Suppression of polarity of insertion mutations within the gal operon of E. coli

An IS4 insertion at the glnA control region of Escherichia coli creates a new promoter by providing the -35 region of its 3'-end

An insertion element (IS)4 insertion selected as suppressor of the rpoN73::Tn5 alelle was located inside the control region of the glnA gene in Escherichia coli. In the rpoN73::Tn5 background the IS4 insertion promotes glnA transcription at a low constitutive level sufficient to sustain glutamine-independent growth. The IS4 insertion mutation in either rpoN73::Tn5 or wild-type backgrounds promotes glnA transcription from a new start site located two bases downstream of the glnAp2 start site. Analysis of sequences flanking the insertion point showed a promoter sequence whose -35 region was located inside the IS4 sequence and the -10 region was inside the glnA control region. Site-directed mutagenesis of relevant nucleotide residues of the newly created promoter impaired transcription of a reporter gene. The results support our contention that IS4 carries a -35 promoter region that is able to create functional hybrid promoters. We propose that this mechanism could be one of the molecular reasons of the suppressor activity previously reported for IS4.

Complete maps of IS1, IS2, IS3, IS4, IS5, IS30 and IS150 locations in Escherichia coli K12

In this paper complete distribution maps are presented of the seven IS elements 1, 2, 3, 4, 5, 30 and 150. These maps were obtained during the construction of an almost complete restriction map of the Escherichia coli genome of K12 strain BHB2600. The positions of IS elements were correlated to this map. The distribution of integration sites of all IS types is nonrandom. Besides a large gap from 79 min to 96 min, there is a pronounced IS cluster at 6 min and another at 97 min, map locations that have low gene incidences on the classical map. One cluster coincides with a region of IS induced rearrangements. The IS distribution pattern was compared to patterns of strains W3110 and HB101.

A transcriptional terminator sequence in the prokaryotic transposable element IS1

The prokaryotic transposable element IS1 is known to exert a strong polar effect upon integration into an operon. To elucidate this polar effect, we constructed a plasmid which has an IS1 integrated between the 5' half of the tet gene for tetracycline resistance and the cat structural gene for chloramphenicol resistance. The cat gene is expressed by the tet promoter and the presence of IS1 in orientation I, in which the IS1 transposase genes insA and insB are in the same orientation as the cat gene, reduced the cat expression. By introducing deletions or insertions within the IS1 sequence, we were able to map a rho-dependent terminator TIS1A between the insA and insB genes. Translational interruption between these ins genes is important for TIS1A to be an active terminator.

Functional promoters created by the insertion of transposable element IS1

We have isolated several insertions of the transposable element IS1 into the proximal promoter (P3) of the beta-lactamase gene of plasmid pBR322, which do not abolish resistance to ampicillin. Using a transcription termination module (omega), we have shown that the gene can be expressed from hybrid promoters, created by the insertion of IS1. The terminal inverted repeats of IS1 carry sequences partially homologous to the "-35" consensus region. Splicing either of these sequences to the existing "-10" region of the beta-lactamase promoter by transposition of IS1 at the proper distance results in the formation of an active hybrid promoter. This interpretation was confirmed by transcription studies in vitro. Gene expression from the hybrid promoters was found to be less efficient than from P3. However, the orientation of IS1 that contributes a "-35" with the greater homology to the known "-35" consensus sequence is significantly more efficient than the other. In addition, we were able to assign a strong determinant of IS1 polarity to a 254 base-pair internal segment of IS1. An examination of the ends of many insertion sequences leads us to expect that the phenomenon described here may occur with several of these transposable elements, and may have an unexpected evolutionary significance.

The characterization of terminators of RNA transcription on IS30 and an analysis of their role in IS element-mediated polarity

Using expression vectors carrying the lacUV5 or Pgal promoters and the galK gene, we have studied terminators of transcription on the prokaryotic mobile genetic element IS30. The long open reading frame, ORF-A, of IS30 contains a relatively Rho-independent terminator, T30A, within its coding sequence. T30A terminates the majority of transcripts initiated at either an external promoter or the IS30-borne promoter P30A. No other terminator functions on this strand of IS30 (orientation left to right). In the orientation right to left, the previously identified terminator T30C, which follows ORF-C, is Rho-independent. T30C together with T30D, a newly identified, strong, partially Rho-dependent terminator near the left end of IS30, permits less than 2% read-through from external promoters. Neither ORF-A nor ORF-C appears to be protected from transcription by external promoters. As a consequence of the internal terminators, the insertion of IS30 into an operon can be expected to reduce the expression of genes downstream of the site of insertion weakly for one orientation of IS30 and strongly for the other orientation.

Antitermination of transcription from an Escherichia coli ribosomal RNA promoter

The Escherichia coli lac and ara promoters and rrnC ribosomal RNA promoter-leader region were fused to lacZYA. Transcription termination signals were introduced into the lac genes of these fusions by Tn9 and IS1 insertions. Measurement of lac enzymes from upstream and downstream of the insertions showed that termination signals resulting from these insertions are very efficient when transcription begins at lac or ara promoters but are very inefficient when transcription begins at the rrnC promoter-leader region. The rrnC promoter-leader region must, therefore, modify RNA polymerase to enable it to read through transcription termination signals.

IS4 transposition in the attenuator region of the Escherichia coli pheS,T operon

A cis-acting mutation which lowers phenylalanyl-tRNA synthetase operon (pheS,T) transcription about tenfold was previously isolated on a multicopy plasmid [Plumbridge and Springer, J. Bacteriol. 152 (1982) 650-668]. This mutation has now been characterized as an IS4 element inserted in orientation II in the terminator stem of the pheS,T attenuator. The identification of the insertion as IS4 is based on (i) the nature and location of restriction sites internal to the insertion element, and (ii) the DNA sequence of both the left and right Escherichia coli::IS4 junctions. The effect of the IS4 transposition on the expression of pheS,T was studied using pheS,T::lac fusions cloned in lambda phages. IS4 integration into the leader region of the pheS,T operon was shown to abolish the miaA (trpX) allele dependence which characterizes the attenuation mechanism regulating pheS,T expression [Fayat et al., J. Mol. Biol. 171 (1983) 239-261; Springer et al., J. Mol. Biol. 171 (1983) 263-279]. The IS4 insertion site described here is compared to the other known sites and the effect of IS4 transposition on the expression of neighbouring genes is discussed.

A control system which causes alternating turn-off/turn-on of transcription on insertion element IS1

Presence of insertion element IS1 within an operon leads to absence of expression of genes distal to its integration site. This strong polar effect is observed irrespective of the orientation of IS1. Here I report on a mutant of E. coli K12 which allows turn-on of genes located distally to IS1. This turn-on is due to activation of transcription starting within IS1. The activation of transcription is under the control of a regulatory locus (sis1) which acts in trans. The regulatory locus itself changes its state, which leads to an alternating turn-off/turn-on of genes located distal to IS1: The rate of turn-off was observed with a frequency of about 0.3% (per cell and per generation), that of turn-on with a frequency of about 0.015% (per cell and per generation).

Efficient read-through of Tn9 and IS1 by RNA polymerase molecules that initiate at rRNA promoters

Transcription and translation are coupled in most Escherichia coli operons. As a consequence, ribosomes must be present on an mRNA molecule while transcription of the mRNA is in progress or else premature termination of transcription may result. This requirement is most clearly manifested when premature nonsense codons result in polarity in multicistronic operons. Polarity can also result from insertions of transposons and insertion sequences. However, since rRNA operons are not translated, some property of these operons must allow transcription to be uncoupled from translation. In this paper we demonstrate that transposon Tn9 and insertion sequence IS1 are nonpolar or incompletely polar in rRNA operons during normal growth. We also show that essentially all expression of rrn sequences distal to IS1 and Tn9 results from transcripts that originate at rRNA promoters. These results suggest either that rRNA operons possess some mechanism which reduces or prevents termination within rRNA operons or that Tn9 and IS1 can be very inefficient at blocking normal transcription. Insertions of Tn10 in rRNA operons are substantially but incompletely polar. We could not determine whether the residual downstream transcription observed results from promoters within Tn10 or from read-through of Tn10. We discuss the meaning of read-through of Tn9 and IS1 and the residual expression of genes downstream from Tn10 with regard to rRNA operon structure and previous experiments in which polarity of transposons or insertion sequences was observed in protein-encoding operons.

Mutants in the y region of bacteriophage lambda constitutive for repressor synthesis: their isolation and the characterization of the Hyp phenotype

Bacteriophage lambdahyp mutants have been isolated as survivors of Escherichia coli K-12 bacteria lysogenic for lambda Nam7am53cI857. The hyp mutants are characterized by (i) their localization in the y region very close to the imm lambda/imm434 boundary, (ii) polarity on O gene expression, (iii) immediate recovery of lambda immunity at 30 degrees C after prolonged growth of lambda Nam7am53cI857 hyp lysogens at 42 degrees C even in the presence of an active cro gene product, (iv) ability of phage lambda v2v3vs326 but not lambda v1v2v3 to propagate on lambda cI+hyp lysogens, (v) inability to express lambda exonuclease activity after prophage induction, and (vi) inviability at any temperature of phage carrying the hyp mutation. All these properties are referred to collectively as the Hyp phenotype. We show that the Hyp phenotype is due to cII-independent constitutive cI-gene-product synthesis originating in the y region, which results in the synthesis of anti-cro RNA species, and constitutive levels of cro gene product present even in lambda cI+hyp lysogens. A model is presented which is consistent with all the experimental observations.

An IS4-encoded protein is synthesized in minicells

A protein of Mr 47,000 is synthesized in Escherichia coli minicells, when these harbor a multicopy plasmid carrying IS4 in either orientation and between different flanking sequences. The protein corresponds to the sequence predicted from the known DNA sequence of IS4, as shown by partial N-terminal radiolabel protein sequence analysis. Its apparent molecular weight, however, as determined from its electrophoretic mobility in SDS polyacrylamide gels, is smaller than predicted. When compared with other plasmid-encoded proteins, the IS4-encoded protein is synthesized in minicells in small amounts. Its synthesis has not been detected in a DNA-dependent cell-free system.

The sequence of IS4

IS-elements are devoid of easily recognizable transacting functions and exert their visible effects in the position cis only (recent reviews Calos and Miller 1980; Starlinger 1980). It has been a matter of debate, whether these elements encode functions for their own transposition. In the case of the E. coli IS-elements this could not easily be determined by genetic methods, because most of these elements are present in several copies (Saedler and Heiss 1973; Deonier et al. 1979). In the case of the IS-elements flanking transposons, evidence has recently been brought forward that these carry the transposition specificity (Rothstein et al. 1980; Kleckner 1980; Grindley 1981). IS4 is present in one copy only in several E. coli K12 strains and should, therefore, be suitable for genetic and physiological studies (Chadwell et al. 1979). It has been cloned from several sites on the E. coli chromosome in pBR322 (Klaer and Starlinger 1980). Here we report the DNA sequence of IS4 which contains an open reading frame for 442 amino acids, and of the junctions of this element with surrounding DNA at three different sites in the E. coli chromosome.

Deletions and DNA rearrangements within the transposable DNA element IS2. A model for the creation of palindromic DNA by DNA repair synthesis

Three derivatives of mutant ga10P-308::IS2-I of Escherichia coli were characterized by DNA sequence analysis. Deletions and DNA sequence rearrangements were observed which apparently were initiated at short A-T rich inverted repeats within IS2. Two of the mutants carried newly synthesized DNA sequences which were inverted copies of already existing IS2 sequences. Thus long stretches with twofold symmetry were formed. It is discussed whether these inverted repeats were formed by DNA repair synthesis which was initiated at the A-T rich palindromes of IS2.

The structure of unstable constitutive revertants of mutant galOP-308::IS2-I

The isolation and characterization of three unstable and constitutive revertants of mutant galOP-308 of E. coli is described. In this mutant an IS2 element is integrated between the promoter and the first structural gene of the galactose operon, and exerts a strong polar effect on the expression of the three galactose genes. In the three revertants under investigation it was observed that relief of polarity and constitutive expression of the gal-operon were accompanied by the deletion of 90% of the IS2 sequence and of various lengths of the adjacent sequences including the gal-promoter. We conclude from this result that the transcription termination signals causing strong polarity were located on the deleted part of IS2, and that in our revertants the galactose genes are now under the control of a new promoter which is apparently unstable.

IS4 at its chromosomal site in E. coli K12

IS4 DNA has been isolated in pure form. Hybridization of this DNA against restricted DNA of several E. coli K12 strains by Southern's blotting technique has shown that, in most strains, only one copy of IS4 is present. Though the restriction fragments around this site differ in size, IS4 can be shown always to be located at the same site. In one strain, one additional copy has been found in a new location. In this strain, IS4 in its original location has been retained.

IS2-61 and IS2-611 arise by illegitimate recombination from IS2-6

A more stable derivative of IS2-6 has been isolated, which had lost 54 bp of the 108 bp long insert characteristic of IS2-6. This new allele of IS2, IS2-61, segregates the remaining 54 bp to yield allele IS2-611. DNA sequence analysis shows that the segregation products of IS2-6 arise by recA-independent, illegitimate recombination at 9 bp long direct sequence repetitions.

IS4 is found between eleven or twelve base pair duplications

Three mutations caused by the integration of IS4 in galT in both possible orientations were shown by DNA sequence analysis to be integrated between a duplication of eleven base pairs of gene galT. IS4 has been cloned from its single position on the E. coli K12 chromosome. Here, 12 base pairs are duplicated adjacent to IS4. This sequence is unrelated to the duplicated sequence in galT.

Close vicinity of IS1 integration sites in the leader sequence of the gal operon of E. coli

Four insertions of IS1 in the leader sequence of the gal operon of E. coli have been analysed. Two of them occur at the same position, but in opposite orientations. The other two are inserted one nucleotide to one side and four nucleotides to the other side, respectively. In each case, nine base pairs of the leader sequence of the gal operon are duplicated directly, and are found flanking the termini of IS1 at its junction with the gal operon. These repeated sequences differ from each other as expected from the different insertion sites.

Polarity of mutations induced by insertion of transposons Tn5, Tn7 and Tn10 into the nif gene cluster of Klebsiella pneumoniae

Three new genes nifM, nifI and nifN have been mapped in the nif gene cluster of Klebsiella pneumoniae and a fourth gene nifJ has been confirmed as being a separate cistron. Polar nif mutations were obtained by transposition of Tn7 to plasmid pRD1, and of Tn5 and Tn10 to plasmid pMF100, a derivative of pRD1. Complementation analysis of the nif::Tn mutants led to the identification of at least six transcriptional units: nifB; nifA; nifJ; nifH, nifD and nifK; nifE and nifI; nifN, nifM and nifF. Biochemical and genetic evidence suggest that the three genes nifH, nifD and nifK, which are probably the structural genes for nitrogenase, belong to the same operon and are transcribed from nifH to nifK. A polypeptide with a molecular weight of approximately 120,000 is presumed to be the nifJ product.

Regional replication of the bacterial chromosome induced by derepression of prophage lambda. III. Role of the replication in escape synthesis of gal operon

Recent evidence suggests that the escape synthesis of gal operon following derepression of the prophage lambda in Escherichia coli K12 involves transcription originating at the lambda promoter (PL) to extend through gal under the conditions in which lambda DNA replication is prevented. Whether the observed expression of gal is due to transcription initiating at PL or at the bacterial promoter for gal (Pgal) was examined in the case of lambda DNA replication being normal. The experiments are based on that two types of transcription are distinguished from each other by the following properties: 1. Pgal-promoted transcription is inhibited by chloramphenicol, while PL-promoted transcription is not. 2. PL-promoted transcription suppresses the polar effect caused by nonsense mutation in a bacterial gene, while Pgal-promoted transcription does not do so. -he results have suggested that gal escape synthesis in lambda-induced lysogen results from transcription which initiates not only at PL but also at Pgal. The Pgal-promoted transcription may be a consequence, direct or indirect, of the concomitant replication of gal DNA.