The effects of esomeprazole combined with aspirin or rofecoxib on prostaglandin E2 production in patients with Barrett's oesophagus.

BACKGROUND: Reducing mucosal cyclo-oxygenase-2 and prostaglandin E(2) production and suppressing intraoesophageal acid may be effective chemopreventive strategies in patients with Barrett's oesophagus. AIM: To compare the effects of aspirin and rofecoxib when administered with esomeprazole on prostaglandin E(2) production, cyclo-oxygenase-2 expression and proliferating cell nuclear antigen expression in patients with Barrett's oesophagus. METHODS: This exploratory, multicentre, randomized, open-label, four-way crossover study in 45 patients with Barrett's oesophagus evaluated prostaglandin E(2) content, proliferating cell nuclear antigen expression, and cyclo-oxygenase-2 expression after 10 days of sequential treatments with: esomeprazole 40 mg twice daily plus aspirin 325 mg once daily (E40 b.d. + A325); E40 b.d. plus rofecoxib 25 mg once daily (E40 b.d. + R25); E40 b.d.; and rofecoxib 25 mg once daily (R25). RESULTS: Prostaglandin E(2) content reduction in Barrett's oesophagus tissue was significantly greater with E40 b.d. + A325 compared with E40 b.d. + R25, E40 b.d. or R25 (P < 0.05). All treatments containing E40 b.d. significantly decreased proliferating cell nuclear antigen expression from baseline (P < 0.05). None of the treatments significantly reduced cyclo-oxygenase-2 expression. CONCLUSIONS: The combined treatment of esomeprazole 40 mg b.d. and aspirin 325 mg significantly decreased mucosal prostaglandin E(2) content and all treatments containing esomeprazole significantly reduced proliferating cell nuclear antigen expression in patients with Barrett's oesophagus.

Insertion of in-frame sequence tags into proteins using transposons.

Several methods based on the use of transposons allow the efficient generation of relatively short (e.g., <35 residues) in-frame insertions in proteins. The analysis of such insertions has provided a simple means to identify sites that tolerate dramatic sequence changes without loss of function ("permissive" sites) and to dissect protein structure-function relationships. In addition, epitope and protease cleavage site "tags" introduced in such insertions have made it possible to analyze the oligomerization state and transmembrane topologies of several proteins. Finally, the DNA inserted by these methods generally carries restriction sites which may facilitate the construction of in-frame deletions and gene fusions encoding a variety of chimeric proteins.

Analysis of F factor TraD membrane topology by use of gene fusions and trypsin-sensitive insertions.

This report describes a procedure for characterizing membrane protein topology which combines the analysis of reporter protein hybrids and trypsin-sensitive 31-amino-acid insertions generated by using transposons ISphoA/in and ISlacZ/in. Studies of the F factor TraD protein imply that the protein takes on a structure with two membrane-spanning sequences and amino and carboxyl termini facing the cytoplasm. It was possible to assign the subcellular location of one region for which the behavior of fused reporter proteins was ambiguous, based on the trypsin cleavage behavior of a 31-residue insertion.

MalK forms a dimer independent of its assembly into the MalFGK2 ATP-binding cassette transporter of Escherichia coli.

The maltose transport complex (MTC) is a member of the ATP-binding cassette superfamily of membrane transport proteins and is a model for understanding the folding and assembly of hetero-oligomeric membrane protein complexes. The MTC is made up of two integral membrane proteins, MalF and MalG, and a peripheral membrane protein, MalK. These proteins associate with a stoichiometry of 1:1:2 to form the complex MalFGK2. In our studies of the oligomerization of this complex, we have shown that the ATP-binding component, MalK, forms a dimer in the absence of MalF and MalG. Epitope-tagged MalK coimmunoprecipitated with wild-type MalK, indicating that the MalK protein forms an oligomer. The relative amounts of tagged and wild-type MalK that were present in the whole cell extracts and in the immunoprecipitated complexes show that the MalK oligomer is a dimer. These hetero-oligomers can also be formed in vitro by mixing two extracts, each containing either tagged or wild-type MalK. The dimerization of MalK was also demonstrated in vivo using the bacteriophage lambda repressor fusion assay. The formation of a MalK dimer in the absence of MalF and MalG may represent an initial step in the assembly pathway of the MTC.

Transposon-mediated random insertions and site-directed mutagenesis prevent the trafficking of a mouse mammary tumor virus superantigen.

Mouse mammary tumor viruses (MMTVs) encode superantigens (Sags) which are critical to the life cycle of infectious virus and can mediate extensive deletion of T lymphocytes when expressed by endogenous proviruses. Little is known about the structure, intracellular trafficking, or nature of Sag association with major histocompatibility (MHC) class II products. In order to gain a better understanding of Sag structure-function relationships, we extensively mutagenized this type II glycoprotein using two different approaches: transposon-mediated random in-frame insertion mutagenesis and site-directed mutagenesis targeting clusters of charged residues. We find that 31 codon insertions are infrequently tolerated in Mtv-7 Sag, with just 1 of 14 insertion mutants functionally presented on the surface of B cells. Surprisingly, similar effects were observed with Sag mutants with substitutions at pairs of charged residues; only 2 of 6 mutants trafficked to the plasma membrane and stimulated T cells, 1 with a temperature-sensitive phenotype. The data suggest that the nonfunctional Mtv-7 Sag mutants are stringently retained in the endoplasmic reticulum due to conformational defects rather than disrupted interactions with MHC class II, thus identifying charged amino acids critical to the structural stability of viral superantigens.

Exploring the role of integral membrane proteins in ATP-binding cassette transporters: analysis of a collection of MalG insertion mutants.

The maltose transport complex of Escherichia coli is a well-studied example of an ATP-binding cassette transporter. The complex, containing one copy each of the integral membrane proteins MalG and MalF and two copies of the peripheral cytoplasmic membrane protein MalK, interacts with the periplasmic maltose-binding protein to efficiently translocate maltose and maltodextrins across the bacterial cytoplasmic membrane. To investigate the role of MalG both in MalFGK2 assembly interactions and in subsequent transport interactions, we isolated and characterized 18 different MalG mutants, each containing a 31-residue insertion in the protein. Eight insertions mapping to distinct hydrophilic regions of MalG permitted either assembly or both assembly and transport interactions to occur. In particular, we isolated two insertions mapping to extracytoplasmic (periplasmic) regions of MalG which preserved both assembly and transport abilities, suggesting that these are permissive sites in the protein. Another periplasmic insertion seems to affect only transport-specific interactions between MalG and maltose-binding protein, defining a novel class of MalG mutants. Finally, four MalG mutant proteins, although stably expressed, are unable to assemble into the MalFGK2 complex. These mutants contain insertions in only two different hydrophilic regions of MalG, consistent with the notion that a restricted number of domains in this protein are critical complex assembly determinants. These MalG mutants will allow us to further explore the intermolecular interactions of this model transporter.

Insertion mutagenesis of the lac repressor and its implications for structure-function analysis.

We recently developed a simple technique for the generation of relatively large (31-codon) insertion mutations in cloned genes. To test whether the analysis of such mutations could provide insight into structure-function relationships in proteins, we examined a set of insertion mutants of the Escherichia coli lac repressor (LacI). Representatives of several LacI mutant classes were recovered, including mutants which exhibit fully active, inducer-insensitive, or weak dominant-negative phenotypes. The various properties of the recovered mutants agree with previous biophysical, biochemical, and genetic data for the protein. In particular, the results support the prior designation of mutationally tolerant spacer regions of LacI as well as proposed differences in dimerization interactions among regions of the protein core domain. These findings suggest that the analysis of 31-codon insertion mutations may provide a simple approach for characterizing structure-function relationships in proteins for which high-resolution structures are not available.

MalFGK complex assembly and transport and regulatory characteristics of MalK insertion mutants.

MalK is a peripheral cytoplasmic membrane protein that has multiple activities in Escherichia coli. It associates with integral cytoplasmic membrane proteins MalF and MalG to form the maltose transport complex (MalFGK), a member of the ATP-binding cassette (ABC) superfamily of proteins. In addition, MalK participates in two different regulatory pathways which modulate mal gene expression and MalFGK transport activity. We have created a set of malK mutations for analysis of the protein's structure and folding. These mutations, distributed throughout malK, are all similar insertions of 31 codons. The ability of each mutant to function in maltose transport and MalK-dependent regulation was characterized. Furthermore, we have exploited a sensitive biochemical assay to classify our MalK insertion mutants into two additional categories: MalFGK complex assembly proficient and complex assembly defective. The regions containing the insertions in the assembly-proficient class should correspond to areas within MalK that are surface exposed within the MalFGK complex. Affected regions in assembly-deficient mutants may be involved in critical structural contacts within the complex. One mutant apparently blocks assembly at an intermediate stage prior to oligomerization of the final MalFGK complex. This work contributes to the analysis of ABC transport proteins and to the study of the assembly process for hetero-oligomeric membrane proteins.

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

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

Membrane protein assembly: genetic, evolutionary and medical perspectives.

Lipid bilayers are delicate structures that are easily disrupted by a variety of amphipathic molecules. Yet the viability of a cell requires the continued assembly of large amphipathic proteins within its membranes without damage. The need to minimize bilayer disruption may account for a number of fundamental features of membrane protein assembly. These include the use of redundant sequence information to establish the topologies and folded structures of membrane proteins, and the existence of efficient mechanisms to rid cells of misassembled proteins. Most missense mutations that inactivate a membrane protein probably do so by altering the folding of the membrane-inserted structure rather than by rearranging the topology or by changing key residues involved directly in function. Such misfolded membrane proteins may be toxic to cells if they escape cellular safeguards. This toxicity may underlie some human degenerative diseases due to mutant membrane proteins.

The topological analysis of integral cytoplasmic membrane proteins.

We review three general approaches to determining the topology of integral cytoplasmic membrane proteins. (i) Inspection of the amino acid sequence and use of algorithms to predict membrane spanning segments allows the construction of topological models. For many proteins, the mere identification of such segments and an analysis of the distribution of basic amino acids in hydrophilic domains leads to correct structure predictions. For others, additional factors must come into play in determining topology. (ii) Gene fusion analysis of membrane proteins, in many cases, leads to complete topological models. Such analyses have been carried out in both bacteria and in the yeast Saccharomyces cerevisiae. Conflicts between results from gene fusion analysis and other approaches can be used to explore details of the process of membrane protein assembly. For instance, anomalies in gene fusion studies contributed evidence for the important role of basic amino acids in determining topology. (iii) Biochemical probes and the site of natural biochemical modifications of membrane proteins give information on their topology. Chemical modifiers, proteases and antibodies made to different domains of a membrane protein can identify which segments of the protein are in the cytoplasm and which are on the extracytoplasmic side of the membrane. Sites of such modifications as glycosylation and phosphorylation help to specify the location of particular hydrophilic domains. The advantages and limitations of these methods are discussed.

Analysis of the topology of a membrane protein by using a minimum number of alkaline phosphatase fusions.

An approach to analyzing the topology of membrane proteins with alkaline phosphatase fusions is described. Precise fusions were constructed by using polymerase chain reaction at the C terminus of each hydrophilic region of the membrane protein. The disruption of topogenic signals is thereby minimized, and predictable anomalous results are avoided. The Escherichia coli MalG protein has been analyzed.

Assembly of a hetero-oligomeric membrane protein complex.

The maltose transporter of Escherichia coli is a hetero-oligomeric complex located in the cytoplasmic membrane of the cell. The in vivo assembly of this complex has been examined by using an assay based on the proteolytic sensitivity of one of its components, MalF. Immediately after synthesis and insertion into the membrane, MalF is sensitive to exogenously added proteases. In a time- and complex assembly-dependent fashion, MalF becomes protease resistant. Using this assay, we show that MalF is inserted into the membrane independently of other components of the transport complex. The assembly of the maltose transport complex occurs subsequently from a pool of freely diffusing protein in the membrane. This assembly process is efficient and occurs with rapid kinetics.

Biochemical characterization of Escherichia coli DNA helicase I.

The gene product of F tral is a bifunctional protein which nicks and unwinds the F plasmid during conjugal DNA transfer. Further biochemical characterization of the Tral protein reveals that it has a second, much lower, Km for ATP hydrolysis, in addition to that previously identified. Measurement of the single-stranded DNA-stimulated ATPase rate indicates that there is co-operative interaction between the enzyme monomers for maximal activity. Furthermore, 18O-exchange experiments indicate that Tral protein hydrolyses ATP with, at most, a low-level reversal of the hydrolytic step during each turnover.

The dynamics of assembly of a cytoplasmic membrane protein in Escherichia coli.

The topology of integral cytoplasmic membrane proteins can be analyzed using alkaline phosphatase fusions by determining which constructs have low and which have high specific activity. We show that in all cases the enzymatic activity is due to the fraction of the alkaline phosphatase moiety of the fusion protein localized to the periplasm. We present evidence that these fusions can also be used to analyze the process of assembly of cytoplasmic proteins into the membrane. The rate of acquisition of protease resistance of the alkaline phosphatase moiety of such hybrid proteins is compared for fusions to periplasmic and cytoplasmic domains. We show that this process, which is assumed to be representative of export of alkaline phosphatase, is significantly slower for fusions to cytoplasmic and certain periplasmic domains than for most periplasmic domains. These results are discussed in the context of the normal assembly of integral membrane proteins.

Nucleotide sequence of the traI (helicase I) gene from the sex factor F.

A 6.9-kilobase region of the Escherichia coli F plasmid containing the 3' half of the traD gene and the entire traI gene (encodes the TraI protein, DNA helicase I and TraI, a polypeptide arising from an internal in-frame translational start in traI) has been sequenced. A previously unidentified open reading frame (tentatively trbH) lies between traD and traI.

The B isozyme of creatine kinase is active as a fusion protein in Escherichia coli: in vivo detection by 31P NMR.

A cDNA encoding the B isozyme of creatine kinase (CKB) has been expressed in Escherichia coli from a fusion with lacZ carried by lambda gt11. Western blots indicate that a stable polypeptide with the appropriate mobility for the beta-galactosidase-creatine kinase (beta-gal-CKB) fusion protein cross-reacts with both beta-gal and CKB antiserum. No significant CK activity is detected in control E. coli; however, extracts from cells containing the lambda gt11-CKB construct have a CK activity of 1.54 +/- 0.07 mumol/min per mg protein. The fusion protein appears to provide this activity because immunoprecipitation of protein with beta-gal antiserum leads to a loss of CK activity from extracts. That the enzyme is active in vivo was demonstrated by detection of a phosphocreatine (PCr) peak in the 31P NMR spectrum from E. coli grown on medium supplemented with creatine. As in mammalian brain and muscle, the PCr peak detected was sensitive to the energy status of the E. coli.

Evidence that DNA helicase I and oriT site-specific nicking are both functions of the F TraI protein.

Site-specific and strand-specific nicking at the origin of transfer (oriT) of the F sex factor is the initial step in conjugal DNA metabolism. Then, DNA helicase I, the product of the traI gene, processively unwinds the plasmid from the nick site to generate the single strand of DNA that is transferred to the recipient. The nick at oriT is produced by the combined action of two Tra proteins, TraY and TraZ. The traZ gene was never precisely mapped, as no available point mutation uniquely affected TraZ-dependent oriT nicking. With several new mutations, we have demonstrated that TraZ activity is dependent upon traI DNA sequences. The simplest interpretation of this finding is that the F TraI protein is bifunctional, with DNA unwinding and site-specific DNA nicking activities.