Isolation and characterisation of lambdatra transducing phages from EDFL223 (Flac traB::EDlambda4)

Role of the propilin leader peptide in the maturation of F pilin

F-pilin maturation and translocation result in the cleavage of a 51-amino-acid leader sequence from propilin and require LepB and TraQ but not the SecA-SecY secretion pathway. The unusual propilin leader peptide and the dependence of its cleavage on TraQ suggested that TraQ recognition may be specific for the leader peptide. An in vitro propilin cleavage assay yielded propilin (13 kDa), the pilin polypeptide (7 kDa), and a 5.5-kDa protein as the traA products. The 5.5-kDa protein comigrates with the full-length 51-amino-acid leader peptide, and [14C]proline labeling confirmed its identity since the only proline residues of propilin are found within the leader peptide. The in vitro and in vivo propilin-processing reactions proceed similarly in a single polypeptide cleavage step. Furthermore, TraQ dependence is a property of F-pilin maturation specifically rather than a property of the leader peptide. A propilin derivative with an amino-terminal signal sequence generated by deleting codons 2 to 28 required TraQ for processing in vivo. On the other hand, a chimeric protein with the propilin wild-type leader peptide fused to the mature portion of beta-lactamase was processed in a TraQ-independent manner. Thus, despite its unusual length, the propilin leader peptide seems to perform a function similar to that of the typical amino-terminal signal sequence. This work suggests that TraQ is not necessary for the proteolysis of propilin and therefore is likely to act as a chaperone-like protein that promotes the translocation of propilin.

Molecular analysis and nucleotide sequence of finQ, a transcriptional inhibitor of the F plasmid transfer genes

We report the cloning of finQ, a gene coding for fertility inhibition of the F plasmid, from the IncI R factor R820a. The finQ gene was mapped precisely within a 1.24 kb region by ptac-transposase + min-kan mutagenesis and its product, FinQp, identified as a single polypeptide by means of SDS-polyacrylamide gel electrophoresis. Nucleotide sequencing of the finQ region allowed elucidation of the FinQp amino acid sequence and determination of its precise molecular weight as 39,895 Da. Analysis of the predicted amino acid sequence indicated that FinQp is a positively charged protein possessing a helix-turn-helix DNA binding motif. We propose a possible model for the mechanism by which FinQp terminates transcription within the F plasmid tra region. DNA-DNA hybridization established that all FinQ+ R factors examined have an homologous finQ gene.

The product of the F plasmid transfer operon gene, traF, is a periplasmic protein

The products of clones carrying the F plasmid transfer operon gene, traF, were analyzed. Proteins expressed in maxicells were labeled with [35S]methionine and examined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography. Clones carrying the wild-type traF gene expressed two polypeptide products that were not products of clones containing the traF13 amber mutation. These migrated with apparent molecular weights (Ma) of 27,000 and 25,000. A pulse-chase experiment suggested that the larger product was a precursor of the smaller one. In the presence of ethanol, the Ma-27,000 polypeptide accumulated and the Ma-25,000 product was not expressed. These results indicated that the traF protein undergoes proteolytic processing associated with export. Cell fractionation experiments further indicated that the greatest concentration of the mature (Ma 25,000) TraF protein was located in the periplasm. The DNA sequence of traF and the position of the transition mutation in traF13 DNA were also determined. Sequence analysis suggested that traF would be expressed as a 247-amino-acid, Mr-28,006 polypeptide. The 19 amino acids at the amino terminus of this polypeptide appear to constitute a typical membrane leader peptide, while the remainder of the molecule (Mr 25,942) is predicted to be primarily hydrophilic in character.

Location of F plasmid transfer operon genes traC and traW and identification of the traW product

As part of an analysis of the conjugative transfer genes associated with the expression of F pili by plasmid F, we have investigated the physical location of the traC and traW genes. We found that plasmid clones carrying a 2.95-kilobase EcoRI-EcoRV F transfer operon fragment were able to complement transfer of F lac traC mutants and expressed an approximately 92,000-dalton product that comigrates with TraC. We also found that traW-complementing activity was expressed from plasmids carrying a 900-base-pair SmaI-HincII fragment. The traW product was identified as an approximately 23,000-dalton protein. The two different F DNA fragments that expressed traC and traW activities do not overlap. Our data indicate that the traC gene is located in a more-tra operon promoter-proximal position than suggested on earlier maps and that traW is distal to traC. These results resolve a long-standing question concerning the relationship of traW to traC. The clones we have constructed are expected to be useful in elucidating the role of proteins TraC and TraW in F-pilus assembly.

Analysis of transfer genes and gene products within the traB-traC region of the Escherichia coli fertility factor, F

A series of plasmids that carry overlapping segments of F DNA encoding the genes in the traB-traC interval was constructed, and a restriction enzyme map of the region was derived. Plasmids carrying deletions that had been introduced at an HpaI site within this interval were also isolated. The ability of these plasmids to complement transfer of F lac plasmids carrying mutations in traB, traV, and traW, and traC was analyzed. The protein products of the plasmids were labeled in UV-irradiated cells and analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography. These analyses showed that the product of traV is a polypeptide that migrates with an apparent molecular weight of 21,000. It was not detected when [35S]methionine was used to label plasmid products, but was readily detected in 14C-amino acid labeling experiments. A 21,500-dalton product appeared to stem from the region assigned to traP. A 9,000-dalton product was found to stem from a locus, named traR, that is located between traV and traC. No traW activity could be detected from the region of tra DNA examined. Our data also indicated that traC is located in a more promoter-proximal position than suggested on earlier maps. The plasmids constructed are expected to be useful in studies designed to identify the specific functions of the traB, -P, -V, -R, and -C products.

A traC mutant that retains sensitivity to f1 bacteriophage but lacks F pili

An F lac pro mutant which was temperature sensitive for infection by the filamentous bacteriophage f1 but resistant to the F-specific icosahedral RNA phage f2 was isolated. Cells carrying the F' mutation failed to elaborate F pili at all temperatures. Mutant cells were able to pair with recipient cells during bacterial conjugation, but transfer of conjugal DNA occurred at a greatly reduced frequency. Complementation analyses showed the F' mutation to be in the traC gene. When a plasmid carrying traC was introduced into hosts harboring the F' mutation, phage sensitivity, the ability to elaborate F pili, and conjugation efficiency were restored. The mutation was named traC1044. The F lac pro traC1044 mutant appears to be unique among traC mutants in retaining host sensitivity to the filamentous phage f1 in the absence of expression of extended F pili. Phage f1 attachment sites appeared to be present at the cell surface in traC1044 mutants. The reduced accessibility of these sites may account for the reduced efficiency of phage f1 infection of traC1044 hosts, although the possibility that a defect was present in the receptor site itself was not eliminated. Membranes of hosts carrying the F' mutation contained a full complement of mature F-pilin subunits, so the product of traC is presumably required for pilus assembly but not for pilin processing. This, together with the deficiency in conjugal DNA transfer, suggests that traC may be part of a membrane-spanning tra protein complex responsible for pilus assembly and disassembly and conjugal DNA transmission.

Analysis of Escherichia coli K12 F factor transfer genes: traQ, trbA, and trbB

The genes that encode the transfer properties of plasmid F, the fertility factor of Escherichia coli K12, are known to be clustered over a large, 33.3-kb segment of F DNA. As the central segment of the transfer region has not previously been well characterized, we constructed a detailed restriction map of the large F EcoRI DNA fragment, fl, and isolated a series of plasmid derivatives that carry various overlapping segments of this F tra operon DNA. We also analyzed the protein products of those clones that carried DNA segments extending over the region between traF and traH. This region was known to include traQ, a gene required for efficient conversion of the direct product of traA to the 7000-Da pilin polypeptide. We identified the traQ product as a polypeptide that migrates as a 12,500-Da protein on sodium dodecyl sulfate-polyacrylamide gels. We also detected the products of two other new genes that we have named trbA and trbB. These polypeptides migrate with apparent molecular weights of 14,200 and 18,400, respectively. Analysis of plasmid deletion derivatives that we constructed in vitro shows that these genes map in the order traF trbA traQ trbB traH. The presence of a plasmid carrying a small 0.43-kb fragment that expressed only the 12,500 traQ product caused the traA product of a co-resident compatible plasmid to be converted to the 7000-Da pilin polypeptide, demonstrating that TraQ is the only tra operon product required for this step of F-pilin biosynthesis.

Overproduction, purification and characterization of the F traT protein

A lambda transducing phage (ED lambda 110) which carries the sex factor F surface exclusion genes, traS and traT, was characterized by both genetic and physiochemical techniques. The transducing segment consists of 5.2 kilobases of F tra DNA, and carries the carboxy-terminal one-half of the upstream traG gene, as well as traS, traT, and the adjacent downstream gene traD. These tra proteins could be identified in infected UV-irradiated cells, and the major part of their synthesis was found to occur from the phage's late promoter pR' under Q control. Lysogens for ED lambda 110 were induced and found to greatly overproduce the traT gene product (TraTp), an outer membrane protein normally found in about 20,000 copies per cell, to levels which exceeded the major outer membrane proteins. This led to the development of a simple purification procedure for TraTp, the most important step of which was the construction of an appropriate ompB derivative to eliminate the major outer membrane porin proteins, which have several physical properties in common with TraTp. Purified TraTp was added to mixtures of donor and recipient cells and found to inhibit mating. The specificity of this assay was demonstrated by using an R100-1 donor, which responds to a heterologous surface exclusion system, and by using an altered TraTp containing a missense amino acid substitution. A mechanism by which TraTp mediates surface exclusion is proposed.

The role of insertions, deletions, and substitutions in the evolution of R6 related plasmids encoding aminoglycoside transferase ANT-(2")

In 7% of gram-negative bacteria resistance to gentamicin is mainly mediated by plasmid-encoded aminoglycoside transferase ANT-(2"). The genome organization of 15 aadB plasmids (42-110 kb) was analyzed by restriction and hybridization techniques. They appeared to be IncFII-like replicons but were distinct from R6 by virtue of small substitutions in the transfer region. Aminoglycoside resistance genes aadB and aadA were located on Tn21 related elements. Only one of them was able to transpose its resistance genes mer sul aadA and aadB ( Tn4000 ), the other elements were naturally occurring defective transposons. In some of these structures deletions were identified at the termini, at sul, aadA , mer or transposition function--insertions adjacent to aadA or mer. The mode of these rearrangements and their site-specificity were considered with respect to the evolution of the Tn21 transposon family.

Synthesis of F-pilin polypeptide in the absence of F traJ product

The products of a lambda transducing phage (ED lambda 101) which carries a segment of the F tra operon expressing F traA , traL , and traE activity from the lambda leftward promoter were examined using a uv-irradiated host system. After infection of an F- host, products of traE (19,500 Da) and traA (14,000 Da) were detectable among the lambda early proteins synthesized. Infection of an Flac host altered the pattern of polypeptides synthesized by the phage in that the 14,000-Da traA product became barely detectable and was replaced by a polypeptide which migrated at 7000 Da. A derivative of ED lambda 101 carrying the traA1 amber mutation was unable to synthesize either the 14,000-Da polypeptide in F- cells or the 7000-Da polypeptide in Flac cells. The 7000-Da polypeptide derived from ED lambda 101 was synthesized in the absence of traJ product in F- cells coinfected with a second transducing phage which carried a tra operon segment including traQ . It was also a product of ED lambda 134 which expresses genes traA through traH . The 7000-Da polypeptide, like F-pilin, associated primarily with the inner membrane, and could be immunoprecipitated with antiserum prepared against purified F-pili. Analysis of membranes from F- cells infected with ED lambda 101 indicated that the 14,000-Da traA product synthesized under these conditions accumulated in the inner membrane. These results show that both the 14,000-Da traA product might be processed to F-pilin in a traQ -dependent reaction which occurs in or on the inner membrane of the Escherichia coli host. However, the possibility that traQ encodes a regulatory product which affects expression of the traA sequence has not been excluded.

RNA-polymerase binding sites within the tra region of the F factor of Escherichia coli K-12

Chimeric plasmids containing the tra operon of the Escherichia coli K-12 F factor were used to map by electron microscopy the RNA polymerase binding sites within the contiguous F EcoRI restriction fragments f6, f16, f1, f17, f19 and f2. [These fragments have been previously cloned in the EcoRI site of pSC101 to give the chimeric plasmids pRS27 (f6, f15), pRS29 (f15, f1) and pRS31 (f17, f19 and f2)]. The results may reflect the presence of a number of previously unrecognized promoters within the traY----Z operon.

Regulation of the F conjugation genes studied by hybridization and tra-lacZ fusion

Hybridization experiments and tra-lacZ fusions were used to obtain further insight into the complex series of control systems that affect F conjugation. We confirmed that the regular IncF FinOP control system represses transcription of traJ, and found that the traJ product is required for transcription of traM as well as of the traY-Z operon. The chromosomal sfrA gene product may be required to prevent premature termination of traJ transcription, while the sfrB gene product prevents premature termination at two sites within the traY-Z operon. The FinQ inhibition system determined by several IncI plasmids caused termination at three different sites in the operon, and that of JR66a at one further site. JR66a and R485 strongly inhibit F transfer, but have weak, or no (respectively) effects on transcription: they may inhibit function of one or more transfer gene products.

The finO gene of antibiotic resistance plasmid R100

Lambda phages carrying the R100 finO gene have been isolated from an R100:: lambda cointegrate in which lambda was inserted into the R100 traD gene at kb coordinate 72.1. Physical analyses of these phages place the finO gene within R100 SalI fragment D, near kb coordinate 82.0. Analysis of proteins synthesized by the phages did not identify the finO gene product, although a constitutive protein of m.w. 30,100 was encoded by R100 DNA between kb coordinates 78.7 and 81.2.

lambda-Transducing phages carrying transfer genes isolated from an abnormal prophage insertion into the traY gene of F

A set of lambda-transducing phages carrying transfer (tra) genes has been isolated from an abnormal lysogen in which a lambda prophage was inserted into the traY gene of Flac. These have been characterized genetically for complementation of Flac tra and finP point mutants and for the presence of oriT. Studies of tra gene expression during lambda repression showed that tra genes on the transducing phages were expressed from the lambda PL promoter as well as from the transfer promoters when these were present. The molecular weights of the traM (14,000) and traJ (23,500) proteins were measured after infection of ultraviolet-irradiated cells with one of the phages, ED lambda 102, and overproduction of the traJ protein upon induction of an ED lambda 102 lysogen was demonstrated. A proportion of this traJ protein was located in the inner membrane and cytoplasmic fractions of the cell, the majority being in the outer membrane. Physical analysis of the DNA carried by the lambda tra phages by determination of the phage buoyant densities in CsCl, by restriction enzyme digestion and by electron microscope heteroduplex analysis, was used to define the DNA segments encoding the tra functions. Correlation of the physical and genetical data improved the positioning of the tra genes within the transfer region. These results were combined with new restriction enzyme cleavage data to construct an improved map of this region.

A new activity in the Ftra operon which is required for F-pilin synthesis

Membrane preparations from a series of Hfr mutant strains of Escherichia coli K12 deleted in the promoter distal end of the F transfer operon were analyzed. Deletions which extended into traG, as expected, had no discernible effect on synthesis of membrane F-pilin. A more extensive deletion in strain K1777 which eliminated traH activity similarly had no effect on F-pilin synthesis. Membranes from three other TraF+ TraH- deletion strains, as well as membranes from all strains carrying deletions extending into traF or further, lacked F-pilin, however. Since traH amber mutations do not affect synthesis of membrane pilin (Moore et al. 1981 b) we conclude that a gene required for F-pilin biosynthesis is located between traF and traH. We have named this gene traQ. Further evidence for traQ and an assay for its activity was obtained by examining the products of a TraM+ TraJ+ TraA+ lambda transducing phage, KI lambda 13, in UV irradiated cells. Infection of F- cells with KI lambda 13 does not result in F-pilin synthesis. Membrane pilin is synthesized as a product of the transducing phage if an Flac or Hfr irradiated host is used, however. Mutant analysis demonstrated that this synthesis is independent of host expression of traA, traL, traE, traK, traB, traV, traW, traC, traU, traF, or traH, but dependent on expression of the traF-traH region. We interpret our data to indicate that an activity encoded by traQ is required for the conversion of traA product to F-pilin.

sfrA and sfrB products of Escherichia coli K-12 are transcriptional control factors

The mechanisms whereby mutations in Escherichia coli K-12 genes sfrA and sfrB reduce expression of the transfer functions of sex factor F have been examined by assaying the levels of tra messenger ribonucleic acid and of tra proteins. The sfrA product was necessary for efficient transcription of the control gene traJ and, directly or indirectly, for transcription of the traY leads to Z operon. In the absence of sfrA, reduced levels of the traJ and traT proteins were observed in the outer membrane. The sfrB product was needed to prevent premature transcription at one or more rho-dependent termination sites. sfrB mutations also reduced synthesis of full-length lipopolysaccharide molecules, of several chromosomally determined outer membrane proteins, and of functional flagella. Thus, the sfrB product may act as an antiterminator in transcription of several operons encording cell envelope components.

Interactions between the F conjugal transfer system and CloDF13::Tna plasmids

It was confirmed that all the F transfer genes required for the formation of stable mating pairs, including traN and traG, are essential for transfer of the two small multicopy plasmids ColE1 and cloDF13, whereas the traM, traI and traZ genes that are required for F conjugal DNA metabolism, are not. Differences between ColE1 and CloDF13 were that the F traD gene was needed for transfer of ColE1 but not of CloDF13, and that R100-1 efficiently transferred CloDF13 but not ColE1. A copy number mutant of CloDF13 inhibited F transfer and reduced plaque formation by the F-specific RNA phage f2, but not by Q beta or by the single-strand DNA phage f1. This phenotype suggests that the inhibition system (FinC) acts on traD, mutations in which give a similar phenotype. Hybridisation experiments with lambda tra phage DNA showed that transcription of traD was not reduced, and FinC probably inhibits function of the traD product rather than its synthesis. FinC-insensitive Flac mutants were isolated and characterised. One was shown to have an uppromoter mutation resulting in increased transcription of traJ and hence of the traY leads to Z operon including traD: the raised level of the traD product presumably then counteracted FinC inhibition.

Tn2301, a transposon construct carrying the entire transfer region of the F plasmid

The largest R . BamHI fragment of the plasmid F, which carries the entire F conjugation system, has been cloned into the single R . BamHI site of the ampicillin (Ap) resistance transposon TN1. pDS1106 (ColE1 mob::Tn1) was the vector plasmid, and the resultant conjugative plasmid, pED830, was characterized both genetically and by restriction enzyme analysis. The transposon construct, denoted Tn2301, was transposable at frequencies similar to Tn1 to small nonconjugative plasmids or to the Escherichia coli host chromosome. In the former case, Apr conjugative plasmids were obtained, whereas in the latter case, Hfr strains resulted. Representative Hfr strains were characterized by quantitative and interrupted mating experiments. Extension of this technique for Hfvr formation should aid chromosome mapping both in E. coli and in other bacterial genera.

Characterisation of a lambda transducing phage carrying the F conjugation gene traG

A lambda transducing phage carrying the traGSTD genes of the E. coli K12 factor F was isolated by an in vivo technique, and characterized in tra complementation tests, by determining its restriction endonuclease fragment sizes, and by measuring heteroduplex molecules. The size and location on the F physical map of the tra transducing segment was thereby determined. Comparison of the proteins synthesized in UV-irradiated cells by this phage and by a derivative carrying the amber traG79 mutation, allowed the traG product to be identified as a protein of molecular weight 100,000. In the same experiments, the sizes of the traT and traD products made by the phage were also measured, being 25,000 and 85,000 daltons respectively.

Transfer-deficient cointegrates of Flac and lambda prophage

Twelve transfer-deficient mutants of the plasmid Flac were obtained by insertion of prophage lambda into secondary attachment sites within the transfer region. Insertions into eight different tra genes were identified. These mutations were strongly polar on expression of tra genes previously mapped "downstream", and thus confirmed that the genes traA through traD form a single operon. However, some continued expression of traI suggested that this was transcribed in part from a promoter located between traD and traI, and in part from the transfer operon promoter. One insertion early in the transfer operon produced a plasmid-specific tra mutation not complemented by R100-1 or R1-19: this insertion was into a new gene (traY), located before traA as the first member of the transfer operon. Partial tra deletion mutants were obtained as 42 degrees C--survivors from several of the Flac tra::ED lambda 4 plasmids, and their properties are described.

Identification of cistrons involved in conjugal transfer of narrow-host-range R plasmid R91-5 of Pseudomonas aeruginosa

The development of a transductional method for complementation tests between transfer-deficient mutants of the narrow-host-range R plasmic R91-5 of Pseudomonas aeruginosa has allowed the indentification of cistrons involved in the conjugal transfer of this plasmid. Complementation tests performed between transfer-deficient mutants characterized phenotypically with respect to sensitivity to donor-specific phage, ability to inhibit the replication of phage G101, and expression of entry-exclusion has identified a minimum of 10 transfer cistrons. Although most mutagen-induced mutants were relatively heterogeneous and appeared to be affected in a single cistron only, a high proportion of mutants isolated after selection for donor-specific phage resistance had deletions but always included tra Y. Mutants selected directly on the basis of transfer deficiency which also became donor-specific phage resistant fell into all 10 cistrons, suggesting that many R91-5 transfer cistrons are concerned with the synthesis of sex pili and other surface structures necessary for conjugal transfer. Conversely, most retaining donor-specific phage sensitivity belonged to one cistron, whereas transfer-deficient mutants which had also lost the ability to inhibit the replication of phage G101 comprised four cistrons.

R.SmaI cleavage map of the transfer region of the E. coli K12 sex factor F

A map of the seventeen R.SmaI sites within the 33·4 kb transfer region of plasmid F has been obtained. The number of R.SmaI sites contrasts sharply with the few sites for other restriction endonucleases with hexanucleotide specificity. Location of the R.SmaI sites in γtratransducing phages allowed physical location of lambda insertions into thetraB,traFandtraHgenes.

Cloned fragments of the plasmid ColV,I-K94 specifying virulence and serum resistance

A cloned BamH1-generated fragment of ColV,I-K94 increased the virulence of Escherichia coli, causing an approximately 100-fold reduction in LD50 for chicks. A genetic determinant for resistance to the bactericidal effects of serum was mapped to a 5,300 base-pair sequence within the fragment. Neither colicin V nor immunity to colicin V affected the pathogenicity of E. coli for chicks.

Investigations of the F conjugation gene traI:traI mutants and lambdatraI transducing phages

A series of traI point and deletion mutants of Flac, and a traM mutant, were characterised. Complementation tests with an amber Flac traI mutant confirmed their genotypes, and in addition all the traI mutants, but not the traM mutant, were complemented by pRS31 (PSC101 traDI) and EDlambda109 (lambdatraI). Judging from the efficiencies of plating of F-specific phages, none of the mutations affected pilus formation. The traI products of F and of the F-like plasmid R1 were interchangeable with each other but not with that of R100, while the traM product of F could not be replaced by those of R1 or of R100. Neither traI nor traM were needed for conjugal transfer of ColE1. Three lambda transducing phages carrying traI were isolated by in vivo or in vitro techniques, and characterised by genetic complementation tests, by analysis of the fragments produced by restriction endonucleases, and by measurement of heteroduplex molecules. The genetic structures together with the sizes and F coordinates, of the transfer regions carried by the phages were thereby determined. Comparison of the proteins synthesised in UV-irradiated cells by one of the lambdatraI phages with those made by a derivative carrying an amber traI mutation, allowed the traI product to be identified as a protein of molecular weight 174,000. In addition, the molecular weights of the traD (84,000), traS (18,000), and traT (25,000) products made by the lambdatraSTD1 phage EDlambda107 were measured. The possible roles of the traI and traM products in conjugation are discussed.