Studies on the control region of the bipolar argECBH operon of Escherichia coli. I. Effect of regulatory mutations and IS2 insertions

Co-evolution with recombination affects the stability of mobile genetic element insertions within gene families of Salmonella

Bacteria can have multiple copies of a gene at separate locations on the same chromosome. Some of these gene families, including tuf (translation elongation factor EF-Tu) and rrl (ribosomal RNA), encode functions critically important for bacterial fitness. Genes within these families are known to evolve in concert using homologous recombination to transfer genetic information from one gene to another. This mechanism can counteract the detrimental effects of nucleotide sequence divergence over time. Whether such mechanisms can also protect against the potentially lethal effects of mobile genetic element insertion is not well understood. To address this we constructed two different length insertion cassettes to mimic mobile genetic elements and inserted these into various positions of the tuf and rrl genes. We measured rates of recombinational repair that removed the inserted cassette and studied the underlying mechanism. Our results indicate that homologous recombination can protect the tuf and rrl genes from inactivation by mobile genetic elements, but for insertions within shorter gene sequences the efficiency of repair is very low. Intriguingly, we found that physical distance separating genes on the chromosome directly affects the rate of recombinational repair suggesting that relative location will influence the ability of homologous recombination to maintain homogeneity.

Biosynthesis of Arginine and Polyamines

Early investigations on arginine biosynthesis brought to light basic features of metabolic regulation. The most significant advances of the last 10 to 15 years concern the arginine repressor, its structure and mode of action in both E. coli and Salmonella typhimurium, the sequence analysis of all arg structural genes in E. coli and Salmonella typhimurium, the resulting evolutionary inferences, and the dual regulation of the carAB operon. This review provides an overall picture of the pathways, their interconnections, the regulatory circuits involved, and the resulting interferences between arginine and polyamine biosynthesis. Carbamoylphosphate is a precursor common to arginine and the pyrimidines. In both Escherichia coli and Salmonella enterica serovar Typhimurium, it is produced by a single synthetase, carbamoylphosphate synthetase (CPSase), with glutamine as the physiological amino group donor. This situation contrasts with the existence of separate enzymes specific for arginine and pyrimidine biosynthesis in Bacillus subtilis and fungi. Polyamine biosynthesis has been particularly well studied in E. coli, and the cognate genes have been identified in the Salmonella genome as well, including those involved in transport functions. The review summarizes what is known about the enzymes involved in the arginine pathway of E. coli and S. enterica serovar Typhimurium; homologous genes were identified in both organisms, except argF (encoding a supplementary OTCase), which is lacking in Salmonella. Several examples of putative enzyme recruitment (homologous enzymes performing analogous functions) are also presented.

An Escherichia coli insertion element (IS2) provides a functional promoter in Bordetella pertussis

The adenylate cyclase (cyaA) gene of Bordetella pertussis is not expressed in Escherichia coli. Using cya-lac fusions, high-expression spontaneous mutants were isolated and shown to have the insertion element IS2 in orientation II integrated into the reading frame of cyaA. Upon transfer of the IS2-activated cya-lac fusion into B. pertussis, we found that the IS2-provided promoter is as efficient in B. pertussis as it is in E. coli. These results provide evidence that an insertion element derived from the E. coli chromosome can activate gene expression in B. pertussis, a taxonomically distant organism.

Turn-on of inactive genes by promoter recruitment in Escherichia coli: inverted repeats resulting in artificial divergent operons

We have characterized two rearrangements consisting of inverted repeats of the argE gene. The promoters (p) of argE and of argCBH face each other over an internal operator. The rearrangements were obtained as reactivations of argE in a strain harboring an argEp deletion on a lambda darg prophage. In both cases the repeat included argE and argCBHp on either side of a unique sequence; the result is a divergent operon in which each copy of argCBHp reads into the adjacent argE repeat. In one case, the pair of repeats adjoins the silent parental gene, forming a triplication (comes from leads to comes from). The other rearrangement consists of a single argE palindrome, but the whole prophage is rearranged into an inverted repeat, analogous to certain lambda dv's. Both structures could be explained by breakage of a replication fork passing argE and by inaccurate rejoining of strands. The lambda dv-like rearrangement would result from breakage at both replication forks of a phage or prophage replicating during transient release of immunity. The triplication would imply breaking of a chromosomal replication fork, formation of a cyclic intermediate by recombination between the daughter duplex molecules and reinsertion into the parental argE gene. Formation of a triplication by replication errors involving appropriate strand switchings and branch migrations can not be excluded however.

Molecular basis for modulated regulation of gene expression in the arginine regulon of Escherichia coli K-12

We compare the nucleotide sequences of the regulatory regions of five genes or groups of genes of the arginine regulon of Escherichia coli K-12: argF, argI, argR, the bipolar argECBH operon and the carAB operon. All these regions harbour one or two copies of a conserved 18 bp sequence which appears to constitute the basic arginine operator sequence (ARG box). We discuss the influence of ARG box copy number, degree of dyad symmetry, base composition, and position relative to the cognate promoter site on the derepression-repression ratios of the genes of the regulon. A novel hypothesis, based on structural considerations, is also put forward to account for the absence ot attenuation control.

The regulatory region of the divergent argECBH operon in Escherichia coli K-12

The nucleotide sequence of the control region of the divergent argECBH operon has been established in the wild type and in mutants affecting expression of these genes. The argE and argCBH promoters face each other and overlap with an operator region containing two domains which may act as distinct repressor binding sites. A long leader sequence - not involved in attenuation - precedes argCBH. Overlapping of the argCBH promoter and the region involved in ribosome mobilization for argE translation explains the dual effect of some mutations. Mutations causing semi-constitutive expression of argE improve putative promoter sequences within argC. Implications of these results regarding control mechanisms in amino acid biosynthesis and their evolution are discussed.

IS3 can function as a mobile promoter in E. coli

We had shown previously (3) that the E. coli argE gene could be turned-on by an IS3 element inserted in orientation II near the 5' end of the gene. Here we show that this effect is due to the presence of an outward promoter located on IS3. The exact site of insertion of IS3 was determined by DNA sequencing. Using the S1 nuclease mapping technique with in vivo transcribed RNA we located the promoter responsible for argE transcription on IS3 itself outside the region involved in the inverted repeats of this element. IS3 may therefore be considered as a mobile promoter.

Transcription initiation sites within an IS2 insertion in a Gal-constitutive mutant of Escherichia coli

Insertion of the insertion sequence Is2(I) directly before the galE gene of the galactose operon results in a Gal minus phenotype (1, 2). The Gal-constitutive allele galc200 (and its deletion derivative galc200 delta 31) arise from such a Gal minus mutant by the insertion of LS2(II) DNA within the LS2(I) sequence (3). We have transcribed in vitro a DNA template representing the IS2-galE region of galc200 delta 31. Gal-directed transcription initiates at two sites within the IS2(I) sequence, 51 and 52 bp from the IS2-galE junction. The promoter for these transcripts, Pgal200 delta 31, is composed of a novel joint between a -10 region from the IS2(I) DNA and a -35 region contributed by the IS2(II) insertion. No promoters intrinsic to the 121 bp of the IS2(II) sequence also present on the template were detected. The relevance of Pgal200 delta 31 to the Galc phenotype of galc200 and to general mechanisms for the constitutive expression of genes adjacent to IS2 is discussed.

Promoter mapping and selection of operator mutants by using insertion of bacteriophage Mu in the argECBH divergent operon of Escherichia coli K-12

The analysis of a large number of Arg mutants obtained by inserting phage Mu in the argECBH cluster of genes confirmed the "facing" arrangement proposed earlier for the promoters of argE (argEp) and argCBH (argCBHp) and clarified remaining ambiguities regarding the localization of argEp. Casadaban and Cohen's Mu d lac phages (M. Casadaban and S. N. Cohen, Proc. Natl. Acad. Sci. U.S.A. 76:4530-4533, 1979) were used to construct strains where either an intact or a truncated lacZ gene was fused to argC or argB. Several operator-constitutive mutations could be selected for in such strains; the mutations affected both arms of the cluster, thereby defining one common operator region for both directions of transcription.

Characterization of beta-lactamase-deficient (bla) mutants of the R plasmid R1 in Escherichia coli K-12 and comparison with similar mutants of RP1

Thirty-eight mutants of R1, an R plasmid specifying the type IIIa (TEM) beta-lactamase, were isolated; these mutants are partially or totally unable to synthesize the type IIIa beta-lactamase. The loss of beta-lactamase activity was associated with a reduction in the level of penicillin resistance conferred by the mutants upon their host strain. At least two of the mutants synthesized a beta-lactamase with altered substrate specificity. These properties are compared with those of two beta-lactamase-deficient mutants of plasmid RP1. The results suggest that, for both R plasmids, penicillin resistance is entirely attributable to the presence of beta-lactamase activity. The properties of two R1 derivatives, pUB251 and pUB252, which have phenotypes similar to that of RP1, support this conclusion.

Immunological and genetic properties of Escherichia coli K12 argE mutants

CRM+ nonsense mutations, as described for E. coli K12 lacZ, in theory permit determination of the direction of transcription of an isolated gene. In the hope of utilising this approach to confirm that the E gene of the E. coli K12 argECBH cluster is transcribed in the opposite direction from the CBH unit, 30 argE mutations were investigated immunologically and genetically. Only three, E1, E25 and E26 (which map close together towards the left-hand end of the gene), were found to be CRM+. Co-suppression of each argE mutation with known strongly polar lacZ amber, ochre and UGA mutations was looked for to distinguish missfense from nonsense argE's, Arg+ revertants being screened for Lac+ and Mel+ phenotypes. Of 16 mutations not hitherto characterised as nonsense, frameshift or large deletions, only three, E1, E25 and E26, appeared to be missense. Three of the nonsense mutations were also streptomycin suppressible. It appears, therefore, that among argE mutants so far studied the correlation between CRM+ and missense is complete, so that the projected method for determining the direction of transcription of argE could not be applied.

Use of bio-lac fusion strains to study regulation of biotin biosynthesis in Escherichia coli

The technique developed by Casadaban (M. J. Casadaban, J. Mol. Biol. 104: 541-555, 1976) has been employed to construct Escherichia coli K-12 derivatives in which the genes determining lactose utilization are fused to the regulatory region of the biotin operon. Fusions of the lac genes to either arm of this divergently transcribed operon have been isolated. When the operon is derepressed, expression of the lac genes is sufficient to permit growth on lactose minimal medium. Repressing conditions prevent growth on lactose. This property of bio-lac fusion strains, as well as the ease of determining the level of operon expression by assaying beta-galactosidase, was used for the isolation and characterization of mutants defective in repression. Preliminary analyses of several newly isolated regulatory mutants are presented. For the several birA mutants examined, there appeared to be no direct correlation between effects on minimum biotin requirement and alterations in repressibility, suggesting a possible dual function for the gene. Parallel attempts to obtain fusions of lac to bioH were unsuccessful, indicating lack of direct biotin control at the bioH locus.

Tandem and inverted repeats of arginine genes in Escherichia coli: structural and evolutionary considerations

Duplications of arg genes produced in the Rec+ and in the recA genetic backgrounds are shown by heteroduplex analysis to be strictly tandem at the level of resolution of this technique. The formation of these particular rearrangements therefore does not require the inclusion of transposons or other sequences of an appreciable size in their final structure. Duplications of short segments (about 2,000 nucleotides) appear unexpectedly stable when compared with duplications of longer segments (about 10,000 nucleotides). One of the structures analyzed displays two inversely repeated argE genes rearranged into an artificial divergent operon. The bearing of this observation on the origin of bipolar operons, of "mirror-image" map symmetries and on the production of inverted repeats in general, is discussed.

Cloning and endonuclease restriction analysis of argF and of the control region of the argECBH bipolar operon in Escherichia coli

A 1.8 kb DNA fragment, liberated by endonuclease HindIII, contains the control region of the argECBH bipolar operon near one end and the weak secondary promoter of argH at the other extremity; it has been cloned in plasmid pBR322. The same plasmid vector has been used to clone the argF gene liberated from the chromosome by endonuclease BamHI. Restriction patterns for the two hybrid plasmids have been determined, using enzymes AluI, BglI, EcoRI, HaeIII, HincII, HindIII, HpaI and II, PstI and SalI. Two AluI sites situated on either side of and close to a HincII target delineate two short fragments covering the whole of the argECBH control region. The argF control elements are located in a region accessible to further dissection by BamHI, EcoRI, PstI and HindIII. Carriers of the argF plasmid produce extremely high amounts of ornithine carbamoyltransferase, a feature useful for purification of this enzyme.