phoA Gene Fusions Research Articles

Secretion of the chlamydial virulence factor CPAF requires the Sec-dependent pathway

The chlamydial protease/proteasome-like activity factor (CPAF) is secreted into the host cytosol to degrade various host factors that benefit chlamydial intracellular survival. Although the full-length CPAF is predicted to contain a putative signal peptide at its N terminus, the secretion pathway of CPAF is still unknown. Here, we have provided experimental evidence that the N-terminal sequence covering the M1–G31 region was cleaved from CPAF during chlamydial infection. The CPAF N-terminal sequence, when expressed in a phoA gene fusion construct, was able to direct the export of the mature PhoA protein across the inner membrane of wild-type Escherichia coli. However, E. coli mutants deficient in SecB failed to support the CPAF signal-peptide-directed secretion of PhoA. Since native PhoA secretion was known to be independent of SecB, this SecB dependence must be rendered by the CPAF leader peptide. Furthermore, lack of SecY function also blocked the CPAF signal-peptide-directed secretion of PhoA. Most importantly, CPAF secretion into the host cell cytosol during chlamydial infection was selectively inhibited by an inhibitor specifically targeting type I signal peptidase but not by a type III secretion-system-specific inhibitor. Together, these observations have demonstrated that the chlamydial virulence factor CPAF relies on Sec-dependent transport for crossing the chlamydial inner membrane, which has provided essential information for further delineating the pathways of CPAF action and understanding chlamydial pathogenic mechanisms.

Membrane topology of theSalmonella entericaserovar Typhimurium Group B O-antigen translocase Wzx

The O-antigen translocase, Wzx, is involved in translocation of bacterial polysaccharide repeat units across the cytoplasmic membrane, and is an unusually diverse, highly hydrophobic protein, with high numbers of predicted alpha-helical transmembrane segments (TMS). The Salmonella enterica serovar Typhimurium Group B O-antigen Wzx was an ideal candidate for topological study as the O-antigen gene cluster is one of only a few that have been well characterized. The topology profile prediction for this protein was determined using five programs, with different recognition parameters, which consistently predict that 12 TMS are present. A membrane topology model was constructed by analysis of lacZ and phoA gene fusions at randomly selected and targeted fusion sites within wzx. Enzyme activity of these, and full-length C-terminal fusion proteins, confirmed the 12-TMS topology for this Wzx, and also indicated that the C-terminus was located within the cytoplasm, which is consistent with the predicted topology.

Structural and functional study of the phenicol-specific efflux pump FloR belonging to the major facilitator superfamily.

The florfenicol-chloramphenicol resistance gene floR from Salmonella enterica was previously identified and postulated to belong to the major facilitator (MF) superfamily of drug exporters. Here, we confirmed a computer-predicted transmembrane topological model of FloR, using the phoA gene fusion method, and classified this protein in the DHA12 family (containing 12 transmembrane domains) of MF efflux transporters. We also showed that FloR is a transporter specific for structurally associated phenicol drugs (chloramphenicol, florfenicol, thiamphenicol) which utilizes the proton motive force to energize an active efflux mechanism. By site-directed mutagenesis of specific charged residues belonging to putative transmembrane segments (TMS), two residues essential for active efflux function, D23 in TMS1 and R109 in TMS4, were identified. Of these, the acidic residue D23 seems to participate directly in the affinity pocket involved in phenicol derivative recognition. A third residue, E283 in TMS9, seems to be necessary for correct membrane folding of the transporter.

Functional Dissection of a Mercuric Ion Transporter, MerC, fromAcidithiobacillus ferrooxidans

Topological analysis with a phoA gene fusion suggested that Acidithiobacillus ferrooxidans MerC, a mercury transporter, has two periplasmic loops and four transmembrane domains. Cys-23 and Cys-26 of the protein were involved in Hg(2+)-recognition/uptake, but Cys-132 and Cys-137 were not. Escherichia coli cells producing the MerC were hypersensitive to CdCl(2). In this case, mutation of His72 rendered the host cells less CdCl(2) sensitive, whereas none of the Cys residues affected it. E. coli cells expressing the gene encoding a mercuric ion transporter (merC)-deletion mutant, in which the coding-sequence of the carboxy-terminal cytoplasmic region was removed, retained Hg(2+) hypersensitivity and showed about 55% HgCl(2) uptake ability compared to that of the one expressing the intact merC, indicating that the region is not essential for Hg(2+) uptake. Coexpression of A. ferrooxidans the gene encoding mercuric reductase (merA) and the merC deletion mutation conferred HgCl(2) tolerance to E. coli host cells. Under this condition, the merC deletion gene product was exclusively present as a monomer.

Four genes are required for the system II cytochrome c biogenesis pathway in Bordetella pertussis, a unique bacterial model.

Unlike other cytochromes, c-type cytochromes have two covalent bonds formed between the two vinyl groups of haem and two cysteines of the protein. This haem ligation requires specific assembly proteins in prokaryotes or eukaryotic mitochondria and chloroplasts. Here, it is shown that Bordetella pertussis is an excellent bacterial model for the widespread system II cytochrome c synthesis pathway. Mutations in four different genes (ccsA, ccsB, ccsX and dipZ) result in B. pertussis strains unable to synthesize any of at least seven c-type cytochromes. Using a cytochrome c4:alkaline phosphatase fusion protein as a bifunctional reporter, it was demonstrated that the B. pertussis wild-type and mutant strains secrete an active alkaline phosphatase fusion protein. However, unlike the wild type, all four mutants are unable to attach haem covalently, resulting in a degraded N-terminal apocytochrome c4 component. Thus, apocytochrome c secretion is normal in each of the four mutants, but all are defective in a periplasmic assembly step (or export of haem). CcsX is related to thioredoxins, which possess a conserved CysXxxXxxCys motif. Using phoA gene fusions as reporters, CcsX was proven to be a periplasmic thioredoxin-like protein. Both the B. pertussis dipZ (i. e. dsbD) and ccsX mutants are corrected for their assembly defects by the thiol-reducing compounds, dithiothreitol and 2-mercaptoethanesulphonic acid. These results indicate that DipZ and CcsX are required for the periplasmic reduction of the cysteines of apocytochromes c before ligation. In contrast, the ccsA and ccsB mutants are not corrected by exogenous reducing agents, suggesting that CcsA and CcsB are required for the haem ligation step itself in the periplasm (or export of haem to the periplasm). Related to this suggestion, the topology of CcsB was determined experimentally, demonstrating that CcsB has four transmembrane domains and a large 435-amino-acid periplasmic region.

Topological analysis and role of the transmembrane domain in polar targeting of PilS, a Pseudomonas aeruginosa sensor kinase.

In Pseudomonas aeruginosa, synthesis of pilin, the major protein subunit of the pili, is regulated by a two-component signal transduction system in which PilS is the sensor kinase. PilS is an inner membrane protein found at the poles of the bacterial cell. It is composed of three domains: an N-terminal hydrophobic domain; a central cytoplasmic linker region; and the C-terminal transmitter region conserved among other sensor kinases. The signal that activates PilS and, consequently, pilin transcription remains unknown. The membrane topology of the hydrophobic domain was determined using the lacZ and phoA gene fusion approach. In this report, we describe a topological model for PilS in which the hydrophobic domain forms six transmembrane helices, whereas the N- and C-termini are cytoplasmic. This topology is very stable, and the cytoplasmic C-terminus cannot cross the inner membrane. We also show that two of the six transmembrane segments are sufficient for membrane anchoring and polar localization of PilS.

Identification of Mycobacterium avium DNA sequences that encode exported proteins by using phoA gene fusions

Setting: Mycobacterium avium is the major cause of disseminated infection in patients with late stage AIDS.Objective: In order to identify M. avium genes that may be involved in bacterial uptake and intracellular survival, a phoA -based reporter system was used to identify genes that encoded surface-expressed or exported proteins.Design: PhoA (alkaline phosphatase) is only active if the protein is exported across the cell membrane into the periplasm. Consequently, detectable PhoA activity requires the fusion of a promoterless phoA gene with a DNA fragment containing a functional promoter and export leader sequence. A M. avium promoter library was constructed in the phoA reporter plasmid pJEM11 and screened in M. smegmatis for expression of active PhoA.Results: More than 100 independent PhoA+recombinants were isolated, of which 15 were sequenced. Most of these exhibited varying degrees of homology with published M. avium, M. tuberculosis, M. bovis and M. leprae sequences. Based on sequence homology, one M. avium sequence was identified as a homologue of the M. tuberculosis phosphate transport gene phoS2 (Ag88). Another M. avium sequence was homolog with a putative M. tuberculosis cutinase gene. Both of these M. avium genes were cloned and sequenced. Several other M. avium sequences were homologous with, as yet, unidentified M. tuberculosis genes.Conclusion: PhoA fusion technology is applicable to the study of atypical slow growing mycobacteria. Most of the M. avium exported proteins identified in this study are highly homologous with genes from M. tuberculosis and M. leprae. In addition, parallels in gene organization were identified between M. avium and members of the M. tuberculosis complex.

A periplasmic location is essential for the role of the ApbE lipoprotein in thiamine synthesis in Salmonella typhimurium.

ApbE is a lipoprotein in Salmonella typhimurium, and mutants unable to make this protein have a reduced ability to make thiamine (vitamin B(1)) and require it as a supplement for optimal growth in minimal glucose medium. Polyclonal antibodies specific to ApbE were used to determine that wild-type ApbE is located exclusively in the inner membrane. The periplasmic, monotopic topology of ApbE was determined by using computer-based hydrophobicity plots, LacZ and PhoA gene fusions, and proteinase protection experiments. This extracellular location of ApbE is required for its function, since a cytoplasmic form (ApbE(cyto)) did not allow an apbE mutant to grow in the absence of thiamine. A periplasmic form of ApbE (ApbE(peri)) lacking the lipoprotein modification allowed an apbE mutant to grow in the absence of thiamine, indicating that soluble ApbE could function in thiamine synthesis and that lipoation and membrane association were not required. Alteration of the amino acid implicated in membrane sorting for other lipoproteins did not result in a relocalization of ApbE to the outer membrane, suggesting that additional sorting determinants exist for ApbE.

Transmembrane Segment (TMS) VIII of the Na+/Citrate Transporter CitS Requires Downstream TMS IX for Insertion in the Escherichia coli Membrane

The amino acid sequence of the sodium ion-dependent citrate transporter CitS of K. pneumoniae contains 12 hydrophobic stretches that could form membrane-spanning segments. A previous analysis of the membrane topology in Escherichia coli using the PhoA gene fusion technique indicated that only nine of these hydrophobic segments span the membrane, while three segments, Vb, VIII and IX, were predicted to have a periplasmic location (Van Geest, M., and Lolkema, J. S. (1996) J. Biol. Chem. 271, 25582-25589). A topology study of C-terminally truncated CitS molecules in dog pancreas microsomes revealed that the protein traverses the endoplasmic reticulum membrane 11 times. In agreement with the PhoA fusion data, segment Vb was predicted to have a periplasmic location, but, in contrast, segments VIII and IX were found to be membrane-spanning (Van Geest, M., Nilsson, I., von Heijne, G., and Lolkema, J. S. (1999) J. Biol. Chem. 274, 2816-2823). In the present study, using site-directed Cys labeling, the topology of segments VIII and IX in the full-length CitS protein was determined in the E. coli membrane. Engineered cysteine residues in the loop between the two segments were accessible to a membrane-impermeable thiol reagent exclusively from the cytoplasmic side of the membrane, demonstrating that transmembrane segments (TMSs) VIII and IX are both membrane-spanning. It follows that the folding of CitS in the E. coli and endoplasmic reticulum membrane is the same. Cysteine accessibility studies of CitS-PhoA fusion molecules demonstrated that in the E. coli membrane segment VIII is exported to the periplasm in the absence of the C-terminal CitS sequences, thus explaining why the PhoA fusions do not correctly predict the topology. An engineered cysteine residue downstream of TMS VIII moved from a periplasmic to a cytoplasmic location when the fusion protein containing TMSs I-VIII was extended with segment IX. Thus, downstream segment IX is both essential and sufficient for the insertion of segment VIII of CitS in the E. coli membrane.

Integration of the colicin A pore-forming domain into the cytoplasmic membrane of Escherichia coli

The pore-forming domain of colicin A (pfColA) fused to a prokaryotic signal peptide (sp-pfColA) inserted into the inner membrane of Escherichia coli and apparently formed a functional channel, when generated in vivo. We investigated pfColA functional activity in vivo by the PhoA gene fusion approach, combined with cell fractionation and protease susceptibility experiments. Alkaline phosphatase was fused to the carboxy-terminal end of each of the ten α-helices of sp-pfColA to form a series of differently sized fusion proteins. We suggest that the α-helices anchoring pfColA in the membrane are first translocated into the periplasm. We identify two domains that anchor pfColA to the membrane in vivo: domain 1, extending from helix 1 to helix 8, which contains the voltage-responsive segment and domain 2 consisting of the hydrophobic helices 8 and 9. These two domains function independently. Fusion proteins with a mutation inactivating the voltage-responsive segment or with a domain 1 lacking helix 8 were peripherally associated with the outside of the inner membrane, and were therefore digested by proteases added to spheroplasts. In contrast, fusion proteins with a functional domain 1 were protected from proteases, suggesting as expected that most of domain 1 is inserted into the membrane or is indeed translocated to the cytoplasm during pfColA channel opening.

Genetic analysis of microcin H47 immunity

Microcin H47 is a bactericidal antibiotic produced by a natural Escherichia coli isolate. The genetic system encoding microcin production and immunity consists of at least seven clustered genes. Four of these are devoted to microcin biosynthesis and two genes are required for its secretion into the extracellular medium. The product of the seventh gene, mchI, determines the cell's self-immunity. This gene was shown to encode a highly hydrophobic 69-residue peptide. Analysis of the MchI amino acid sequence, as well as the characterization of MchI–PhoA hybrid proteins, indicated that the microcin immunity product is probably exported out of the cytoplasm and remains an integral membrane peptide. This localization of the immunity peptide points to the cellular membrane as the site of action of microcin H47. Key words: microcin H47, microcin immunity, phoA gene fusion, membrane peptide.

20] Analysis of transporter topology using deletion and epitope tagging

Publisher Summary This chapter describes the analysis of transporter topology using deletion and epitope tagging. Several strategies have been employed to elucidate the structure and transmembrane topology of transport proteins. An understanding of transporter structure is crucial for determining the correlation between transporter structure and function. In addition, structural knowledge aids in the design of more specific transporter reagents, which may prove therapeutically useful. Current studies of the transmembrane topology of integral membrane proteins using deletion analysis and epitope tagging derive from gene fusion methods designed to study secretion and topology of bacterial proteins. In these original experiments, a modified form of the Escherichia coli phoA gene, which encodes the secreted periplasmic enzyme alkaline phosphatase, was fused to the C-terminal portion of a protein of interest. Therefore, the level of alkaline phosphatase activity is a direct indication of the location of the enzyme in bacteria and a useful tool for discerning the secretion or topogenic properties of bacterial proteins. The phoA gene fusion method has been used to determine the transmembrane topology of the C-terminal half of the bacterial glutamate transporter in E. coli .

Mycobacterium tuberculosis Des protein: an immunodominant target for the humoral response of tuberculous patients.

The phoA gene fusion methodology permitted the identification of a new Mycobacterium tuberculosis exported protein, Des. This protein has significant sequence similarities to plant acyl-acyl carrier protein desaturases, which are enzymes involved in general fatty acid biosynthesis as well as in mycolic acid biosynthesis in mycobacteria. As shown by Western blot and enzyme-linked immunosorbent assay experiments, the Des protein is a major B-cell antigen that was recognized by all the tuberculous M. tuberculosis- and M. bovis-infected human patients tested.

Topological Analysis of NhaA, a Na+/H+ Antiporter from Escherichia coli

Analysis of the hydropathic profile of the amino acid sequence of NhaA, a Na+/H+ antiporter from Escherichia coli has previously suggested the existence of 11 putative transmembrane segments (Taglicht, D., Padan, E., and Schuldiner, S. (1991) J. Biol. Chem. 266, 11289-11294). In the present work to test the location of the C terminus, right-side-out and inside-out membrane vesicles were digested with carboxypeptidase B and probed with an antibody raised against a synthetic peptide whose sequence was based on the C terminus sequence. The results demonstrate that the C terminus is facing the cell interior because it is available for digestion only from the inside. Previous evidence from an NhaA-beta-galactosidase fusion to loop 5 of NhaA indicated that this loop is also facing the cytoplasm (Karpel, R., Alon, T., Glaser, G., Schuldiner, S., and Padan, E. (1991) J. Biol. Chem. 266, 21753-21759) and therefore was not consistent with the position of the C terminus in an 11-transmembrane segment model. Therefore, the model was re-evaluated. For this purpose, 10 nhaA'-'phoA gene fusions were constructed and assayed for alkaline phosphatase activity. The results support a 12-transmembrane segment model with the N and C termini located in the cytoplasm. The evidence indicates that two very short segments, 14 and 16 amino acids long, must cross the membrane in an unknown conformation.

Membrane Topology of the C-terminal Half of the Neuronal, Glial, and Bacterial Glutamate Transporter Family

Secondary glutamate transporters in neuronal and glial cells in the mammalian central nervous system remove the excitatory neurotransmitter glutamate from the synaptic cleft and prevent the extracellular glutamate concentration to rise above neurotoxic levels. Secondary structure prediction algorithms predict 6 transmembrane helices in the first half of the transporters but fail in the C-terminal half where no clear helix-loop-helix motif is resolved in the hydropathy profile of the primary sequences. A number of previous studies have emphasized the importance of the C-terminal half of the molecules for the function. Here we determine the membrane topology of the C-terminal half of the glutamate transporters by applying the phoA gene fusion technique to the homologous bacterial glutamate transporter of Bacillus stearothermophilus. High sequence conservation and very similar hydropathy profiles in the C-terminal half warrant a similar folding as in the glutamate transporters of the mammalian central nervous system. The C-terminal half contains four putative transmembrane helices. The strong hydrophobic moment and substitution moment of the most C-terminal helix X that point to opposite faces of the helix suggest that the helix faces the lipid environment with its least conserved, hydrophobic face and the interior of the protein with its well conserved, hydrophilic face. Residues that were shown before to be critical for function cluster in helix X and VII.

Mutational Analysis of the Predicted First Transmembrane Segment of Each Homologous Half of Human P-glycoprotein Suggests That They Are Symmetrically Arranged in the Membrane

A recent study of P-glycoprotein membrane topology using phoA gene fusions provided evidence that the orientation of the first transmembrane segment of each homologous half of P-glycoprotein was different (Béjà, O., and Bibi, E. (1995) J. Biol. Chem. 270, 12351-12354). To test this hypothesis, we compared the functional consequences of mutations to residues in transmembrane segments (TMs) TM1 and TM7. Mutations to 3 residues occupying homologous positions in TM1 and TM7 resulted in mutant P-glycoproteins that were inactive. These mutants were found to be misprocessed. By contrast, mutations to other residues in TM1 resulted in functional P-glycoproteins. When putative TM1 was replaced with TM7 or TM7 with TM1 to yield TM7/TM7 or TM1/TM1 chimeras, both constructs yielded P-glycoproteins that were capable of conferring drug resistance in transfected cells. The purified P-glycoproteins from mutants TM7/TM7 and TM1/TM1 retained 59 and 28% of verapamil-stimulated ATPase activity, respectively. By contrast, interchanging TM6 and TM12 to yield TM6/TM6, TM12/TM12, or TM12/TM6 constructs resulted in P-glycoproteins that did not have any detectable ATPase activity and did not confer drug resistance in transfected cells. These results suggest that TM1 and TM7 likely have similar structural and functional roles in P-glycoprotein and that they have identical topologies.

Identification of mycoplasma membrane proteins by systematic Tn phoA mutagenesis of a recombinant library.

Wall-less prokaryotes in the genus Mycoplasma include over 90 species of infectious agents whose pathogenicity for humans and other animals is currently being assessed. Molecular characterization of surface proteins is critical in this regard but is hampered by the lack of genetic systems in these organisms. We used TnphoA transposition to systematically mutagenize, in Escherichia coli, a genomic plasmid library constructed from Mycoplasma fermentans, a potential human pathogen. The strategy circumvented problems of expressing mycoplasma genes containing UGA (Trp) codons and relied on the construction of the vector pG7ZCW, designed to reduce TnphoA transposition into vector sequences. Functional phoA gene fusions directly identified genes encoding 19 putative membrane-associated proteins of M. fermentans. Sequences of fusion constructs defined three types of export sequence: (1) non-cleavable, membrane-spanning sequences, (2) signal peptides with signal peptidase (SPase) I-like cleavage sites, and (3) signal peptides with SPase II-like lipoprotein-cleavage sites which, like most other mycoplasmal lipoprotein signals analysed to date, differed from those in several Gram-negative and Gram-positive eubacteria in their lack of a Leu residue at the -3 position. Antibodies to synthetic peptides that were deduced from two fusions to predicted lipoproteins, identified corresponding amphiphilic membrane proteins of 57 kDa and 78 kDa expressed in the mycoplasma. The P57 sequence contained a proline-rich N-terminal region analogous to an adhesin of Mycoplasma gallisepticum. The P78 protein was identical to a serologically defined phase-variant surface lipoprotein. TnphoA mutagenesis provides an efficient means of systematically characterizing functionally diverse lipoproteins and other exported proteins in mycoplasmas.

Characterization of the Mycobacterium tuberculosis erp gene encoding a potential cell surface protein with repetitive structures.

Using the phoA gene fusion methodology adapted to mycobacteria, several Mycobacterium tuberculosis DNA fragments encoding exported proteins were recently identified. In this paper, the molecular cloning, genomic positioning, nucleotide sequence determination and transcriptional start site mapping of a new M. tuberculosis gene, identified by this methodology, are reported. This gene was called erp (for exported repetitive protein) and has a sequence similar to that of the Mycobacterium leprae 28 kDa antigen irg gene M. tuberculosis erp gene contains a putative iron box close to the mapped transcriptional start site. The predicted Erp protein displays a typical N-terminal signal sequence, a hydrophobic domain at the C-terminus and harbours repeated amino acid motifs. These structural features are reminiscent of cell-wall-associated surface proteins from Gram-positive bacteria. We found that these repeats are conserved among M. tuberculosis isolates, and are absent from the published M. leprae irg gene sequence. In addition to being present in M. leprae, erp sequences were found in other members of the M. tuberculosis complex, but not in other mycobacteria tested. These results suggest that erp might encode a cell surface component shared by major pathogenic mycobacteria.

Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter.

We have constructed a series of plasmid vectors (pBAD vectors) containing the PBAD promoter of the araBAD (arabinose) operon and the gene encoding the positive and negative regulator of this promoter, araC. Using the phoA gene and phoA fusions to monitor expression in these vectors, we show that the ratio of induction/repression can be 1,200-fold, compared with 50-fold for PTAC-based vectors. phoA expression can be modulated over a wide range of inducer (arabinose) concentrations and reduced to extremely low levels by the presence of glucose, which represses expression. Also, the kinetics of induction and repression are very rapid and significantly affected by the ara allele in the host strain. Thus, the use of this system which can be efficiently and rapidly turned on and off allows the study of important aspects of bacterial physiology in a very simple manner and without changes of temperature. We have exploited the tight regulation of the PBAD promoter to study the phenotypes of null mutations of essential genes and explored the use of pBAD vectors as an expression system.

Multidrug Resistance Protein (Mdr)-alkaline Phosphatase Hybrids in Escherichia coli Suggest a Major Revision in the Topology of the C-terminal Half of Mdr

Recent studies reveal that the organization of the multidrug resistance protein (Mdr) in the membrane is probably not exactly as predicted from hydropathy profiling. When expressed in Escherichia coli, phoA gene fusions can be utilized to study the membrane topology of Mdr. Using this approach, it was proposed recently that the N-terminal hydrophobic domain of Mdr spans the membrane six times, in a different fashion from that predicted by hydropathy analysis (Bibi, E. and Béjà, O. (1994) J. Biol. Chem. 269, 19910-19915). In this study, we analyze mdr-phoA fusions constructed in the C-terminal half of Mdr. Overall, the results presented here lead to a significant revision in the membrane topology model of the C-terminal half of Mdr. The new topology is discussed with regard to the hydropathy profiles of the well characterized ABC proteins MalG and MalF, which are strikingly similar to those of the N- and C-terminal halves of Mdr, respectively.