The Gifsy phages: Gifsy1 and Gifsy2

Gifsy 1 and Gifsy 2 are temperate phages present in the vast majority of Salmonella enterica serovar Typhimurium strains; the genomic positioning of the prophages is illustrated in Figure 1. This strain of pathogenic bacteria infects a broad spectrum of animal species, from reptiles to mammals [1].

Figure 1: shows the positions of the prophage inserts into the Salmonella genome [1].

Phage Repressor System

Maya Lisa anja

Alpha-repressor

The C1-repressor is responsible for repressing transcription of the lytic genes, thereby maintaining the stable lysogenic state. The induction of the lytic state is caused by activated RecA, which stimulates the self-cleavage of the C1-repressor. We will be using the C1-repressor in our system.

Phage Anti-Termination system

(INTRO)

Anti-Termination is the process by which the termination of gene transcription is prevented. Such control of gene transcription can be found in the phage Lambda system. The mechanism is controlled by proteins, such as the lambda N or lambda Q-proteins. The expression of early genes and late genes are both regulated by the anti-termination mechanism, controlled by the lambda N-protein and the lambda Q-protein, respectively.

The N-protein is able to suppress transcription termination at both factor-dependent and factor-independent termination sites. N anti-termination is strongly stimulated by the NusA protein. Unlike the N-protein, the Q-protein specifically binds to a DNA sequence immediately upstream of the pR´ promoter.

A more detailed explanation of these anti-termination mechanisms will be posted later on. The mechanism of N-protein nut-site termination have been studied heavily the last years and the current best descriped mechanism have been done in a couple of reviews (XXXXX,XXXX,XXXX) The anti-termination function by introduction of the N-protein (or equivalent) that interacts with nusA and disrupt the termination. Of known systems can be mentioned lambda, p21, p22 FUNCTION XXXXXXXXXXXX shown in the figure below. In the known systems the nut site is placed from XXX bp to XXX bp upstream of the termination steam loop. (REFERENCES !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! IMPORTANT - read two gottersman 2010 – crystallography papers)))) figures from papers on antitermination. Few papers descripe and test the the actual needed distance from the termination steam loop. From other systems and mechanism it is known that XXX bp is needed for regulation of RNAP or DNAP. (MOGENS ABOUT REFERENCES AND SYSTEMS SEE MICRO-BIO-TEXT BOOKS_) .

N-protein plasmid

The N protein were isolated from salmonella genomic DNA with specific designed primers. We used the natural occurring RBS site, as a High expression of N have shown non specific anti-termination effect on a global scale on the genome. [[#References References]]

nut sites

Severel papers analyse the function of the nut-site. It has been shown that this mechanism can be manipulated in different manners and that the function can be canceled and reactivated by counter-mutations in XXXXX (REFFFFF). Futher it has been shown that the specificity of the N-proteins can be changed from lambda to P22 by only a few mutations showing a possible coevolution, or possible interactions to increase possible genomic randomization (REFFF). (Complexicity)