General Information/ClpX, ClpP, and Lon
Certain factors involved in protein "management" such as ClpX, ClpP, and Lon have been implicated in transposition. ClpX is essential for bacteriophage Mu growth where it is required for disassembling the transposase-DNA complex or the transpososome strand transfer complex in preparation for the assembly of a replication complex. Recognition of Mu transposase, pA, by ClpX requires the terminal 10 amino acids of pA. Together with ClpP, ClpX also plays a role in proteolysis of the Mu repressor. The Lon protease is implicated in proteolysis of the IS903 transposase.
At present the involvement of these proteins in the transposition of other elements has not been well documented.
SOS system, RecA, RecBC
The third class of host factor includes host cell systems which act to limit DNA damage and maintain chromosome integrity. Studies with IS10 (see ) and IS1 have demonstrated that high levels of Tpase in the presence of suitable terminal IRs lead to induction of the host SOS system. As discussed previously, some controversy still exists concerning the role of RecA in Tn5 (IS50) transposition. Reznikoff and colleagues have provided genetic evidence that transposition is inhibited by induction of the SOS system in a manner which does not require the proteolytic activity of RecA. On the other hand, Tessman and collaborators using a different transposition assay have found that constitutive SOS conditions actually enhance Tn5 transposition. Moreover, using yet another assay system, Ahmed has concluded that intermolecular transposition of Tn5 is stimulated by RecA. Further investigation is clearly required to understand these apparently incompatible results.
Ahmed has also concluded that intermolecular transposition of the IS1-based transposon, Tn9, behaves in a similar way to that of Tn5 with respect to the recA allele. In contrast, however, the frequency of adjacent deletions mediated by IS1 was significantly increased in the absence of RecA. This has received some independent support using a physical assay where it was shown that deletion products accumulate in a recA but not in a wildtype host. Moreover, like IS1 induction of the SOS system, accumulation of such adjacent deletions was dependent on recBC (Zablweska et al., unpublished observations). The recBC genes are also implicated in the behavior of transposons such as Tn10 and Tn5 where they affect precise and imprecise excision in a process independent of transposition per se. This is more pronounced with composite transposons in which the component insertion sequences IS10 and IS50 are present as inverted repeats, and is stimulated when the transposon is carried by a transfer-proficient conjugative plasmid. It seems probable that such excisions occur by a process involving replication fork slippage (see  for further discussion).
PolI and gyrase
Both DNA polymerase I  and DNA gyrase are implicated in the transposition of Tn5. While the effect of gyrase may reflect a requirement for optimal levels of supercoiling, the role of PolI remains a matter of speculation. It may be involved in DNA synthesis necessary to repair the single strand gaps resulting from staggered cleavage of the target and which gives rise to the DRs. DNA gyrase has also been shown to be important in transposition of bacteriophage Mu.
Another host function, the Dam DNA methylase can be important in modulating both Tpase expression and activity. IS10, IS50 and IS903 all carry methylation sites (GATC) in the transposase promoter regions and in each case, promoter activity is increased in a dam-host. Additional evidence has been presented that the methylation status of GATC sites within the terminal inverted repeats also modulates the activity of these ends. For IS50, this can now be understood in terms of steric interference in the transposase active site, as recently revealed by the determination of the crystal structure of a synpatic complex including its Tpase and a pair of precleaved transposon ends. Similar methylation sites have been previously observed in IS3, IS4, and IS5. A survey of the elements included in the data base has shown that most groups or families contain members which have GATC sites within the first 50 bp of one or both extremities. The IS3, IS5 and IS256 families include the most members carrying such sites. Except for IS3 itself where strong stimulation of transposition has been observed in a dam-host, in most of these cases the biological relevance of these sites is unknown. Moreover, it should be pointed out that the probability that any 100 bp DNA sequence carries the GATC tetranucleotide is about 40%. The role of Dam methylation in IS10 and IS50 transposition is described in detail in the appropriate sections dealing with these elements.
Metabolic control elements
In a screen of over 20,000 independent insertion mutants for host factors that influence IS903 transposition the Derbyshire lab isolated more than 100 mutants that increased or decreased transposition and also altered its timing during colony growth. These included independent mutations in a gene required for fermentative metabolism during anaerobic growth resulting in “early” transposition during colony growth and was suppressed by addition of fumarate, and other mutations in genes associated with DNA metabolism, intermediary metabolism, transport, cellular redox, protein folding and proteolysis. Other mutations were isolated in pur genes involved in purine biosynthesis. Further analysis suggested that this phenotype was due to a requirement for GTP in IS903 transposition. It should be noted that some of these mutants also affected transposition of IS10 and of Tn552.
Certain transposons appear to be subject to a mode of regulation known as over-expression inhibition. This was first observed with the eukaryotic transposons Tc1/mariner Lampe where increasing the concentration of transposase results in a reduction in the level of transposition. It was subsequently observed with the sleeping beauty transposon. It also occurs in vivo in mice.
The biological rational for this is that “infection” of a naïve cell by the transposon results in a burst of transposition which is then attenuated by overproduction inhibition. This is then followed by gradual decay of the transposon.
The Chalmers lab has provided an interesting and compelling explanation of this effect. Using the mariner family transposon Hsmar1 they present convincing data implying that overproduction inhibition occurs during transpososome assembly and is due to a combination of the multimeric state of the transposase coupled with competition for transposase binding sites at the Hsmar1 ends. The model (assembly-site-occlusion model) is based on the presence of transposase multimers (dimers) to the exclusion of monomers – in other words, end-binding required a dimeric transposase. At low transposase/transposon ratios, one dimer can bind both transposon ends resulting in the ordered assembly of the transpososome. An increase in the transposase dimer/transposon ratio results in binding of dimers to both transposon ends, preventing transpososome assembly. The model not only explains the in vivo transposase dose-response for Hsmar1 but also for the related Sleeping Beauty (SB) and piggyBac (PB) transposons. As yet, no information is at present available concerning the relevance of this mode of regulation to prokaryotic transposable elements.
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