Switch in the transposition products of Mu DNA mediated by proteins: Cointegrates versus simple insertions

Mu-driven transposition of recombinant mini-Mu unit DNA in the Corynebacterium glutamicum chromosome

A dual-component Mu-transposition system was modified for the integration/amplification of genes in Corynebacterium. The system consists of two types of plasmids: (i) a non-replicative integrative plasmid that contains the transposing mini-Mu(LR) unit bracketed by the L/R Mu ends or the mini-Mu(LER) unit, which additionally contains the enhancer element, E, and (ii) an integration helper plasmid that expresses the transposition factor genes for MuA and MuB. Efficient transposition in the C. glutamicum chromosome (≈ 2 × 10⁻⁴ per cell) occurred mainly through the replicative pathway via cointegrate formation followed by possible resolution. Optimizing the E location in the mini-Mu unit significantly increased the efficiency of Mu-driven intramolecular transposition–amplification in C. glutamicum as well as in gram-negative bacteria. The new C. glutamicum genome modification strategy that was developed allows the consequent independent integration/amplification/fixation of target genes at high copy numbers. After integration/amplification of the first mini-Mu(LER) unit in the C. glutamicum chromosome, the E-element, which is bracketed by lox-like sites, is excised by Cre-mediated fashion, thereby fixing the truncated mini-Mu(LR) unit in its position for the subsequent integration/amplification of new mini-Mu(LER) units. This strategy was demonstrated using the genes for the citrine and green fluorescent proteins, yECitrine and yEGFP, respectively.

Application of the bacteriophage Mu-driven system for the integration/amplification of target genes in the chromosomes of engineered Gram-negative bacteria--mini review

The advantages of phage Mu transposition-based systems for the chromosomal editing of plasmid-less strains are reviewed. The cis and trans requirements for Mu phage-mediated transposition, which include the L/R ends of the Mu DNA, the transposition factors MuA and MuB, and the cis/trans functioning of the E element as an enhancer, are presented. Mini-Mu(LR)/(LER) units are Mu derivatives that lack most of the Mu genes but contain the L/R ends or a properly arranged E element in cis to the L/R ends. The dual-component system, which consists of an integrative plasmid with a mini-Mu and an easily eliminated helper plasmid encoding inducible transposition factors, is described in detail as a tool for the integration/amplification of recombinant DNAs. This chromosomal editing method is based on replicative transposition through the formation of a cointegrate that can be resolved in a recombination-dependent manner. (E-plus)- or (E-minus)-helpers that differ in the presence of the trans-acting E element are used to achieve the proper mini-Mu transposition intensity. The systems that have been developed for the construction of stably maintained mini-Mu multi-integrant strains of Escherichia coli and Methylophilus methylotrophus are described. A novel integration/amplification/fixation strategy is proposed for consecutive independent replicative transpositions of different mini-Mu(LER) units with “excisable” E elements in methylotrophic cells.

Specificity of bacteriophage Mu excision

To study the excision of bacteriophage Mu at the DNA sequence level, the Mu-derived phage lambda placMu3 was transposed to the transcribed but non-translated leader region of a plasmid-borne tetracycline (tet) resistance gene. Revertants (excision products) were then selected by Tet+ restoration of Tet+ and characterized. Of 21 independent Tet+ revertants, 17 contained simple deletions of most or all of lambda placMu3, while the other four contained more complex rearrangements in which one end of lambda placMu3 had been transposed, and most of the prophage had been deleted. The deletion endpoints were found in short direct repeats in each of the complex rearrangements and in 11 of the 17 simple deletion excisants. The results suggest models of slipped mispairing of template and nascent DNA strands facilitated by proteins of the Mu transposition machinery.

Structural domains in phage Mu transposase: identification of the site-specific DNA-binding domain

Limited proteolysis of phage Mu transposase with three proteases of differing specificities produced a common pattern of fragmentation. The fragments were mapped by using a combination of immunoblotting and amino acid sequence analysis. Our results suggest that the transposase molecule is organized principally into three domains: an amino-terminal domain of molecular mass 30 kDa, a core region of approximately 35 kDa, and a carboxyl-terminal domain of approximately 10 kDa. The amino-terminal domain has at least two additional sites that are partially accessible to proteases. Filter binding and nuclease protection studies were done to determine the functions of the isolated domains. Site-specific binding to Mu DNA was localized to the amino-terminal domain. The core domain showed nonspecific DNA-binding activity.

Primary structure of phage mu transposase: homology to mu repressor

The phage Mu transposase is essential for integration, replication-transposition, and excision of Mu DNA. We present the complete nucleotide and derived amino acid sequence of the transposase and analyze implications for transposase/DNA interaction. The NH2 terminus of the Mu transposase has considerable sequence homology with the Mu repressor and with the NH2 terminus of the transposase of the Mu-like phage D108. These three proteins are known to share binding sites on DNA. The protein sequence and predicted secondary structural similarities at the NH2 termini of the three proteins suggest a common DNA-binding region similar to the regions found in proteins of known structure. An internal sequence in the Mu A protein also shares these features. We anticipate that these regions will be involved in DNA recognition during transposition.

DNA sequences at the ends of the genome of bacteriophage Mu essential for transposition

We have determined the minimal DNA sequences at the ends of the genome of bacteriophage Mu that are required for its transposition. A mini-Mu was constructed on a multicopy plasmid that enabled the manipulation of the DNA sequences at its ends without affecting the genes essential for transposition. The genes A and B, which were cloned outside the ends of the mini-Mu on the same plasmid, were both needed for optimal transposition. In our experimental system the predominant end products of the transposition are cointegrates both in the presence and in the absence of B. Two regions ending approximately 25 and 160 bp from the left end and one ending approximately 50 bp from the right end appear to be essential for optimal transposition. Overlapping with these regions, a 22-base-pair sequence was recognized with the consensus Y-G-T-T-C-A-Y-T-N-N-A-A-R-Y-R-C-G-A-A-A-A, where Y and R represent any pyrimidine and purine, respectively. At the left end these sequences occur as direct repeats; at the right end this sequence is inverted with respect to those at the left end.

The nucleotide sequence of the B gene of bacteriophage Mu

Bacteriophage Mu is a highly efficient transposon which requires the products of the Mu A and B genes in order to transpose at a normal frequency. We have determined the nucleotide sequence of the B gene as well as that of the A-B intergenic region upstream of B. The protein product of the gene contains 312 amino acids and has a predicted molecular weight of 35,061. As expected, there do not appear to be any potential promoter sequences in the intergenic region prior to the gene, but it is preceded by a strong Shine-Dalgarno sequence. The intergenic region does not contain any obvious transcription termination sequences. The frequency of optimal codon usage is similar to that for other transposon and phage genes, and the amino acid composition is comparable to that of an "average" E. coli protein. A region near the amino terminus of the protein resembles the highly conserved bihelical fold which is involved in DNA contact and sequence specific recognition in a number of DNA binding proteins.

Transposition without duplication of infecting bacteriophage Mu DNA

Most models of DNA transposition invoke replication of the transposable element, but it is not clear whether a 'co-integrate' is an obligatory intermediate in the pathway leading to the production of simple insertions during transposition. Such an intermediate can be accounted for only by a replicative transposition scheme. Bacteriophage Mu is a temperate phage that can either lysogenize or lyse its host, and it encodes at least two modes of transposition as judged by the end-products generated by the process. During the lytic development of the integrated prophage, co-integrates are the predominant end-products; transposition is coupled to replication during this phase. A small number of simple insertions are also produced during the lytic growth, but during transposition from the infecting phage into the host chromosome, simple insertions are the main end-products. Conditions can be found where the choice between the two kinds of end-products depends on a delicate balance between the essential transposition functions encoded by Mu. Experiments have suggested that the simple insertions which arise during transposition from the infecting phage may do so without Mu DNA replication. Here I demonstrate using an infecting phage with completely methylated DNA, a dam- (DNA adenine methylase) host and a combination of restriction enzymes that can cut either fully methylated or unmethylated DNA but not hemi-methylated DNA, that transposition of the phage DNA into the host chromosome does not involve a duplication of its DNA. This result may also have significance for other transposons that do not appear to go through a co-integrate intermediate during transposition.

The E. coli K-12 chromosome flanked by two IS10 sequences transposes

Transposon are commonly found among prokaryotes and usually range up to 20 kilobases. In this study, we were interested to determine whether a larger DNA segment could transpose. We observed that the E. coli K-12 chromosome, 4,000 kilobases in size, when flanked by two IS10 sequences, could transpose to pACYC177 at a frequency of 10(-8) per cell per generation. We suggest that this transposition event occurs independently of the size and without duplication of the entire DNA sequence flanked by the IS10 elements.

Lambda placMu: a transposable derivative of bacteriophage lambda for creating lacZ protein fusions in a single step

We isolated a plaque-forming derivative of phage lambda, lambda placMu1 , that contains sequences from bacteriophage Mu enabling it to integrate into the Escherichia coli chromosome by means of the Mu transposition system. The Mu DNA carried by this phage includes both attachment sites as well as the cI, ner (cII), and A genes. Lambda placMu1 also contains the lacZ gene, deleted for its transcription and translation initiation signals, and the lacY gene of E. coli, positioned next to the terminal 117 base pairs from the S end of Mu. Because this terminal Mu sequence is an open reading frame fused in frame to lacZ, the phage can create lacZ protein fusions in a single step when it integrates into a target gene in the proper orientation and reading frame. To demonstrate the use of this phage, we isolated lacZ fusions to the malB locus. These showed the phenotypes and regulation expected for malB fusions and could be used to isolate specialized transducing phages carrying the entire gene fusion as well as an adjacent gene (malE). They were found to be genetically stable and rarely (less than 10(-7] gave rise to secondary Lac+ insertions. We also isolated insertions into high-copy-number plasmids. The physical structure of these phage-plasmid hybrids was that expected from a Mu-dependent insertion event, with the lambda placMu prophage flanked by the Mu attachment sites. Lac+ insertions into a cloned recA gene were found at numerous positions and produced hybrid proteins whose sizes were correlated with the position of the fusions in recA.

Transposition of Tn554 does not generate a target duplication

Transposable elements from prokaryotic and eukaryotic organisms are discrete DNA segments bounded by inverted or directly repeated sequences that insert into non-homologous DNA in a reaction that is independent of the general recombination functions of the host. The mechanisms proposed generally involve a staggered double-stranded scission of the target DNA, ligation to the nicked ends of the transposable element, and replication of the element, resulting in the generation of a directly repeated oligonucleotide target sequence flanking the new copy of the element. Most transposons have a relatively low degree of target site specificity coupled with a low insertion frequency. Tn554, a Staphylococcus aureus transposon which specifies resistances to erythromycin and spectinomycin, displays an unusually high degree of insertion specificity. Tn554 transposes with high efficiency to a unique ('primary') site in the S. aureus chromosome and only rarely (less than 10(-6) per transductant) to other, secondary sites. We report here the nucleotide sequences surrounding the junctions of Tn554 in three independent 'primary' insertions and two 'secondary' insertions of the transposon. Two unusual features are revealed: first, the termini of Tn554 contain neither inverted nor directly repeated sequences. Second, transposition of Tn554 does not generate the short direct repeats of the target DNA that are characteristic of other transposable elements. These results suggest that the mechanism of Tn554 insertion may be significantly different from that of other transposons.