Integration and excision of bacteriophage lambda

All-in-one construct for genome engineering using Cre-lox technology

Mycoplasma genitalium is an appealing model of a minimal cell and synthetic biology study, and it was one of the first organisms whose genome was fully sequenced and chemically synthesized. Despite its usefulness as a model organism, many genetic tools well established for other microorganisms are not currently available in mycoplasmas. We have developed several vectors to adapt the Cre-lox technology for genome engineering in M. genitalium, providing an all-in-one construct that could be also useful to obtain unmarked genetic modifications in many other slow growing microorganisms. This construct contains a modified promoter sequence based in TetR system that exhibits an enhanced control on Cre recombinase expression, virtually abolishing the presence of this recombinase in the absence of inducer. This allows to introduce the Cre recombinase gene and the desired genetic modification in a single transformation step. In addition, this inducible promoter may be a very promising tool for a wide range of molecular applications.

Site-specific recombinational cloning using gateway and in-fusion cloning schemes

The comprehensive study of protein structure and function, or proteomics, depends on the obtainability of full-length cDNAs in species-specific expression vectors and subsequent functional analysis of the expressed protein. Recombinational cloning is a universal cloning technique based on site-specific recombination that is independent of the insert DNA sequence of interest, which differentiates it from classical restriction enzyme-based cloning methods. Recombinational cloning enables rapid and efficient parallel transfer of DNA inserts into multiple expression systems. This unit summarizes strategies for generating expression-ready clones using the most popular commercial recombinational cloning technologies, Gateway (Life Technologies) and In-Fusion (Clontech).

The terminal a sequence of the herpes simplex virus genome contains the promoter of a gene located in the repeat sequences of the L component

The herpes simplex virus DNA genome consists of two covalently linked components, L and S. The unique sequences of the L component are flanked by 9-kilobase-pair inverted repeat sequences ab and b'a', whereas those of the S component are flanked by 6.5-kilobase-pair inverted repeat sequences c'a' and ca. We report that the 500-base-pair a sequence contains the promoter-regulatory domain and the transcription initiation site of a diploid gene, the coding sequences of which are located in the b sequences of the inverted repeats of the L component. The chimeric gene constructed by fusion of the a sequence to the coding sequences of the thymidine kinase gene and recombined into the viral genome was regulated as a gamma 1 gene. The size of the protein predicted from its sequence is 358 amino acids; it was designated as infected cell protein (ICP) 34.5. Thus, the inverted repeats flanking the unique sequences of the L component contain two genes specifying ICP0 and ICP34.5, respectively. Moreover, in addition to the cis-acting sites for the inversion of L and S components relative to each other, for cleavage of unit length DNA molecules from head-to-tail concatemers, and for packaging of the DNA into capsids, the a sequence also contains the promoter-regulatory domain and transcription initiation sites of a gene.

Two-micrometer circle site-specific recombination: the minimal substrate and the possible role of flanking sequences

The 2-mum circle DNA of yeast encodes a site-specific recombination system (FLP recombination). The recombination region had been mapped earlier to a 65-base-pair (bp) segment within the 599-bp-long inverted repeats of the molecule. I have shown that the "minimal" FLP substrate resides in a 13-bp dyad symmetry plus an 8-bp core located within the 65-bp recombination region. Further, as determined by different in vivo assays, sequences extraneous to the minimal FLP site and the 65-bp recombination region can affect the efficiency of the recombination reaction.

Transposon Tn1721: site-specific recombination generates deletions and inversions

Transposon Tn1721 contains genes for transposase (tnpA), resolvase (tnpR) and a resolution site (res). The closely linked loci were localized within a 3.8 kb region their order being res - tnpR - tnpA with res at the translational start of tnpR. Genes tnpR and tnpA have identical transcriptional polarity but independent promoters. The tnpR promoter had 40% of lac promoter efficiency its activity being autoregulated by binding of resolvase to res, as shown by fusion to the galactokinase gene. The weak tnpA promoter was only detectable in the transposase-mediated transposition reaction. Resolvase-catalyzed, site-specific recombination was analyzed in hybrid plasmids with either direct or inverted repeats of res. The rate of the reaction was dependent on the relative orientation of the two sites and on the provision of tnpR in cis or in trans. Direct repeats were rapidly resolved leading to deletions of intervening DNA, if the tnpR gene was provided in cis, but required approximately 60 generations for completion of the reaction, if tnpR was located on a second plasmid (in trans). The reaction involving inverted repeats of res (leading to inversion of intervening DNA) was only detectable if tnpR was furnished in cis. After 50 generations about 10% of plasmid DNA showed the inversion. The reaction was reversible.

Recombination between two IS/s flanking the r-determinant of R100-1: involvement of dor and recA gene functions in Salmonella typhimurium

Drug resistance genes of the r-determinant component of a composite R plasmid R100-1 were frequently lost in Salmonella typhimurium. Various deletion mutants were analyzed by restriction endonuclease cleavage, Southern blotting, and hybridization techniques. The loss of the r-determinant was found to be the result of a reciprocal recombination between the two IS/s flanking the r-determinant. This recombination depended upon both dor and recA gene functions.

Posttranscriptional control of bacteriophage lambda gene expression from a site distal to the gene

The bacteriophage lambda int gene product, integrase, recombines the phage DNA with the host DNA at specific sites on each to accomplish lysogeny. The int gene is transcribed from two promoters, PL and PI, each regulated positively by lambda proteins. The expression of integrase is also controlled from a site, sib, in the b region of the phage genome. This is a unique regulatory site because it is located distal to the structural gene in relation to the promoters. The expression of int from the PL promoter is inhibited when sib is present. This effect appears to be specific for PL because sib does not cause inhibition of PI-dependent int synthesis. lambda mutants that contain alterations in the site have been isolated. Sequence analyses of the mutations reveal single base changes, spanning 37 base pairs (bp) in the b region, some 240 bp beyond the int gene. Another mutant, hef13, which has a phenotype similar to that of sib, introduces a nucleotide change within the same 37-bp region. The sib and hef mutations cluster within a region of dyad symmetry. Regulation of int synthesis by sib occurs after transcription of the int gene. There is no difference in the rate of PL-promoted int mRNA synthesis in either sib+ or sib- phage infections, yet int mRNA is less stable in the sib+ infection. Because RNase III host mutants are defective in sib regulation, processing of the PL mRNA at sib by this endoribonuclease may cause int mRNA decay and decrease int synthesis.

Resolution of cointegrates between transposons gamma delta and Tn3 defines the recombination site

Transposition of the genetically related insertion elements gamma delta and Tn3 is thought to involve two steps. In the case of transposition from one replicon to another, the first step is fusion of the parent and target replicons with the element appearing in direct orientation at the two junctions. In a subsequent reaction, the cointegrate structure is resolved via a site-specific recombination event. I have constructed two plasmids, each carrying segments of gamma delta and Tn3, that contain the internal resolution site. The tnpR gene product encoded by either Tn3 or gamma delta mediates intramolecular recombination between these two sites. The product of this recombination is a hybrid region that contains gamma delta and Tn3 sequences fused at the point of crossover. DNA sequence analysis of such recombinants indicates that the recombination occurs within a 19-base-pair (bp) region of exact homology between gamma delta and Tn3. The site lies in the 160-bp center intercistronic region, 50 bp before the beginning of the tnpA gene. My results therefore suggest a model for the coupled regulation of the repressor (tnpR) and the transposase (tnpA) genes and site-specific recombination of transposition intermediates. The Tn3/gamma delta recombination system and bacteriophage lambda integration are compared.

Integrative recombination of bacteriophage lambda: extent of the DNA sequence involved in attachment site function

We have investigated the minimum extent of DNA sequence required for the attachment site of bacteriophage lambda to function in integrative recombination. A DNA fragment carrying the phage attachment site (attP) of bacteriophage lambda was trimmed, recloned, and tested for recombination proficiency. In order to recombine with the bacterial attachment site (attB), the phage attachment site must retain about 250 base pairs of its original sequence. On the left side, the essential sequence extends beyond 106 base pairs from the center of the 15-base-pair common core sequence but not beyond 152 base pairs. On the right side the required sequence extends beyond 68 base pairs but not beyond 99 base pairs from the center of the core. A trimmed site that has lost part of the sequence mentioned above cannot function as the phage attachment site. However, depending on which part of the sequence is present, such a site can still act in reactions normally requiring one of the prophage attachment sites or the bacterial attachment site. The results also suggest that the essential suquence of the bacterial attachment site consists only of the sequence common to the phage and bacterial attachment sites.

Site-specific recombination functions of bacteriophage lambda: DNA sequence of regulatory regions and overlapping structural genes for Int and Xis

Site-specific recombination in bacteriophage lambda is mediated by two phage-encoded proteins, Int and Xis. The structural genes encoding these proteins are located immediately to the right of their site of action, the phage att site. The DNA sequence for both the structural and regulatory regions of these genes has been determined. The location and reading frame of the xis gene were ascertained by sequence comparisons with the b538 deletion (that ends within xis) and with the xis6 amber mutation. From the DNA sequence Xis has a molecular weight of 8630; it is rich in basic amino acids with lysine and arginine comprising 25% of the 72 amino acids. Identification of the int reading frame was also unambiguous. From the DNA sequence, Int has a molecular weight of 40,330; of the 356 amino acids, 69 are basic and 46 are acidic. In the NH(2)-terminal portion of Int, 35% of the first 20 amino acids are basic. The site-specific recombination functions form a very tight cluster (att-int-xis) on the lambda chromosome. The combined protein-encoding sequences of xis and int start 1347 base pairs, and terminate 84 base pairs, from the center of the phage att site. The two genes overlap one another by 20 base pairs (xis is upstream of int) and a possible means of controlling the relative synthesis rates of Int and Xis at the level of translation is proposed. Control at the level of transcription is also considered. The mutation intc226 leads to constitutive production of Int, independent of cII/cIII activator proteins normally required for transcription from the p(I) promoter. It is shown that this mutation is the result of a single base change (in the fMet codon of the xis gene) that generates an improved promoter heptamer sequence. This result, in conjunction with comparisons with other promoter sequences and other sequences responding to cII/cIII action, leads to a tentative identification of the p(I) promoter and site of cII/cIII action.

DNA sequence of the int-xis-Pi region of the bacteriophage lambda; overlap of the int and xis genes

The DNA sequence of the int and xis genes of lambda bacteriophage, as well as that of the PI promoter and a region of unknown function beyond this, was determined by the chain termination procedure. The Pribnow box sequence of the PI promoter lies just within the xis gene, and both possible sites of mRNA initiation from PI are within the xis gene. The end of the xis gene in its turn overlaps the start of the int gene by 23 base pairs, in a different reading frame. This overlap may play a role in ensuring efficient excision of the prophage in response to natural induction signals.