Transposon Tn951 (TnLac) is defective and related to Tn3

The Tn3-family of Replicative Transposons

Transposons of the Tn3 family form a widespread and remarkably homogeneous group of bacterial transposable elements in terms of transposition functions and an extremely versatile system for mediating gene reassortment and genomic plasticity owing to their modular organization. They have made major contributions to antimicrobial drug resistance dissemination or to endowing environmental bacteria with novel catabolic capacities. Here, we discuss the dynamic aspects inherent to the diversity and mosaic structure of Tn3-family transposons and their derivatives. We also provide an overview of current knowledge of the replicative transposition mechanism of the family, emphasizing most recent work aimed at understanding this mechanism at the biochemical level. Previous and recent data are put in perspective with those obtained for other transposable elements to build up a tentative model linking the activities of the Tn3-family transposase protein with the cellular process of DNA replication, suggesting new lines for further investigation. Finally, we summarize our current view of the DNA site-specific recombination mechanisms responsible for converting replicative transposition intermediates into final products, comparing paradigm systems using a serine recombinase with more recently characterized systems that use a tyrosine recombinase.

Catabolic transposons

The structure and function of transposable elements that code for catabolic pathways involved in the biodegradation of organic compounds are reviewed. Seven of these catabolic transposons have structural features that place them in the Class I (composite) or Class II (Tn3-family) bacterial elements. One is a conjugative transposon. Another three have been found to have properties of transposable elements but have not been characterized sufficiently to assign to a known class. Structural features of the toluene (Tn4651/Tn4653) and naphthalene (Tn4655) elements that illustrate the enormous potential for acquisition, deletion and rearrangement of DNA within catabolic transposons are discussed. The recently characterized chlorobenzoate (Tn5271) and chlorobenzene (Tn5280) catabolic transposons encode different aromatic ring dioxygenases, however they both illustrate the constraints that must be overcome when recipients of catabolic transposons assemble and regulate complete metabolic pathways for environmental pollutants. The structures of the chlorobenzoate catabolic transposon Tn5271 and the related haloacetate dehalogenase catabolic element of plasmid pUO1 are compared and a hypothesis for their formation is discussed. The structures and activities of catabolic transposons of unknown class coding for the catabolism of halogenated alkanoic acids (DEH) and chlorobiphenyl (Tn4371) are also reviewed.

Conduction of pEC22, a plasmid coding for MR.EcoT22I, mediated by a resident Tn3-like transposon, Tn5396

pEC22 is a small plasmid that encodes the restriction-modification system MR.EcoT22I. Restriction and functional analysis of the plasmid identified the positions of genes encoding that system. The plasmid is able to be conducted by conjugal plasmids, a process mediated by a transposon contained within pEC22. This cryptic transposon, called Tn5396, was isolated from pEC22 and partially sequenced. The sequence of Tn5396 is for the most part typical of transposons of the Tn3 family and is most similar to that of Tn1000. The transposon differs from closely related transposons in that it lacks well-conserved sequences in the inverted-repeat region and has an unusually long terminal inverted repeat. Consideration of regions of internal sequence similarity in this and other transposons in the Tn3 family supports a theory of the mechanism by which the ends of Tn3-like transposons may maintain substantial identity between their inverted repeats over the course of evolutionary time.

Activation of the lac genes of Tn951 by insertion sequences from Pseudomonas cepacia

We have identified three transposable gene-activating elements from Pseudomonas cepacia on the basis of their abilities to increase expression of the lac genes of the broad-host-range plasmid pGC91.14 (pRP1::Tn951). When introduced into auxotrophic derivatives of P. cepacia 249 (ATCC 17616), this plasmid failed to confer the ability to utilize lactose. The lac genes of Tn951 were poorly expressed in P. cepacia and were not induced by isopropyl-beta-D-thiogalactopyranoside. Lac+ variants of the pGC91.14-containing strains which formed beta-galactosidase at high constitutive levels as a consequence of transposition of insertion sequences from the P. cepacia genome to sites upstream of the lacZ gene of Tn951 were isolated. Certain of the elements also increased gene expression in other bacteria. For example, IS407 strongly activated the lacZ gene of Tn951 in Pseudomonas aeruginosa and Escherichia coli, and IS406 (but not IS407) did so in Zymomonas mobilis. The results indicate that IS elements from P. cepacia have potential for turning on the expression of foreign genes in a variety of gram-negative bacteria.

Nucleotide sequences and operon structure of plasmid-borne genes mediating uptake and utilization of raffinose in Escherichia coli

The plasmid-borne raf operon encodes functions required for inducible uptake and utilization of raffinose by Escherichia coli. Raf functions include active transport (Raf permease), alpha-galactosidase, and sucrose hydrolase, which are negatively controlled by the Raf repressor. We have defined the order and extent of the three structural genes, rafA, rafB, and rafD; these are contained in a 5,284-base-pair nucleotide sequence. By comparisons of derived primary structures with known subunit molecular weights and an N-terminal peptide sequence, rafA was assigned to alpha-galactosidase (708 amino acids), rafB was assigned to Raf permease (425 amino acids), and rafD was assigned to sucrose hydrolase (476 amino acids). Transcription was shown to initiate 13 nucleotides upstream of rafA; a putative promoter, a ribosome-binding site, and a transcription termination signal were identified. Striking similarities between Raf permease and lacY-encoded lactose permease, revealed by high sequence conservation (76%), overlapping substrate specificities, and similar transport kinetics, suggest a common origin of these transport systems. alpha-Galactosidase and sucrose hydrolase are not related to host enzymes but have their counterparts in other species. We propose a modular origin of the raf operon and discuss selective forces that favored the given gene organization also found in the E. coli lac operon.

Site-specific recombinations between direct and inverted res sites of Tn2501

The resolvase gene and the putative res site of Tn2501 are not closely related to any of the previously described resolution functions. In view of this divergence, we designed genetic experiments to confirm the localization of the res site. We analyzed the activity of the Tn2501-encoded resolvase on substrates containing either directly or invertedly repeated res sites. These experiments confirm the localization of the res site that was predicted from nucleotide sequence data and show that the Tn2501 resolvase promotes site-specific inversions in vivo.

Behavior of the IncW plasmid Sa in Zymomonas mobilis

The stability of the broad-host-range IncW R plasmid Sa in Zymomonas mobilis ZM6100(Sa) was monitored using three antibiotic resistance markers carried by Sa. When grown in batch culture without selection, ZM6100(Sa) rapidly lost the Sa plasmid. When grown with selection for either kanamycin or spectinomycin resistance, the three Sa markers were retained in at least 90% of the population, with spontaneous loss of chloramphenicol resistance being observed in the rest of the population. When ZM6100(Sa) was grown with selection for chloramphenicol resistance, the Sa plasmid either formed a cointegrate plasmid, designated pNSW301, with a native ZM6100 plasmid or was lost except for the chloramphenicol resistance marker. Possible transportation of the chloramphenicol resistance region of Sa to the Z. mobilis chromosome was indicated by hybridization data. The cointegrate plasmid, pNSW301, was maintained stably, except for spontaneous loss of chloramphenicol resistance, in Z. mobilis without selection for 300 generations. pNSW301 was able to replicate in Escherichia coli and was capable of conjugal transfer.

Tn951 derivatives designed for high-frequency plasmid-specific transposition and deletion mutagenesis

We describe the construction of a system allowing high-frequency transposition and deletion mutagenesis with class-II transposons containing a kanamycin or a chloramphenicol-resistance marker. The system utilizes the transposition function of Tn3 and the resolution function of Tn951/Tn2501 which leads to an uncoupling of the resolution and repression functions. It consists of defective transposons inserted into conjugative, replication thermosensitive plasmids. The properties of the system are: easily selectable resistance markers, high transposition frequencies onto plasmids, low transposition frequencies onto the host chromosome, placement of the tnpA gene outside the transposons so that "second-generation" transposition does not occur, possibility to transpose the whole system onto other plasmid vectors with different selection strategies, consecutive use of two transposons for deletion mutagenesis and restriction mapping.

Evolutionary relationship between Tn21-like elements and pBP201, a plasmid from Klebsiella pneumoniae mediating resistance to gentamicin and eight other drugs

We have characterized pBP201 one of the plasmids from a collection of 46 strains producing adenylyltransferase ANT(2") (Schmidt 1984). It confers resistance to sulphonamides and produces aminoglycoside adenylyltransferases AAD(3") and ANT(2") and beta-lactamase TEM-1. Plasmid pBP201 has a size of 24.8 kilobases (kb) and contains TnA and a Tn21-related element, Tn4000 delta, with deletions in mer and the termini and a substitution at tnpR. In complementation assays with transposition-deficient mutants of Tn21 the element in pBP201 appears to be TnpA+ but TnpR-. It represents a naturally occurring defective transposon. The sequence organization of pBP201 has been compared with that of Tn21-related elements such as Tn2410, Tn2603, Tn2424, Tn1696, and Tn4000. In these transposons the integration sites of resistance genes cat, bla, aacA, aacC or aadB have been identified at two preferential locations; these are at the termini of the streptomycin resistance gene aadA. Two additional sites have been localized in the Tn21 backbone to the right of the mer operon and at res (internal resolution site) and are probably involved in the evolution of these elements. Based on these results a model for the possible genealogy of class II transposons is presented.

Detection and characterization of Tn2501, a transposon included within the lactose transposon Tn951

The DNA sequence spanning coordinates 9.9 to 16.4 kilobases of the lactose transposon Tn951 ( Cornelis et al., Mol. Gen. Genet. 160:215-224, 1978) constitutes a transposable element by itself. Unlike Tn951 ( Cornelis et al., Mol. Gen. Genet. 184:241-248, 1981), this element, called Tn2501 , transposes in the absence of any other transposon. Transposition of Tn2501 proceeds through transient cointegration and duplicates 5 base pairs of host DNA. Tn2501 is flanked by nearly perfect inverted repeats (44 of 48), related to the inverted repeats of Tn21 ( Zheng et al., Nucleic Acids Res. 9:6265-6278, 1982). Unlike Tn21 , Tn2501 does not confer mercury resistance.

The role of insertions, deletions, and substitutions in the evolution of R6 related plasmids encoding aminoglycoside transferase ANT-(2")

In 7% of gram-negative bacteria resistance to gentamicin is mainly mediated by plasmid-encoded aminoglycoside transferase ANT-(2"). The genome organization of 15 aadB plasmids (42-110 kb) was analyzed by restriction and hybridization techniques. They appeared to be IncFII-like replicons but were distinct from R6 by virtue of small substitutions in the transfer region. Aminoglycoside resistance genes aadB and aadA were located on Tn21 related elements. Only one of them was able to transpose its resistance genes mer sul aadA and aadB ( Tn4000 ), the other elements were naturally occurring defective transposons. In some of these structures deletions were identified at the termini, at sul, aadA , mer or transposition function--insertions adjacent to aadA or mer. The mode of these rearrangements and their site-specificity were considered with respect to the evolution of the Tn21 transposon family.

Study of the incompatibility and replication of the 70-kb virulence plasmid of Yersinia

The 70-kb virulence plasmid, vir, from four Yersinia enterocolitica and one Y. pseudotuberculosis strains are incompatible with IncFI plasmids F'Lac and R386 while they are compatible with plasmids representing nine other incompatibility groups. Hybridization experiments carried out on one of these virulence plasmids showed that it contains the F incompatibility determinant D, incD. This determinant was cloned onto pACYC184 and the recombinant clone expressed incompatibility with F'Lac. We conclude that the incompatibility observed between F or R386 and the 70-kb virulence plasmid of Y. enterocolitica and Y. pseudotuberculosis is mediated by incD. Replication genes (rep) from the same plasmid were cloned independently in Escherichia coli. Rep and incD map on two different BamHI fragments. Surprisingly, the replicon isolated is not sensitive to inc D incompatibility. Apart from incD, vir and F share extremely little homology. In particular, there is no evidence for the presence of an F-like transfer operon on vir.

Plasmid-mediated uptake and metabolism of sucrose by Escherichia coli K-12

The conjugative plasmid pUR400 determines tetracycline resistance and enables cells of Escherichia coli K-12 to utilize sucrose as the sole carbon source. Three types of mutants affecting sucrose metabolism were derived from pUR400. One type lacked a specific transport system (srcA); another lacked sucrose-6-phosphate hydrolase (scrB); and the third, a regulatory mutant, expressed both of these functions constitutively (scrR). In a strain harboring pUR400, both transport and sucrose-6-phosphate hydrolase were inducible by fructose, sucrose, and raffinose; if a scrB mutant was used, fructose was the only inducer. These data suggested that fructose or a derivative acted as an endogenous inducer. Sucrose transport and sucrose-6-phosphate hydrolase were subject to catabolite repression; these two functions were not expressed in an E. coli host (of pUR400) deficient in the adenosine 3-,5'-phosphate receptor protein. Sucrose uptake (apparent Km = 10 microM) was dependent on the scrA gene product and on the phosphoenolpyruvate-dependent sugar:phosphotransferase system (PTS) of the host. The product of sucrose uptake (via group translocation) was identified as sucrose-6-phosphate, phosphorylated at C6 of the glucose moiety. Intracellular sucrose-6-phosphate hydrolase catalyzed the hydrolysis of sucrose-6-phosphate (Km = 0.17 mM), sucrose (Km = 60 mM), and raffinose (Km = 150 mM). The active enzyme was shown to be a dimer of Mr 110,000.