-type TonA, fractionated with the Sarkosyl-soluble fraction of the cell envelope, indicating that these proteins are blocked in assembly as inner membrane (translocation) intermediates or as outer membrane (maturation) intermediates unable to form Sarkosyl-resistant complexes. We have also examined the kinetics of assembly of wild-type TonA into the outer membrane and the results indicate that, following cleavage of the N-terminal signal peptide, the protein passes through an apparently membrane-free intermediate form and only appears in the outer membrane after a delay of at least 50 seconds, following the completion of synthesis. From these results, we propose that the assembly of TonA involves translocation (with concomitant cleavage of the signal sequence) directly into the periplasm, followed by partitioning into the outer membrane. We further propose that the C terminus of TonA is essential for final maturation in the outer membrane in Sarkosyl-resistant form but that the C-terminal half of the molecule probably does not contain any topogenic sequences required for partitioning to the outer membrane.

Prokaryotic gene expression in vitro: transcription-translation coupled systems

Transcription-translation coupled systems have been developed to study prokaryotic gene expression. Several types of expression system have been described. The original system consists of a crude unfractionated Escherichia coli extract, which supports protein synthesis directed by a template DNA. Control of gene expression at the transcriptional stage has been studied using this unfractionated system. In this respect, two examples of particular interest, lactose and tryptophan operons, are described. Other systems are either partially reconstituted or highly defined, containing up to 30 purified factors necessary for transcription (RNA polymerase) and translation (aminoacyl-tRNA synthetases, initiation, elongation and release factors). Additional differences between the various systems relate to the analysis of the gene products. Whereas most methods involve analysis of the totally synthesized protein, a particular system implies the formation of only the N-terminal di- or tripeptide of the gene product. Reconstituted systems have proved useful in studies on transcriptional, e.g., discovery and role of L factor, as well as translational regulation of gene expression, e.g., autogenous control of ribosomal protein synthesis.

A vector for the construction of translational fusions to TEM beta-lactamase and the analysis of protein export signals and membrane protein topology

A plasmid vector, pJBS633, that facilitates the construction of translational fusions of genes of interest to the coding region of the mature form of TEM beta-lactamase has been developed. Transformants containing in-frame fusions can be identified by their ability to grow when plated at high inocula on agar containing ampicillin (Ap). The cellular location of the beta-lactamase moiety of the fusion proteins can then be determined since only those that direct the translocation of the beta-lactamase across the cytoplasmic membrane to the periplasm result in the ability of individual cells of Escherichia coli to form isolated colonies in the presence of Ap. Conversely, those fusion proteins in which the beta-lactamase moiety remains cytoplasmic do not protect individual cells against Ap. Transformants expressing the latter class of fusion proteins can, however, be identified when plated at high inocula since, as cells start to lyse, the cytoplasmic beta-lactamase activity is released and provides Ap resistance to the surrounding cells. The vector contains the origin of replication of f1 phage so that single-stranded plasmid DNA can be obtained in the appropriate orientation to allow sequencing across the fusion junction using a universal primer complementary to the start of the coding region of mature TEM beta-lactamase. pJBS633 should be useful as a general vector for the construction of beta-lactamase fusions and, in particular, for the analysis of protein export signals and the determination of the organisation of proteins in the E. coli cytoplasmic membrane.

The nucleotide sequences of the ponA and ponB genes encoding penicillin-binding protein 1A and 1B of Escherichia coli K12

Penicillin-binding proteins 1A and 1B of Escherichia coli are the major peptidoglycan transglycosylase-transpeptidases that catalyse the polymerisation and insertion of peptidoglycan precursors into the bacterial cell wall during cell elongation. The nucleotide sequence of a 2764-base-pair fragment of DNA that contained the ponA gene, encoding penicillin-binding protein 1A, was determined. The sequence predicted that penicillin-binding protein 1A had a relative molecular mass of 93 500 (850 amino acids). The amino-terminus of the protein had the features of a signal peptide but it is not known if this peptide is removed during insertion of the protein into the cytoplasmic membrane. The nucleotide sequence of a 2758-base-pair fragment of DNA that contained the ponB gene, encoding penicillin-binding protein 1B, was also determined. Penicillin-binding protein 1B consists of two major components which were shown to result from the use of alternative sites for the initiation of translation. The large and small forms of penicillin-binding protein 1B were predicted to have relative molecular masses of 94 100 and 88 800 (844 and 799 amino acids). The amino acid sequences of penicillin-binding proteins 1A and 1B could be aligned if two large gaps were introduced into the latter sequence and the two proteins then showed about 30% identity. The amino acid sequences of the proteins showed no extensive similarity to the sequences of penicillin-binding proteins 3 or 5, or to the class A or class C beta-lactamases. Two short regions of amino acid similarity were, however, found between penicillin-binding proteins 1A and 1B and the other penicillin-binding proteins and beta-lactamases. One of these included the predicted active-site serine residue which was located towards the middle of the sequences of penicillin-binding proteins 1A, 1B and 3, within the conserved sequence Gly-Ser-Xaa-Xaa-Lys-Pro. The other region was 19-40 residues to the amino-terminal side of the active-site serine and may be part of a conserved penicillin-binding site in these proteins.

In vitro translocation of bacterial proteins across the plasma membrane of Escherichia coli

Precursors to two periplasmic proteins and one outer membrane protein were synthesized in a membrane-free extract from Escherichia coli programmed with plasmid DNA. In the presence of inverted plasma membrane vesicles from E. coli up to 25% of the precursor molecules were converted into their mature forms. Using externally added proteinase K as a probe, we found the processed proteins segregated within the membrane vesicles. By the same criteria, a small amount of each precursor also proved to be translocated, indicating that translocation and signal sequence cleavage are not necessarily coupled processes. Furthermore, we present conclusive evidence that the translocation step can occur post-translationally even as late as 60 min after the beginning of translation.

Biochemical and genetic characterization of the tet determinant of Bacillus plasmid pAB124

A fragment of Bacillus plasmid pAB124 carrying the genes encoding tetracycline resistance was previously cloned into Escherichia coli plasmid pSF2124 (S.J. Eccles, A. Docherty, I. Chopra, S. Shales, and P. Ball, J. Bacteriol. 145:1417-1420, 1981). The cloned pAB124 tet fragment conferred low-level resistance in E. coli, but exposure of this strain to a subinhibitory level of tetracycline led to selection of a mutant plasmid in which high-level resistance, associated with decreased drug accumulation, was expressed constitutively. In this plasmid, the Bacillus tet determinant appeared to be transcribed from a promoter on the vector. Construction of tetracycline-sensitive derivatives of this plasmid by transposon insertion mutagenesis allowed identification of a 32,000-dalton membrane-located protein, which apparently promoted decreased accumulation of tetracycline. This protein was also synthesized as a 32,000-dalton polypeptide in a coupled, in vitro transcription-translation system directed by plasmid DNA. The pAB124 tet determinant differed from the tetA through tetD determinants found in gram-negative bacteria in DNA-DNA hybridization and in the ability to prevent accumulation of different tetracycline derivatives, but was closely related to the tet determinant of another plasmid isolated from Bacillus species, pBC16.

Cirrhosis associated with multiple transfusions in thalassaemia

The study of surgical liver biopsy specimens obtained during splenectomy in 86 children with thalassaemia indicated that such patients may develop liver disease that evolves into cirrhosis. Histological characteristics suggest that it is post-necrotic cirrhosis. Onset of cirrhosis in some patients may occur as early as 7-8 years old, and at age about 15-16 years most children with thalassaemia show features of cirrhosis. In addition to fibrosis, hepatitis, or even aggressive hepatitis may develop as has also been observed in patients without thalassaemia who have undergone multiple transfusions. This study presents the current probable evolution of liver disease in patients with thalassaemia and may thus serve as a reference from which to evaluate any future progress in the treatment and care of patients with Cooley's disease.

[Biosynthesis and transport of envelope proteins of Escherichia coli]

Bacterial protein synthesis takes place in the cytoplasm, thus periplasmic and outer membrane proteins pass through the cytoplasmic membrane during their dispatch to the cell envelope. The exported proteins are synthesized as precursor that contains an extra amino-terminal sequence of amino-acids. This sequence, termed "signal sequence", is essential for transport of the envelope proteins through the inner membrane and is cleaved during the exportation process. Various hypotheses for the mechanism have been presented, and it is likely that no signal model will be suitable to the export of all cell envelope proteins. This review is focused on the relationship between the cytoplasmic membrane and the precursor form. The physiological state of the membrane - fluidity, membrane potential for instance - is the strategic requirement of exportation process. Precursors can be accumulated in whole cells with various treatments which alter the cytoplasmic membrane. This inhibition of processing is obtained by modification of unsaturated to saturated fatty acids ratio or with phenylethyl alcohol which perturbs the membrane fluidity, with uncoupler agents such as carbonyl cyanide m-chlorophenyl hydrazone which dissipate the proton motive force, or with hybrid proteins which get jamming in the membrane. However, little is known about the early steps of translocation process across the cytoplasmic membrane ; for instance, it is not clear yet whether energy is required for either or both of the first interaction membrane-precursor and the crossing through the membrane. Several studies have recently shown the presence of exportation sites and of proteins which might play a prominent role in the export process, but the mechanism of discrimination between outer membrane proteins and periplasmic proteins is unknown. Considerable work has been done by genetic or biochemical methods and we have now the first lights of the expert mechanism.

Identification of the rodA gene product of Escherichia coli

Plasmids that carry the Escherichia coli cell shape gene rodA directed the synthesis of a cytoplasmic membrane protein (Mr, 31,000 [31K protein] ) in minicells, maxicells, and an in vitro-coupled transcription-translation system. The 31K protein was identified as the rodA gene product, because it was not synthesized from the vector plasmids or from a plasmid in which the rodA gene was inactivated by insertion of Tn1000. Furthermore, a purified 1.6-kilobase KpnI-BamHI DNA fragment that contained the intact rodA gene directed the synthesis of only the 31K protein in an in vitro system. The apparent molecular weight of the protein was identical whether synthesized in vivo or in vitro, indicating that the rodA gene product is not made as a preprotein. The direction of transcription of rodA was from the KpnI site towards the BamHI site. The 31K protein was unusual in that it could only be detected when cell membranes were solubilized at low temperature (e.g., 37 degrees C) before sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Apparently the rodA gene product aggregates after being boiled in sodium dodecyl sulfate and fails to enter a polyacrylamide gel.

Organization and subcloning of the dacA-rodA-pbpA cluster of cell shape genes in Escherichia coli

The transducing bacteriophage lambda pBS10 carries a small cluster of Escherichia coli penicillin-binding protein/cell shape genes, including pbpA, rodA, and dacA. Deletion mapping and subcloning showed that these genes, and the gene for a cytoplasmic membrane protein of molecular weight 54,000, are located within a 5.6-kilobase region and are probably contiguous. The dacA gene, which codes for penicillin-binding protein 5, was cloned on a 1.5-kilobase fragment into a low-copy-number plasmid vector, but insertion into high-copy-number plasmids produced deleterious effects on bacterial growth, and the plasmids could not be stably maintained. The direction of transcription of dacA was determined. The rodA gene was cloned on a 1.6-kilobase fragment into both low- and high-copy-number plasmids, and the identification of its gene product is described in the accompanying paper (Stoker et al., J. Bacteriol. 155:854-859). The pbpA gene, which codes for penicillin-binding protein 2, was cloned on a 3.7-kilobase fragment in low-copy-number plasmids, but insertion of the fragment into high-copy-number plasmids resulted in deleterious effects on bacterial growth, and the plasmids could not be stably maintained.

On the process of cellular division in Escherichia coli: nucleotide sequence of the gene for penicillin-binding protein 3

We determined the nucleotide sequence of a DNA fragment containing the ftsI gene coding for the penicillin-binding protein 3 (PBP-3), an indispensable enzyme for cell division of Escherichia coli. The entire ftsI gene was within the 2.8 kilobase PvuII fragment derived from the chromosomal segment on pLC26-6 (Nishimura et al. 1977). The coding region for PBP-3 was identified by comparison with the N-terminal amino acid sequence of in vitro synthesized PBP-3. The structural gene for ftsI consisted of 1,764 base-pairs coding for a 588 amino acid residue-polypeptide with a molecular weight of 63,850. PBP-3 synthesized in vitro showed a lower mobility in SDS-gel electrophoresis than that of the authentic PBP-3, suggesting that the primary translation product of the ftsI gene may be processed to yield mature PBP-3.

Insertion of a MalE beta-galactosidase fusion protein into the envelope of Escherichia coli disrupts biogenesis of outer membrane proteins and processing of inner membrane proteins

The synthesis of a membrane-bound MalE beta-galactosidase hybrid protein, when induced by growth of Escherichia coli on maltose, leads to inhibition of cell division and eventually a reduced rate of mass increase. In addition, the relative rate of synthesis of outer membrane proteins, but not that of inner membrane proteins, was reduced by about 50%. Kinetic experiments demonstrated that this reduction coincided with the period of maximum synthesis of the hybrid protein (and another maltose-inducible protein, LamB). The accumulation of this abnormal protein in the envelope therefore appeared specifically to inhibit the synthesis, the assembly of outer membrane proteins, or both, indicating that the hybrid protein blocks some export site or causes the sequestration of some limiting factor(s) involved in the export process. Since the MalE protein is normally located in the periplasm, the results also suggest that the synthesis of periplasmic and outer membrane proteins may involve some steps in common. The reduced rate of synthesis of outer membrane proteins was also accompanied by the accumulation in the envelope of at least one outer membrane protein and at least two inner membrane proteins as higher-molecular-weight forms, indicating that processing (removal of the N-terminal signal sequence) was also disrupted by the presence of the hybrid protein. These results may indicate that the assembly of these membrane proteins is blocked at a relatively late step rather than at the level of primary recognition of some site by the signal sequence. In addition, the results suggest that some step common to the biogenesis of quite different kinds of envelope protein is blocked by the presence of the hybrid protein.

A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane

Gene III protein of bacteriophage f1 is inserted into the host cell membrane where it is assembled into phage particles. A truncated form of gene III protein, encoded by a recombinant plasmid and lacking the carboxyl terminus, does not remain in the membrane but instead appears to slip through it. Fusion of a hydrophobic "membrane anchor" from another membrane protein, the gene VIII protein, to the truncated gene III protein (by manipulation of the recombinant plasmid) restores membrane anchoring. A model for the relationship of gene III protein with the Escherichia coli membrane is discussed.

Complete nucleotide sequence and identification of membrane components of the histidine transport operon of S. typhimurium

The nucleotide sequence of the entire histidine transport operon from Salmonella typhimurium has been determined and is shown to consist of four genes, hisJ, hisQ, hisM and hisP. This operon provides the only example of a binding protein-dependent transport system for which the total number of protein components is known. Determination of the amino acid compositions and sequences of these four transport proteins, together with analysis of various transport mutants, allows us to propose a molecular model for binding protein-dependent transport.

Synthesis of penicillin-binding protein 6 by stationary-phase Escherichia coli

The level of penicillin-binding protein 6, a D-alanine carboxypeptidase I, was found to be 2- to 10-fold higher in stationary-phase cells than in exponentially growing cells of Escherichia coli. This increase appeared to be due to de novo synthesis rather than to an unmasking of preexisting material. There was no comparable change in the amount of any of the other six penicillin-binding proteins.