TraJ Protein Research Articles

Silencing and activating type IV secretion genes of the F-like conjugative resistance plasmid R1

Expression of DNA transfer (tra) genes of F-type conjugative plasmids is required for the assembly of a functional type IV secretion machinery and subsequent plasmid DNA transfer from donor to recipient cells. Transcription of tra genes depends on the activation of a single promoter, designated PY, by the plasmid encoded TraJ protein. We here determine plasmid specificity of TraJ proteins from various subgroups of F-like plasmids and find that plasmid R1 conjugation and PY promoter activation can be achieved only by its cognate activator and by TraJ of the Salmonella plasmid pSLT and not by F or R100 TraJ proteins. In addition, we characterize the PY promoter of plasmid R1. We show that TraJ binds to PY DNA in vivo and that H-NS acts as a silencer of the PY promoter. In the natural plasmid context, H-NS silences transfer gene expression and horizontal plasmid DNA transfer. In contrast to what was found for the F plasmid, lack of H-NS did not abolish the requirement for ArcA and TraJ to reach full tra gene expression and DNA transfer activity. We propose that, besides a passive de-silencing activity, both ArcA and TraJ play a direct role in synergistically stimulating tra operon transcription and subsequent DNA transfer.

Prevalence and distribution of nucleotide sequences typical for pMEA-like accessory genetic elements in the genus Amycolatopsis

The prevalence and distribution of pMEA-like elements in the genus Amycolatopsis was studied. For this purpose, a set of 95 recently isolated Amycolatopsis strains and 16 Amycolatopsis type strains were examined for the presence of two unique pMEA-sequences (repAM and traJ), encoding proteins essential for replication and conjugative transfer. Homologues of repAM and traJ were found in 10 and 26 of 111 investigated strains, respectively, a result which shows that pMEA-like sequences, though not very abundant, can be found in several Amycolatopsis strains. Phylogenetic analysis of the deduced RepAM and TraJ protein sequences revealed clustering with the protein sequences of either pMEA300 or pMEA100. Furthermore, two geographically different populations of pMEA-like elements were distinguished, one originating in Europe and the other in Australia and Asia. Linkage between the distribution of repAM and traJ and the chromosomal identifier, the 16S rRNA gene, indicated that these elements coevolved with their hosts, suggesting that they evolved in an integrated form rather than by horizontal gene transfer of the free replicating form.

H-NS and Lrp serve as positive modulators of traJ expression from the Escherichia coli plasmid pRK100.

Conjugative transfer of F-like plasmids is a tightly regulated process. The TraJ protein is the main positive activator of the tra operon which encodes products required for conjugative transfer of F-like plasmids. Nucleotide sequence analysis revealed potential Lrp and H-NS binding sites in the traJ regulatory region. Expression of a traJ-lacZ fusion in hns and lrp mutant strains showed that both are positive modulators of traJ expression. Competitive RT-PCR demonstrated that H-NS and Lrp exert their effect at the transcriptional level. Electrophoretic mobility-shift assays showed that H-NS and Lrp proteins bind to the traJ promoter. Conjugative transfer of pRK100 was decreased in hns but not in lrp mutant strains. Together, the results indicate H-NS and Lrp function as activators of traJ transcription.

The cyclic AMP-cyclic AMP receptor protein complex regulates activity of the traJ promoter of the Escherichia coli conjugative plasmid pRK100.

The TraJ protein is a central activator of F-like plasmid conjugal transfer. In a search for regulators of traJ expression, we studied the possible regulatory role of the cyclic AMP (cAMP)-cAMP receptor protein (CRP) complex in traJ transcription using a traJ-lacZ reporter system. A comparison of the enzyme activities in the wild-type Escherichia coli strain MC4100 with those in cya and crp mutants indicated that disruption of the formation of the cAMP-CRP complex negatively influenced the activity of the traJ promoter of the F-like plasmid pRK100. The defect in the cya mutant was partially restored by addition of exogenous cAMP. Competitive reverse transcription-PCR performed with RNA isolated from the wild-type and mutant strains showed that the cAMP-CRP complex exerted its effect at the level of transcription. Electrophoretic mobility shift assays with purified CRP demonstrated that there was direct binding of CRP to the traJ promoter region. DNase I footprint experiments mapped the CRP binding site around position -67.5 upstream of the putative traJ promoter. Targeted mutagenesis of the traJ promoter region confirmed the location of the CRP binding site. Consistent with the demonstrated regulation of TraJ by the cAMP-CRP complex, mutants with defects in cya or crp exhibited reduced conjugal transfer from pRK100.

In Vitro Analysis of the Interaction between the FinO Protein and FinP Antisense RNA of F-like Conjugative Plasmids

The FinO protein regulates the transfer potential of F-like conjugative plasmids through its interaction with FinP antisense RNA and its target, traJ mRNA. FinO binds to and protects FinP from degradation and promotes duplex formation between FinP and traJ mRNA in vitro. The FinP secondary structure consists of two stem-loop domains separated by a 4-base spacer and terminated by a 6-base tail. Previous studies suggested FinO bound to the smooth 14-base pair helix of stem-loop II. In this investigation, RNA mobility shift analysis was used to study the interaction between a glutathione S-transferase (GST)-FinO fusion protein and a series of synthetic FinP and traJ mRNA variants. Mutations in 16 of the 28 bases in stem II of FinP that are predicted to disrupt base pairing did not significantly alter the GST-FinO binding affinity. Removal of the single-stranded regions on either side of stem-loop II led to a dramatic decrease in GST-FinO binding to FinP and to the complementary region of the traJ mRNA leader. While no evidence for sequence-specific contacts was found, the results suggest that FinO recognizes the overall shape of the RNA and is influenced by the length of the single-stranded regions flanking the stem-loop.

Regulatory mechanisms in expression of the traY-I operon of sex factor plasmid R100: involvement of traJ and traY gene products.

The plasmid R100 encodes tra genes essential for conjugal DNA transfer in Escherichia coli. Genetic evidence suggests that the traJ gene encodes a positive regulator for the traY-I operon, which includes almost all the tra genes located downstream of traJ. The molecular mechanism of regulation by TraJ, however, is not yet understood. traY is the most proximal gene in the traY-I operon. TraY promotes DNA transfer by binding to a site, sbyA, near the origin of transfer. TraY is suggested to have another role in regulation of the traY-I operon, since it binds to two other sites, named sbyB and sbyC, located in the region preceding traY-I. Using a traY-lacZ fusion gene, we showed that the traY-I operon was expressed only in the presence of traJ. The TraJ-dependent expression of traY-I required the E. coli arcA gene, which encodes a host factor required for conjugation. TraJ-dependent transcription occurred from a promoter (named pY) located upstream of traY-I. The isolated TraJ protein was found to bind to a dyad symmetry sequence, named sbj (specific binding site of TraJ), which existed in the intergenic region between traJ and traY-I. We also demonstrated that TraY repressed the TraJ-dependent expression of traY-I at the TraY binding sites, sbyB and sbyC, which overlapped with pY. TraJ is a protein which binds to the sbj site in the region upstream of the promoter pY and positively regulates expression of the traY-I operon in the presence of the E. coli arcA gene. Since sbj is located 93bp upstream of pY in the intergenic region between traJ and traY-I, TraJ presumably contacts with a transcription apparatus to promote transcription from pY. TraY, which is known to activate the initiation of conjugal DNA transfer, has a new role in the transcriptional autoregulation of traY-I expression. At levels which are sufficient to initiate conjugal DNA transfer, TraY represses traY-I transcription in the presence of TraJ.

Contributions of promoter context and structure to regulated expression of the F plasmid traY promoter in Escherichia coli K‐12

Expression of the F plasmid traY promoter in vivo requires both host (E. coli) and plasmid encoded proteins. As judged by transcript size and primer extension analyses, the F plasmid traY promoter was utilized in vitro by purified E. coli sigma 70 RNA polymerase in the absence of other proteins. However, in vitro transcription required supercoiled templates. Endonuclease protection experiments showed that RNA polymerase is unable to form a stable complex at the traY promoter in linear or relaxed circular templates. In vitro transcription with linear templates could be elicited by altering the traY -10 and -35 hexamers to the consensus sequences. Alterations that reduced the effect of template supercoiling on apparent promoter strength in vitro also reduced the effect of the F plasmid TraJ protein on traY expression in vivo. Apparent traY promoter strength in vitro, estimated in template competition experiments, was unaltered by deletion of tra DNA normally upstream of the promoter, a change in promoter context that elicited high levels of promoter activity in TraJ- cells. These data suggest a model for regulated traY promoter activity in which a nucleoprotein complex involving tra DNA immediately upstream locally relaxes traY promoter DNA. TraJ and perhaps other activators could disrupt the complex, allowing promoter DNA to equilibrate at the prevailing negative superhelical density and thereby eliciting transcription initiation.

Accumulation of the F plasmid TraJ protein in cpx mutants of Escherichia coli

We report here studies of the cellular control of F plasmid TraJ protein levels, focusing on the effects of chromosomal cpx mutations. The principal conclusion from our results is that the cpx mutations impair accumulation of the TraJ protein, thereby reducing tra gene expression. We measured TraJ activity in vivo by expression of a traY'-'lacZ fusion gene and TraJ protein by immuno-overlay blot. In strains with normal TraJ levels, traY expression and donor-related functions were reduced in cells carrying any of four cpxA mutations. In the strain background used to isolate cpx mutants, these reductions were especially evident in cells grown to high density, when traY expression and donor activity both increased in cpx+ cells. In each of the four cpxA mutants tested, TraJ levels were lower than in the otherwise isogenic cpxA+ strain. In cells grown to high density, the differences ranged from 4-fold in the cpxA6 strain to > 10-fold in the cpxA2, cpxA5, and cpxA9 strains. The cpxA2 mutation had little or no effect on traY expression or on donor-related functions when TraJ was present in excess of its limiting level in F' or Hfr cells or on a mutant traY promoter whose expression in vivo was independent of TraJ.

In vitro assembly of relaxosomes at the transfer origin of plasmid RP4.

During initiation of conjugative transfer of DNA containing the transfer origin (oriT) of the promiscuous plasmid RP4, the proteins TraI, TraJ, and TraH interact and assemble a specialized nucleoprotein complex (the relaxosome) at oriT. The structure can be visualized on electron micrographs. Site- and strand-specific nicking at the transfer origin in vitro is dependent on the proteins TraI and TraJ and on Mg2+ ions. Substrate specificity is directed exclusively towards the cognate transfer origin: the RP4-specified TraJ protein cannot recognize the closely related oriT of plasmid R751. After nicking, TraI protein remains attached to the 5'-terminal 2'-deoxycytidyl residue at the nic site [Pansegrau, W., Ziegelin, G. & Lanka, E. (1990) J. Biol. Chem. 265, 10637-10644]. Nicking and relaxosome formation require supercoiled DNA. Thus, a complicated structure involving multiple plasmid-specified proteins and a defined region of DNA must be formed at the transfer origin to prepare the plasmid for generating the single strand to be transferred.

Covalent association of the traI gene product of plasmid RP4 with the 5'-terminal nucleotide at the relaxation nick site.

Formation of relaxosomes is the first step in the initiation of transfer DNA replication during bacterial conjugation. This nucleoprotein complex contains all components capable of introducing a site- and strand-specific nick at a cognate transfer origin (oriT) on supercoiled plasmid DNA, thus providing the substrate for generation of the strand to be transferred. Characterization of the terminal nucleotides at the oriT nick site revealed that relaxation occurs by hydrolysis of a single phosphodiester bond between a 2'-deoxyguanosyl and a 2'-deoxycytidyl residue. The relaxation nick site and a 19-base pair invert repeat sequence that is recognized by asymmetric binding of the RP4 TraJ protein are interspaced by 8 base pairs. The nicking reaction results in covalent attachment of the RP4 TraI protein to the 5'-terminal 2'-deoxycytidyl residue of the cleaved strand. The arrangement of the TraJ binding site and the relaxation nick site on the same side of the DNA double helix suggests that protein-protein interactions between TraJ and TraI are a prerequisite for oriT specific nicking. In accordance with the current model of transfer DNA replication, the 3' end remains accessible for primer extension by DNA polymerase I, enabling replacement strand synthesis in the donor cell by a rolling circle-type mechanism.

TraJ protein of plasmid RP4 binds to a 19-base pair invert sequence repetition within the transfer origin

Transfer of plasmid RP4 during bacterial conjugation requires the plasmid-encoded TraJ protein, which binds to the transfer origin (Fürste, J. P., Pansegrau, W., Ziegelin, G., Kröger, M., and Lanka, E. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 1771-1775). As indicated by traJ mutants, the TraJ protein is a constituent of the relaxosome, the initiation complex of transfer DNA replication. The traJ gene maps adjacent to the transfer origin (oriT). The structural gene consists of a 372-base pair sequence encoding a polypeptide of 122 amino acids (13,282 Da). TraJ was purified from an Escherichia coli strain overproducing the protein. DNA footprinting experiments involving DNase I demonstrated that the purified protein binds to the right arm of a 19-base pair inverted repeat within oriT. Hydroxyl radical footprints of the DNA-protein complex revealed that TraJ protein is bound to only one side of the DNA helix.

The origin of conjugative IncP plasmid transfer: Interaction with plasmid-encoded products and the nucleotide sequence at the relaxation site

To characterize protein-DNA interactions involved in the initiation of conjugative transfer replication we isolated and dissected the transfer origins ( oriT) of the promiscuous IncP plasmids RP4 and R751. Essential features of oriT are conserved: symmetric sequence repeats, the nic site and a pair of potential promoter sites that allow for divergent transcription of two tra opersons. The relaxation nick and the end of a 19 bp inverted repeat are interspaced by eight basepairs. The 5′-terminal nucleotide at the nick is modified by an alkali-resistant residue and the 3′-nucleotide is accessible to extension by DNA polymerase I. Transfer gene products essential for the formation of the initiation complex (relaxosome) of conjugative DNA synthesis map adjacent to oriT. Two of these products, TraJ and TraK confer specificity to their homologous oriT exclusively. Proteins TraJ and TraK are the only components of the RP4 and R751 transfer machinery which cannot be interchanged. TraJ and at least two additional plasmid-encoded products are necessary for specific relaxation. The purified TraJ protein of RP4 possesses oriT-binding ability. The recognition sequence contains a palindromic sequence located within the right arm of the 19 bp inverted repeat. The TraJ binding site and the nic site are located on one side of the DNA double helix. We presume that this nucleoprotein structure is the initial complex in the pathway to the assembly of functional relaxosomes.

Identification and characterization of the products from the traJ and traY genes of plasmid R100.

The nucleotide sequence of part of the tra region of R100 including traJ and traY was determined, and the products of several tra genes were identified. The nucleotide sequence of traJ, encoding a protein of 223 amino acids, showed poor homology with the corresponding segments of other plasmids related to R100, but the deduced amino acid sequences showed low but significant homology. The first four amino acids at the N-terminal region of the TraJ protein were not essential for positive regulation of expression of traY, the first gene of the traYZ operon. The nucleotide sequence of traY shows that this gene may use TTG as the initiation codon and that it encodes a protein of 75 amino acids. Analysis of the traY gene product, which was obtained as the fusion protein with beta-galactosidase, showed that the N-terminal region of the product has an amino acid sequence identical to that deduced from the assigned frame but lacks formylmethionine. traY of plasmid F, which encodes a larger protein than the TraY protein of R100, is thought to use ATG as an initiation codon. However, a TTG initiation codon was found in the preceding region of the previously assigned traY coding frame of F. Interestingly, when translation of traY of F was initiated from TTG, the amino acid sequence homologous to the TraY protein of R100 appeared in tandem in the TraY protein of F. This may suggest that traY of F has undergone duplication of a gene like the traY gene of R100.

Characterization of the F plasmid TraJ protein synthesized in F' and Hfr strains of Escherichia coli K-12.

Using purified F plasmid TraJ protein (Cuozzo, M., Silverman, P., and Minkley, E. (1984) J. Biol. Chem. 259, 6659-6666), we prepared rabbit anti-TraJ protein antibodies to analyze for the first time the TraJ protein as it is synthesized in normal F' and Hfr conjugal donor strains. Using affinity-purified antibody, we identified the protein on immuno-overlay blots of whole cell proteins separated by sodium dodecyl sulfate/polyacrylamide gel electrophoresis. In contrast to the TraJ protein synthesized in large quantity by heat-induced lambda (traJ) lysogens, the TraJ protein synthesized in normal donor cells was soluble, even after sedimentation at 100,000 X g. The soluble protein was found with the cytoplasmic fraction after separation of cytoplasmic and periplasmic proteins. Velocity sedimentation analysis indicated an S20,w of 3.5 for the single molecular species composed of or including all the TraJ polypeptide in crude extracts. Quantitative analyses showed that conjugal donor strains normally contain 2000-4000 TraJ monomers/cell. However, that level depended on other plasmid and chromosomal genes.

Shadow promoters in the F plasmid transfer operon.

The in vivo transcription start site for PYZ, the promoter of the F plasmid transfer operon, has been located. When transcription start sites for PYZ are deleted, two additional shadow promoters, upstream of PYZ, are activated in vivo. The shadow promoters correspond to those previously identified by in vitro run-off transcription experiments. The activated shadow promoters are stimulated by TraJ protein, a positive regulator of the transfer operon.

Promoters in the transfer region of plasmid F.

Regulation of the conjugation (tra) genes of IncF plasmids occurs by a complex, 2-stage process. Most IncF plasmids carry 2 fertility inhibition genes, finO and finP, the products of which act in concert to prevent transcription of traJ, a gene which has its own promoter (6, 22). F itself lacks finO but carries both a finP gene and the site at which FinOP regulation occurs, fisO. In turn, the traJ protein (pTraJ) is required for transcription of the major 32-kb traY→Z operon (10,22). The transfer region contains 2 further promoters, that for traM (21,23), and a weak promoter that also transcribes traI and traZ (1,23). There have also been suggestions that the F traT surface exclusion gene has its own promoter (18), as does the traT gene of R100 (16), although the polarity on surface exclusion and traD of Mu insertions into the traYZ operon argues against this (8,10). These regulatory stages were reviewed by Willetts and Skurray (24).

Overproduction in Escherichia coli K-12 and purification of the TraJ protein encoded by the conjugative plasmid F.

The TraJ protein encoded by the conjugative plasmid F has been designated an Escherichia coli K-12 envelope protein that participates in a mechanism of gene regulation. We have purified the TraJ protein, using an Flac::lambda traJ lysogen that overproduces the protein after heat induction of the prophage. Sufficient TraJ protein was synthesized within 40 min after induction to follow the purification by sodium dodecyl sulfate/polyacrylamide gel electrophoresis. Our purification exploited the observation that the TraJ protein remains insoluble after repeated Triton X-100/EDTA extractions of crude envelope fractions. The protein was then solubilized in sodium dodecyl sulfate at 60 degrees C and fractionated further by gel filtration and hydroxylapatite chromatography, both in the presence of sodium dodecyl sulfate. After hydroxylapatite chromatography, the protein was greater than 95% pure. The identity of the purified protein was confirmed by analysis of its NH2-terminal amino acid sequence, which was the same as that predicted from the partial nucleotide sequence of the traJ gene (Thompson, R., and Taylor, L. (1982) Mol. Gen. Genet. 188, 513-518). This analysis also indicated that the TraJ protein is localized in the cell without proteolytic modification of its NH2-terminus. We discuss the possible significance of these observations with respect to the cellular functions of the TraJ protein.

Identification of the dye gene product, mutational loss of which alters envelope protein composition and also affects sex factor F expression in Escherichia coli K-12.

The product of the dye gene of Escherichia coli, mapping at 99-100 min, is required for expression of the sex factor F, and also appears to be involved in the regulation of envelope proteins. Mutation of dye thus results in loss of expression of the F-factor ( Fex -), i.e. male sterility, and dye sensitivity (Dyes). We have isolated a plasmid, pRB38 , in which a 6 kb SalI fragment carrying the dye+ gene was cloned into the plasmid pACYC184. This 6 kb SalI fragment also carries two nearby markers, chlG , involved in the synthesis of the molybdenum cofactor, and phoM, required for constitutive expression of alkaline phosphatase. Some of the polypeptides synthesised by pRB38 were identified using the maxi-cell procedure. The product of the dye gene was found to be a polypeptide of Mr = 29,000. Thus derivatives of pRB38 in which the transposon gamma delta was inserted into dye, resulting in a Dyes Fex - phenotype when these plasmids were in a delta dye strain, failed to a produce this polypeptide and in some cases produced a truncated product. Such insertions also resulted in a Chlr and Pho- phenotype when the plasmid was in a delta (dye- chlG -phoM) phoR strain, although complementation tests suggested that the phoM+ and chlG + genes were still intact. Insertions of gamma delta into the promoter distal end of dye did not result in a Dyes Fex - phenotype, although a truncated Dye protein was synthesised, and a Chlr Pho- phenotype was produced. It has been suggested ( Gaffney et al. 1983) that the dye (= sfrA ) gene product is necessary for F-factor expression because it is required for translocation of the F-factor TraJ protein to the outer membrane.(ABSTRACT TRUNCATED AT 250 WORDS)

The control region of the F plasmid transfer operon: DNA sequence of the traJ and traY genes and characterisation of the traY → Z promoter

The complete nucleotide sequence of the F plasmid transfer genes traJ and traY, together with the promoterproximal region of the traA gene has been determined. The traJreading frame has been confirmed by sequencing the traJ90 amber mutant allele. The predicted amino acid sequence of the TraJ protein shows that this outer-membrane protein lacks a signal sequence. The pattern of codon usage within the traJ gene is different from that of genes for abundant outer-membrane proteins and is closer to that of genes that are expressed at relatively low levels. We have located the traY → Z operon promoter by in vitro run-offtranscription experiments and have developed in vivo assays for the activity of the promoter by fusing it to galactokinase and kanamycinresistance genes.

λ-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.