Use of the rep technique for allele replacement to construct new Escherichia coli hosts for maintenance of R6K gamma origin plasmids at different copy numbers

Escherichia coli hosts were constructed for maintenance of vectors containing the gamma replication origin of the R6K plasmid (oriRR6K gamma) at different copy numbers (15 or 250/cell). Such vectors require the trans-acting II protein (the pir gene product) for replication. New hosts carry pir+ or pir-116 on the chromosome within uidA, the E. coli gene encoding beta-glucuronidase. They were made using the rep technique for allele replacement and KmR M13 delta uid A::pir+ or M13 delta uidA::pir-116 phage. Because M13 cannot replicate in a rep mutant, KmR transductants arose by integration into the chromosomal uidA locus. Segregants lacking M13 sequences (which were selected as deoxycholate-resistant (DocR) ones) frequently contained delta uidA::pir+ or delta uidA::pir-116 on the chromosome. In principle, this procedure could be used for the introduction of any foreign gene into any nonessential gene on the E. coli chromosome. The delta uidA::pir+ and delta uidA::pir-116 loci were subsequently transferred to a variety of E. coli strains. One such strain is a suppressor-negative one that is especially useful for transposon (Tn) mutagenesis. This strain has an integrated RP4 derivative for conjugative transfer of oriRR6K gamma plasmids also containing oriT from RP4. In addition, new oriRR6K gamma, oriT+ vectors carrying the TcR-encoding genes tetAR from Tn10 are described. These can be used for allele replacement by conjugative transfer of an oriRR6K gamma, oriT+, tetAR plasmid containing a mutated gene into a non-pir recipient and by subsequent selection for Tc-sensitive exconjugants.

Evidence for a fourteen-gene, phnC to phnP locus for phosphonate metabolism in Escherichia coli

The Escherichia coli phn (psiD) locus consists of a large gene cluster encoding proteins necessary for the use of phosphonates (Pn) as a sole phosphorus source. On the basis of nucleotide (nt) sequence analysis, the phn locus contains a 12.6-kb operon of seventeen genes named, in alphabetical order, phnA to phnQ [Chen et al., J. Biol. Chem. 265 (1990) 4461-4471]. New Pn+ plasmids were made which are suitable for mutational analysis of this gene cluster. These plasmids contain the R6K origin for DNA replication, can be conjugatively transferred, contain the tetAR genes, and therefore provide a way for allele replacement. The construction of these plasmids showed that phnA and phnB have no role in Pn metabolism. Also, these plasmids were employed to introduce nonpolar phnD::lacZ and phnD::uidA fusions into the chromosome, which allowed us to show that phnD probably has a role in transport. In addition, it was shown that phnP is the most distal gene required for Pn use. This was done by testing the effect of phn::uidA insertions in or near the 3' end of phnP on Pn use. Altogether, these results show that all genes required for Pn use are in the 10.9-kb, fourteen-gene, phnCDEFGHIJKLMNOP locus.

Construction of new beta-glucuronidase cassettes for making transcriptional fusions and their use with new methods for allele replacement

Five cassettes carrying uidA, encoding beta-glucuronidase, were made for the construction of insertion mutants with transcriptional fusions to uidA. Three uidA cassettes contain antibiotic-resistance genes, for chloramphenicol (Cm), for kanamycin (Km) and neomycin (Nm), or for streptomycin (Sm) and spectinomycin (Sp). Some cause polar insertions while others provide a promoter for downstream gene expression. The expression of these uidA cassettes was compared to the expression of lacZ at the same site in phnD, a phosphate-regulated gene for phosphonate use. Several phn::uidA or phn::lacZ insertions were recombined onto the chromosome to test mutational effects and to measure gene expression in single copy. This was done using one of three methods for allele replacement. A new method involved recombination of mutations in M13 onto the chromosome by infection of an Escherichia coli rep mutant that fails to propagate single-stranded DNA phages. Merodiploid recombinants were selected using a resistance marker carried by the M13 phage; segregants lacking M13 sequences were then selected as deoxycholate-resistant (DocR) ones. An improved method for recombination of mutations in pir-dependent, oriR6K vectors involved the use of plasmids containing genes for tetracycline resistance (TcR). Merodiploid recombinants were selected by conjugative transfer of such plasmids into a recipient lacking pir (encoding the pi protein of the R6K plasmid); segregants lacking vector sequences were subsequently selected as Tc-sensitive ones. Both procedures are efficient and allow for recombining marked as well as unmarked mutations onto the chromosome. In addition, some insertions with an antibiotic-resistance marker were directly recombined onto the chromosome by transformation of a recD mutant with linear DNA.(ABSTRACT TRUNCATED AT 250 WORDS)

Mutational analysis of an Escherichia coli fourteen-gene operon for phosphonate degradation, using TnphoA' elements

All genes for phosphonate (Pn) utilization in Escherichia coli are in a large cluster of 14 genes named, in alphabetical order, phnC to phnP. Plasmids carrying these genes were mutagenized by using TnphoA'-1, and 43 mutants containing simple insertions were studied in detail. Their insertion sites were defined by restriction mapping and by DNA sequencing. One or more mutations in each phn gene was identified. In 23 mutants, expression of the TnphoA'-1 lacZ gene was phosphate starvation inducible. These mutants had TnphoA'-1 oriented in line behind the phnC promoter, i.e., in the + orientation. In 20 mutants, the TnphoA'-1 lacZ gene was expressed at a low basal level. These mutants had insertions in the opposite orientation. All 43 phn::TnphoA'-1 insertions were recombined onto the chromosome to test for mutational effects, and their structures on the chromosome were verified by DNA hybridization. Those in the + orientation were switched to TnphoA'-9, which has an outward promoter for expression of downstream genes. These insertions were tested for polar effects by measuring beta-glucuronidase synthesis from a uidA gene transcriptionally fused to the 3' end of the phnP gene. The results indicate the following: (i) the phnC-to-phnP gene cluster is an operon of 14 genes, and the phnC promoter is the sole psi promoter; (ii) three gene products (PhnC, PhnD, and PhnE) probably constitute a binding protein-dependent Pn transporter; (iii) seven gene products (PhnG, PhnH, PhnI, PhnJ, PhnK, PhnL, and PhnM) are required for catalysis and are likely to constitute a membrane-associated carbon-phosphorus (C-P) lyase; (iv) two gene products (PhnN and PhnP) are not absolutely required and may therefore be accessory proteins for the C-P lyase; and (v) two gene products (PhnF and PhnO) are not required for Pn use and may have a regulatory role because they have sequence similarities to regulatory proteins. The mechanism for breaking the C-P bond by a lyase is discussed in light of these results.

Molecular genetic studies of a 10.9-kb operon in Escherichia coli for phosphonate uptake and biodegradation

Bacteria that use phosphonates as a phosphorus source must be able to break the stable carbon-phosphorus bond. In Escherichia coli phosphonates are broken down by a C-P lyase that has a broad substrate specificity. Evidence for a lyase is based on in vivo studies of product formation because it has been proven difficult to detect the activity in vitro. By using molecular genetic techniques, we have studied the genes for phosphonate uptake and degradation in E. coli, which are organized in an operon of 14 genes, named phnC to phnP. As expected for genes involved in P acquisition, the phnC-phnP operon is a member of the PHO regulon and is induced many hundred-fold during phosphate limitation. Three gene products (PhnC, PhnD and PhnE) comprise a binding protein-dependent phosphonate transporter, which also transports phosphate, phosphite, and certain phosphate esters such as phosphoserine; two gene products (PhnF and PhnO) may have a role in gene regulation; and nine gene products (PhnG, PhnH, PhnI, PhnJ, PhnK, PhnL, PhnM, PhnN, and PhnP) probably comprise a membrane-associated C-P lyase enzyme complex. Although E. coli can degrade many different phosphonates, the ability to use certain phosphonates appears to be limited by the specificity of the PhnCDE transporter and not by the specificity of the C-P lyase.

Evidence for two phosphonate degradative pathways in Enterobacter aerogenes

We screened mini-Mu plasmid libraries from Enterobacter aerogenes IFO 12010 for plasmids that complement Escherichia coli phn mutants that cannot use phosphonates (Pn) as the sole source of phosphorus (P). We isolated two kinds of plasmids that, unexpectedly, encode genes for different metabolic pathways. One kind complements E. coli mutants with both Pn transport and Pn catalysis genes deleted; these plasmids allow degradation of the 2-carbon-substituted Pn alpha-aminoethylphosphonate but not of unsubstituted alkyl Pn. This substrate specificity is characteristic of a phosphonatase pathway, which is absent in E. coli. The other kind complements E. coli mutants with Pn catalysis genes deleted but not those with both transport and catalysis genes deleted; these plasmids allow degradation of both substituted and unsubstituted Pn. Such a broad substrate specificity is characteristic of a carbon-phosphorus (C-P) lyase pathway, which is common in gram-negative bacteria, including E. coli. Further proof that the two kinds of plasmids encode genes for different pathways was demonstrated by the lack of DNA homology between the plasmids. In particular, the phosphonatase clone from E. aerogenes failed to hybridize to the E. coli phnCDEFGHIJKLMNOP gene cluster for Pn uptake and degradation, while the E. aerogenes C-P lyase clone hybridized strongly to the E. coli phnGHIJKLM genes encoding C-P lyase but not to the E. coli phnCDE genes encoding Pn transport. Specific hybridization by the E. aerogenes C-P lyase plasmid to the E. coli phnF, phnN, phnO, and phnP genes was not determined. Furthermore, we showed that one or more genes encoding the apparent E. aerogenes phosphonatase pathway, like the E. coli phnC-to-phnP gene cluster, is under phosphate regulon control in E. coli. This highlights the importance of Pn in bacterial P assimilation in nature.

Involvement of the Escherichia coli phn (psiD) gene cluster in assimilation of phosphorus in the form of phosphonates, phosphite, Pi esters, and Pi

The phn (psiD) gene cluster is induced during Pi limitation and is required for the use of phosphonates (Pn) as a phosphorus (P) source. Twelve independent Pn-negative (Pn-) mutants have lesions in the phn gene cluster which, as determined on the basis of recombination frequencies, is larger than 10 kbp. This distance formed the basis for determining the complete DNA sequence of a 15.6-kbp BamHI fragment, the sequences of which suggested an operon with 17 open reading frames, denoted (in alphabetical order) the phnA to phnQ genes (C.-M. Chen, Q.-Z. Ye, Z. Zhu, B. L. Wanner, and C. T. Walsh, J. Biol. Chem. 265:4461-4471, 1990) Ten Pn- lesions lie in the phnD, phnE, phnH, phnJ, phnK, phnO, and phnP genes. We propose a smaller gene cluster with 14 open reading frames, phnC to phnP, which probably encode transporter and regulatory functions, in addition to proteins needed in Pn biodegradation. On the basis of the effects on phosphite (Pt), Pi ester, and Pi use, we propose that PhnC, PhnD, and PhnE constitute a binding protein-dependent Pn transporter which also transports Pt, Pi esters, and Pi. We propose that PhnO has a regulatory role because a phnO lesion affects no biochemical function, except for those due to polarity. Presumably, the 10 other phn gene products mostly act in an enzyme complex needed for breaking the stable carbon-phosphorus bond. Interestingly, all Pn- mutations abolish the use not only of Pn but also of Pt, in which P is in the +3 oxidation state. Therefore, Pn metabolism and Pt metabolism are related, supporting a biochemical mechanism for carbon-phosphorus bond cleavage which involves redox chemistry at the P center. Furthermore, our discovery of Pi-regulated genes for the assimilation of reduced P suggests that a P redox cycle may be important in biology.

Identification of phosphate starvation-inducible genes in Escherichia coli K-12 by DNA sequence analysis of psi::lacZ(Mu d1) transcriptional fusions

Twenty-four independent phosphate starvation-inducible (psi) transcriptional fusions made with Mu d1(lacZbla) were analyzed by sequencing the psi::lacZ(Mu d1) chromosomal junctions by using DNAs amplified with the polymerase chain reaction or mini-Mu cloning. Our DNA sequence analysis showed that the MuR DNA in Mu d1 has an unexpected structure that is comprised of 104 bases of MuR DNA in the form of a large inverted repeat, which we denoted Mu d1-R. Also, Mu d1s in the phoA and phn (psiD) loci of the phosphate regulon showed regional specificities for the insertion sites despite the randomness of Mu d1 insertions into the genome as a whole. Gene products or open reading frames were identified for seven unknown psi::lacZ(Mu d1) transcriptional fusions by searching DNA data bases with the sequences adjacent and upstream of the Mu d1s. One psiC::lacZ(Mu d1) lies in the ugpB gene of the ugpBAEC operon, which encodes a periplasmic sn-glycerol-3-phosphate-binding protein; two psiQ::lacZ(Mu d1)s lie in the gltB gene, and one psiQ::lacZ(Mu d1) lies in the gltD gene of the gltBDF operon, encoding the large and small subunits of glutamate synthase, respectively; and the psi-51::lacZ(Mu d1) lies in the glpB gene of the glpABC operon, which codes for the anaerobically regulated glycerol-3-phosphate dehydrogenase. psiE and psiF::lacZ(Mu d1)s lie in uncharacterized open reading frames near the xylE and phoA genes, respectively. Six other psi::lacZ(Mu d1)s lie in yet unreported Escherichia coli sequences.