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Chapter 27 : Potential Mechanisms for Linking Phage Mu Transposition with Cell Physiology

Authors: Stella H. North1, Hiroshi Nakai2
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Affiliations: 1: Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Rd. NW, Washington, DC 20007; 2: Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Rd. NW, Washington, DC 20007
Content Type: Monograph
Publication Year: 2005

Category: Microbial Genetics and Molecular Biology; Bacterial Pathogenesis

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Abstract:

This chapter discusses potential mechanisms for linking phage Mu transposition with cell physiology. Derepression of transposition can potentially benefit the host under conditions of stress, and these mechanisms can be part of the cellular stress response. Bacteriophage Mu is a model of regulated transposition, for it functions within its host as a fully active transposon as well as a virus. Transposition of the Mu genome into the host chromosome establishes lysogeny and replicates Mu DNA for lytic development. Upon completion of strand exchange, the transpososome remains in a tight complex with the two Mu ends in what is known as the type II transpososome or the strand-transfer complex (STC), posing as an impediment to the assembly of a replisome. The processes in DNA replication relevant to potential mechanisms in Mu derepression and those properties providing insights about Mu's relationship with its host are summarized in this chapter. Two types of repressor mutants which induce lytic development in Mu lysogens have provided insight as to how Mu derepression may be triggered. The C-terminal domain (CTD) of Rep plays an important role not only in eliciting thermolability of DNA binding domain (DBD) mutations present in but also in promoting Rep degradation induced by Vir expressed in . Recent evidence implicates a role for the Mu repressor CTD in S derepression and regulation of transposition. The CTD’s influence on DNA binding as well as repressor degradation represents two potential pathways by which derepression may be triggered.

Citation: North S, Nakai H. 2005. Potential Mechanisms for Linking Phage Mu Transposition with Cell Physiology, p 499-512. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch27

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Potential Mechanisms for Linking Phage Mu Transposition with Cell Physiology
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Citation: North S, Nakai H. 2005. Potential Mechanisms for Linking Phage Mu Transposition with Cell Physiology, p 499-512. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch27
/content/10.1128/9781555817640.chap27.fig27-1
Figure 1

Bacteriophage Mu genome. Regions for Mu DNA transposition include a 200-bp left-end () sequence and a 100- bp right-end () sequence, which contain binding sites for domain Ibg of MuA and make up attachment sites to host DNA. The operator sequences (O1, O2, and O3) are contained within a 200-bp region and regulate the P and P promoters. They contain binding sites for the Mu repressor, encoded by the c gene. O1 and O2 also include an internal transpositional enhancer that is recognized by domain Ia of MuA and required for the assembly of transposase under physiological conditions.

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Figure 1

Bacteriophage Mu genome. Regions for Mu DNA transposition include a 200-bp left-end () sequence and a 100- bp right-end () sequence, which contain binding sites for domain Ibg of MuA and make up attachment sites to host DNA. The operator sequences (O1, O2, and O3) are contained within a 200-bp region and regulate the P and P promoters. They contain binding sites for the Mu repressor, encoded by the c gene. O1 and O2 also include an internal transpositional enhancer that is recognized by domain Ia of MuA and required for the assembly of transposase under physiological conditions.

Citation: North S, Nakai H. 2005. Potential Mechanisms for Linking Phage Mu Transposition with Cell Physiology, p 499-512. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch27
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Figure 2

Mu replicative transposition. The Mu transposition reaction catalyzed in vitro is depicted. (a) MuA transposase binds to sites on the left and right ends of mini-Mu DNA, which is harbored on a supercoiled plasmid vector (thick black lines). In the presence of the histone-like protein HU, MuA is assembled into a stable tetramer that holds the two Mu ends together in a synaptic complex. MuB plays an accessory role, functioning in target DNA capture and activating transposase activity. (b) MuA introduces nicks at the Mu ends and transfers them to phosphodiester linkages that are 5 bp apart (indicated by full arrows) on target DNA (thick gray lines) to form STC1. (c) Strand exchange produces a fork at each Mu end, the target DNA providing 30-OH ends (indicated by half arrows) that can be potentially used as primer for leading strand synthesis. The molecular chaperone ClpX then destabilizes the quaternary interactions of the MuA transpososome to convert STC1 to STC2. (d) Factors present in a host extract (MRFα2) displace the transpososome and form the prereplisome STC3. PriA binds to one of the forked structures formed by strand exchange (e), and this initiates the assembly of the primosome by bringing PriB, DnaT, and DnaBC to the fork (f and g). (f) The 3′ to 5′ helicase of PriA can function to unwind the lagging strand arm of the fork to create a binding site for the DnaB helicase. DnaC disassembles from the DnaBC complex as the DnaB is loaded onto the lagging strand template (g), and DNA polymerase III holoenzyme is bound to the fork to complete the formation of the replisome (h).

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Figure 2

Mu replicative transposition. The Mu transposition reaction catalyzed in vitro is depicted. (a) MuA transposase binds to sites on the left and right ends of mini-Mu DNA, which is harbored on a supercoiled plasmid vector (thick black lines). In the presence of the histone-like protein HU, MuA is assembled into a stable tetramer that holds the two Mu ends together in a synaptic complex. MuB plays an accessory role, functioning in target DNA capture and activating transposase activity. (b) MuA introduces nicks at the Mu ends and transfers them to phosphodiester linkages that are 5 bp apart (indicated by full arrows) on target DNA (thick gray lines) to form STC1. (c) Strand exchange produces a fork at each Mu end, the target DNA providing 30-OH ends (indicated by half arrows) that can be potentially used as primer for leading strand synthesis. The molecular chaperone ClpX then destabilizes the quaternary interactions of the MuA transpososome to convert STC1 to STC2. (d) Factors present in a host extract (MRFα2) displace the transpososome and form the prereplisome STC3. PriA binds to one of the forked structures formed by strand exchange (e), and this initiates the assembly of the primosome by bringing PriB, DnaT, and DnaBC to the fork (f and g). (f) The 3′ to 5′ helicase of PriA can function to unwind the lagging strand arm of the fork to create a binding site for the DnaB helicase. DnaC disassembles from the DnaBC complex as the DnaB is loaded onto the lagging strand template (g), and DNA polymerase III holoenzyme is bound to the fork to complete the formation of the replisome (h).

Citation: North S, Nakai H. 2005. Potential Mechanisms for Linking Phage Mu Transposition with Cell Physiology, p 499-512. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch27
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Figure 3

Domains of the Mu repressor. Depicted are the DNA binding domain (DBD), which makes up approximately 80 Nterminal residues; the leucine-rich domain (LRD [L121 to L162]), which is thought to function in repressor oligomerization; and the C-terminal domain (CTD), which modulates repressor degradation by ClpXP protease and DNA binding (I170 to V196). The indicated mutations in the DBD result in temperature-sensitive DNA binding (). Deletion of the last 18 amino acids () from the C terminus suppresses the DBD mutations and confers dominance over .

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Figure 3

Domains of the Mu repressor. Depicted are the DNA binding domain (DBD), which makes up approximately 80 Nterminal residues; the leucine-rich domain (LRD [L121 to L162]), which is thought to function in repressor oligomerization; and the C-terminal domain (CTD), which modulates repressor degradation by ClpXP protease and DNA binding (I170 to V196). The indicated mutations in the DBD result in temperature-sensitive DNA binding (). Deletion of the last 18 amino acids () from the C terminus suppresses the DBD mutations and confers dominance over .

Citation: North S, Nakai H. 2005. Potential Mechanisms for Linking Phage Mu Transposition with Cell Physiology, p 499-512. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch27
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Figure 4

Dominant-negative forms of repressor. The sequence within the Rep CTD is shown. Vir3060 and Vir3051 are produced by frameshift mutations that alter the last 11 to 26 residues of the C terminus. The residues of the Vir proteins that differ from Rep are marked with an asterisk.

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Image of Figure 4
Figure 4

Dominant-negative forms of repressor. The sequence within the Rep CTD is shown. Vir3060 and Vir3051 are produced by frameshift mutations that alter the last 11 to 26 residues of the C terminus. The residues of the Vir proteins that differ from Rep are marked with an asterisk.

Citation: North S, Nakai H. 2005. Potential Mechanisms for Linking Phage Mu Transposition with Cell Physiology, p 499-512. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch27
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