Ezra Yagil

Identifying Determinants of Recombination Specificity: Construction and Characterization of Chimeric Bacteriophage Integrases

Bacteriophage integrases are members of a family of structurally related enzymes that promote recombination between DNA molecules that carry specific sites. Phages lambda and HK022 encode closely related integrases that recognize different sets of sequences within the core regions of their respective attachment sites. To locate the amino acid residues that determine this difference in specificity, we isolated recombinant phages that produce chimeric integrases and measured the ability of these chimeras to promote recombination of lambda and HK022 sites in vivo. A chimera that is of lambda origin except for one HK022 residue at position 99 and 12 HK022 residues located between positions 279 and 329 had wild-type HK022 specificity and activity for both integrative and excisive recombination. Chimeras containing certain subsets of these 13 residues had incomplete specificity. The region around position 99 is not well-conserved in other members of the integrase family, but the 279-329 segment includes residues that are highly conserved and believed to be directly involved in catalysis. Many chimeras were inactive in recombining either HK022 or lambda sites. Selection for mutants that restored activity to these chimeras revealed sets of residues that are likely to interact with each other.

Lambda integrase cleaves DNA in cis.

In the Int family of site‐specific recombinases, DNA cleavage is accomplished by nucleophilic attack on the activated scissile phosphodiester bond by a specific tyrosine residue. It has been proposed that this tyrosine is contributed by a protomer bound to a site other than the one being cleaved (‘trans’ cleavage). To test this hypothesis, the difference in DNA binding specificity between closely related integrases (Ints) from phages lambda and HK022 was exploited to direct wild type Ints and cleavage‐ or activation‐defective mutants to particular sites on bispecific substrates. Analysis of Int cleavage at individual sites strongly indicates that DNA cleavage is catalyzed by the Int bound to the cleaved site (‘cis’ cleavage). This conclusion contrasts with those from previous experiments with two members of the Int family, FLP and lambda Int, that supported the hypothesis of trans cleavage. We suggest explanations for this difference and discuss the implications of the surprising finding that Int‐family recombinases appear capable of both cis and trans mechanisms of DNA cleavage.

Transcriptional analysis of the pst operon of Escherichia coli

Abstract. The pst operon of Escherichia coli, which encodes the phosphate-specific transport system, is composed of five genes, pstS, pstC, pstA, pstB and phoU, whose transcription is induced by phosphate starvation. A phosphate-regulated promoter located upstream of the most proximal gene (pstS) controls the transcription of the entire operon. Though the full-length pst mRNA could be detected by an improved RT-PCR protocol, Northern analysis using several pst-specific probes failed to reveal this transcript. Instead, smaller but distinct pst mRNA species were evident. Primer-extension experiments localized the 5′ ends of pst mRNAs within the operon. The data suggest that the full-length mRNA is rapidly processed post-transcriptionally.

The Integration Host Factor (IHF) Affects the Expression of the Phosphate-Binding Protein and of Alkaline Phosphatase in Escherichia coli

Abstract. The genes encoding alkaline phosphatase (phoA) and the inducible inorganic phosphate transport system Pst (pstS,C,A,B,U) belong to the PHO regulon. Mutants of Escherichia coli lacking the global regulatory protein integration host factor (IHF) show an increased level of alkaline phosphatase and a decreased level of Pst. IHF binds weakly but specifically to a DNA fragment containing the promoter region of the pst operon but does not bind to a fragment that includes the promoter region of phoA. It is proposed that IHF is a positive regulator of the pst operon and as such controls indirectly the expression of phoA.

A new type of alkaline phosphatase-negative mutants in Escherichia coli K12

SummaryA new type of phosphatase-negative mutants (phoT) has been isolated. Genetic mapping and complementation tests show that the phoT locus is independent of phoA and of phoR.

Phosphorylation of the integrase protein of coliphage HK022.

The integrase (Int) proteins of coliphages HK022 and lambda, are phosphorylated in one or more of their tyrosine residues. In Int of HK022 the phosphorylated residue(s) belong to its core-binding/catalytic domains. Wzc, a protein tyrosine kinase of Escherichia coli, is not required for Int phosphorylation in vivo, however, it can transphosphorylate the conserved Tyr(342) catalytic residue of Int in vitro. Int purified from cells that overexpress Wzc has a reduced activity in vitro. In vivo, the lysogenization of wild type HK022 as well as of lambda is not affected by the overexpression of Wzc. However, the nin5 mutant of lambda, which lacks a protein-tyrosine phosphatase gene, shows a significantly reduced lysogenization. It is suggested that phosphorylation of Int by Wzc down regulates the activity of Int.

Site-specific recombination in Arabidopsis plants promoted by the Integrase protein of coliphage HK022.

The gene encoding the wild type Integrase protein of coliphage HK022 was integrated chromosomally and expressed in Arabidopsis thaliana plants. Double-transgenic plants cloned with the int gene as well as with a T-DNA fragment carrying the proper att sites in a tandem orientation showed that Int catalyzed a site-specific integration reaction (attP × attB) as well as a site-specific excision reaction (attL × attR). The reactions took place without the need to provide any of the accessory proteins that are required by Int in the bacterial host. When expressed in tobacco plants a GFP-Int fusion exhibits a predominant nuclear localization.

Genetic Mapping of the phoR Regulator Gene of Alkaline Phosphatase in Escherichia coli

SUMMARY: Genetic mapping of the structural phoA and the linked regulatory phoR genes for alkaline phosphatase synthesis in Escherichia coli was carried out by conjugation. Distal markers were selected and the segregation of proximal markers was determined. The gene order lac-phoA-phoR-tsx is proposed.

The effect of IHF on σS selectivity of the phoA and pst promoters of Escherichia coli

The pst operon, a member of the PHO regulon of Escherichia coli, encodes a high-affinity phosphate transport system whose expression is induced when the cells enter a phase of phosphate starvation. The expression of pst is stimulated by the integration host factor (IHF). Transcription of the PHO regulon genes is initiated by the RNA polymerase complexed with σD (EσD). Owing to a cytosine residue at position −13 of the pst promoter its transcription can also be initiated by EσS. Here, we show that inactivation of IHF in vivo abolishes the σS-dependent transcription initiation of the pst operon, indicating that both −13C residue and IHF are required to confer on pst the ability to be transcribed by EσS. Introduction of a −13C residue in the promoter region of phoA, another PHO regulon gene that is not directly affected by IHF, did not affect its exclusive transcription initiation by EσD.

Core-binding specificity of bacteriophage integrases.

Abstract The site-specific recombination systems of bacteriophages λ and HK022 share the same mechanism and their integrase proteins show strong homology. Nevertheless the integrase protein of each phage can only catalyze recombination between its own att sites. Previous work has shown that the specificity determinants in the att sites are located within the sequences that bind the integrase to the core of att. DNA fragments that carry attL and attR sites of each phage were challenged with each of the two integrases and the DNA-protein complexes were examined by the gel- retardation technique. The results show that each integrase can form higher-order DNA-protein complexes only with its cognate att sites, suggesting that differences in the mode of binding to the core are responsible for the specificity difference between the two integrases.