General Information/ClpX, ClpP, and Lon

From TnPedia
Jump to navigation Jump to search

General

Certain factors involved in protein "management" such as ClpX, ClpP, and Lon have been implicated in transposition. ClpX is essential for bacteriophage Mu growth[1] 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[2][3]. Recognition of Mu transposase, pA, by ClpX requires the terminal 10 amino acids of pA[4]. Together with ClpP, ClpX also plays a role in proteolysis of the Mu repressor[5][6]. The Lon protease is implicated in proteolysis of the IS903 transposase[7].

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 [8]) and IS1[9] 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[10], some controversy still exists concerning the role of RecA in Tn5 (IS50) transposition[11][12][13]. 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[13]. On the other hand, Tessman and collaborators[11][12][14] using a different transposition assay have found that constitutive SOS conditions actually enhance Tn5 transposition. Moreover, using yet another assay system, Ahmed[15] 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[15]. 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like IS1 induction of the SOS system, accumulation of such adjacent deletions was dependent on recBC (Zablweska et al., unpublished observations).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[15] 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 [16][17] for further discussion).

PolI and gyrase

Both DNA polymerase I [18][19][20] and DNA gyrase[21][22] 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[23][24].

Dam methylase

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[25][26]. Additional evidence has been presented that the methylation status of GATC sites within the terminal inverted repeats also modulates the activity of these ends[25]. 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[27]. 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[28]. 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[29]. It should be noted that some of these mutants also affected transposition of IS10 and of Tn552.

Hfq

Finally, the RNA chaperone Hfq has also been implicated in the regulation of Tn10 transposition by promoting RNAout interaction with transposase mRNA[30][31][32].

Over-production inhibition

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[33][34][35] where increasing the concentration of transposase results in a reduction in the level of transposition. It was subsequently observed with the sleeping beauty transposon[36][37]. It also occurs in vivo in mice[38][39].

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[40] 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[41][42]. 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.

Bibliography

  1. ↑ Mhammedi-Alaoui A, Pato M, Gama MJ, Toussaint A . A new component of bacteriophage Mu replicative transposition machinery: the Escherichia coli ClpX protein. - Mol Microbiol: 1994 Mar, 11(6);1109-16 [PubMed:8022280] [DOI]
  2. ↑ Kruklitis R, Welty DJ, Nakai H . ClpX protein of Escherichia coli activates bacteriophage Mu transposase in the strand transfer complex for initiation of Mu DNA synthesis. - EMBO J: 1996 Feb 15, 15(4);935-44 [PubMed:8631314]
  3. ↑ Levchenko I, Luo L, Baker TA . Disassembly of the Mu transposase tetramer by the ClpX chaperone. - Genes Dev: 1995 Oct 1, 9(19);2399-408 [PubMed:7557391] [DOI]
  4. ↑ Levchenko I, Yamauchi M, Baker TA . ClpX and MuB interact with overlapping regions of Mu transposase: implications for control of the transposition pathway. - Genes Dev: 1997 Jun 15, 11(12);1561-72 [PubMed:9203582] [DOI]
  5. ↑ Laachouch JE, Desmet L, Geuskens V, Grimaud R, Toussaint A . Bacteriophage Mu repressor as a target for the Escherichia coli ATP-dependent Clp Protease. - EMBO J: 1996 Jan 15, 15(2);437-44 [PubMed:8617219]
  6. ↑ Welty DJ, Jones JM, Nakai H . Communication of ClpXP protease hypersensitivity to bacteriophage Mu repressor isoforms. - J Mol Biol: 1997 Sep 12, 272(1);31-41 [PubMed:9299335] [DOI]
  7. ↑ Derbyshire KM, Kramer M, Grindley ND . Role of instability in the cis action of the insertion sequence IS903 transposase. - Proc Natl Acad Sci U S A: 1990 Jun, 87(11);4048-52 [PubMed:2161528] [DOI]
  8. ↑ Kleckner N, Chalmers RM, Kwon D, Sakai J, Bolland S . Tn10 and IS10 transposition and chromosome rearrangements: mechanism and regulation in vivo and in vitro. - Curr Top Microbiol Immunol: 1996, 204;49-82 [PubMed:8556869] [DOI]
  9. ↑ Lane D, Cavaillé J, Chandler M . Induction of the SOS response by IS1 transposase. - J Mol Biol: 1994 Sep 30, 242(4);339-50 [PubMed:7932694] [DOI]
  10. ↑ Mahillon J, Chandler M . Insertion sequences. - Microbiol Mol Biol Rev: 1998 Sep, 62(3);725-74 [PubMed:9729608]
  11. ↑ 11.0 11.1 Kuan CT, Liu SK, Tessman I . Excision and transposition of Tn5 as an SOS activity in Escherichia coli. - Genetics: 1991 May, 128(1);45-57 [PubMed:1648004]
  12. ↑ 12.0 12.1 Kuan CT, Tessman I . LexA protein of Escherichia coli represses expression of the Tn5 transposase gene. - J Bacteriol: 1991 Oct, 173(20);6406-10 [PubMed:1655708] [DOI]
  13. ↑ 13.0 13.1 Weinreich MD, Makris JC, Reznikoff WS . Induction of the SOS response in Escherichia coli inhibits Tn5 and IS50 transposition. - J Bacteriol: 1991 Nov, 173(21);6910-8 [PubMed:1657870] [DOI]
  14. ↑ Kuan CT, Tessman I . Further evidence that transposition of Tn5 in Escherichia coli is strongly enhanced by constitutively activated RecA proteins. - J Bacteriol: 1992 Nov, 174(21);6872-7 [PubMed:1328165] [DOI]
  15. ↑ 15.0 15.1 15.2 Ahmed A . Evidence for replicative transposition of Tn5 and Tn9. - J Mol Biol: 1986 Sep 5, 191(1);75-84 [PubMed:3025455] [DOI]
  16. ↑ Nagel R, Chan A . Enhanced Tn10 and mini-Tn10 precise excision in DNA replication mutants of Escherichia coli K12. - Mutat Res: 2000 May 31, 459(4);275-84 [PubMed:10844241] [DOI]
  17. ↑ Reddy M, Gowrishankar J . Characterization of the uup locus and its role in transposon excisions and tandem repeat deletions in Escherichia coli. - J Bacteriol: 2000 Apr, 182(7);1978-86 [PubMed:10715006] [DOI]
  18. ↑ Sasakawa C, Uno Y, Yoshikawa M . The requirement for both DNA polymerase and 5' to 3' exonuclease activities of DNA polymerase I during Tn5 transposition. - Mol Gen Genet: 1981, 182(1);19-24 [PubMed:6267432] [DOI]
  19. ↑ Syvanen M, Hopkins JD, Clements M . A new class of mutants in DNA polymerase I that affects gene transposition. - J Mol Biol: 1982 Jun 25, 158(2);203-12 [PubMed:6288966] [DOI]
  20. ↑ Sasakawa C, Uno Y, Yoshikawa M . lon-sulA regulatory function affects the efficiency of transposition of Tn5 from lambda b221 cI857 Pam Oam to the chromosome. - Biochem Biophys Res Commun: 1987 Feb 13, 142(3);879-84 [PubMed:3030303] [DOI]
  21. ↑ Isberg RR, Syvanen M . DNA gyrase is a host factor required for transposition of Tn5. - Cell: 1982 Aug, 30(1);9-18 [PubMed:6290084] [DOI]
  22. ↑ Sternglanz R, DiNardo S, Voelkel KA, Nishimura Y, Hirota Y, Becherer K, Zumstein L, Wang JC . Mutations in the gene coding for Escherichia coli DNA topoisomerase I affect transcription and transposition. - Proc Natl Acad Sci U S A: 1981 May, 78(5);2747-51 [PubMed:6265907] [DOI]
  23. ↑ Pato ML, Karlok M, Wall C, Higgins NP . Characterization of Mu prophage lacking the central strong gyrase binding site: localization of the block in replication. - J Bacteriol: 1995 Oct, 177(20);5937-42 [PubMed:7592347] [DOI]
  24. ↑ Pato ML, Banerjee M . The Mu strong gyrase-binding site promotes efficient synapsis of the prophage termini. - Mol Microbiol: 1996 Oct, 22(2);283-92 [PubMed:8930913] [DOI]
  25. ↑ 25.0 25.1 Roberts D, Hoopes BC, McClure WR, Kleckner N . IS10 transposition is regulated by DNA adenine methylation. - Cell: 1985 Nov, 43(1);117-30 [PubMed:3000598] [DOI]
  26. ↑ Yin JC, Krebs MP, Reznikoff WS . Effect of dam methylation on Tn5 transposition. - J Mol Biol: 1988 Jan 5, 199(1);35-45 [PubMed:2451025] [DOI]
  27. ↑ Davies DR, Mahnke Braam L, Reznikoff WS, Rayment I . The three-dimensional structure of a Tn5 transposase-related protein determined to 2.9-A resolution. - J Biol Chem: 1999 Apr 23, 274(17);11904-13 [PubMed:10207011] [DOI]
  28. ↑ Twiss E, Coros AM, Tavakoli NP, Derbyshire KM . Transposition is modulated by a diverse set of host factors in Escherichia coli and is stimulated by nutritional stress. - Mol Microbiol: 2005 Sep, 57(6);1593-607 [PubMed:16135227] [DOI]
  29. ↑ Coros AM, Twiss E, Tavakoli NP, Derbyshire KM . Genetic evidence that GTP is required for transposition of IS903 and Tn552 in Escherichia coli. - J Bacteriol: 2005 Jul, 187(13);4598-606 [PubMed:15968071] [DOI]
  30. ↑ Ross JA, Ellis MJ, Hossain S, Haniford DB . Hfq restructures RNA-IN and RNA-OUT and facilitates antisense pairing in the Tn10/IS10 system. - RNA: 2013 May, 19(5);670-84 [PubMed:23510801] [DOI]
  31. ↑ Ellis MJ, Trussler RS, Haniford DB . Hfq binds directly to the ribosome-binding site of IS10 transposase mRNA to inhibit translation. - Mol Microbiol: 2015 May, 96(3);633-50 [PubMed:25649688] [DOI]
  32. ↑ Ellis MJ, Trussler RS, Ross JA, Haniford DB . Probing Hfq:RNA interactions with hydroxyl radical and RNase footprinting. - Methods Mol Biol: 2015, 1259;403-15 [PubMed:25579599] [DOI]
  33. ↑ Lampe DJ, Grant TE, Robertson HM . Factors affecting transposition of the Himar1 mariner transposon in vitro. - Genetics: 1998 May, 149(1);179-87 [PubMed:9584095]
  34. ↑ Lohe AR, Hartl DL . Autoregulation of mariner transposase activity by overproduction and dominant-negative complementation. - Mol Biol Evol: 1996 Apr, 13(4);549-55 [PubMed:8882498] [DOI]
  35. ↑ Hartl DL, Lozovskaya ER, Nurminsky DI, Lohe AR . What restricts the activity of mariner-like transposable elements. - Trends Genet: 1997 May, 13(5);197-201 [PubMed:9154003] [DOI]
  36. ↑ Geurts AM, Yang Y, Clark KJ, Liu G, Cui Z, Dupuy AJ, Bell JB, Largaespada DA, Hackett PB . Gene transfer into genomes of human cells by the sleeping beauty transposon system. - Mol Ther: 2003 Jul, 8(1);108-17 [PubMed:12842434] [DOI]
  37. ↑ Zayed H, Izsvák Z, Walisko O, Ivics Z . Development of hyperactive sleeping beauty transposon vectors by mutational analysis. - Mol Ther: 2004 Feb, 9(2);292-304 [PubMed:14759813] [DOI]
  38. ↑ Karsi A, Moav B, Hackett P, Liu Z . Effects of insert size on transposition efficiency of the sleeping beauty transposon in mouse cells. - Mar Biotechnol (NY): 2001 May, 3(3);241-5 [PubMed:14961361] [DOI]
  39. ↑ Mikkelsen JG, Yant SR, Meuse L, Huang Z, Xu H, Kay MA . Helper-Independent Sleeping Beauty transposon-transposase vectors for efficient nonviral gene delivery and persistent gene expression in vivo. - Mol Ther: 2003 Oct, 8(4);654-65 [PubMed:14529839] [DOI]
  40. ↑ Claeys Bouuaert C, Lipkow K, Andrews SS, Liu D, Chalmers R . The autoregulation of a eukaryotic DNA transposon. - Elife: 2013 Jun 18, 2;e00668 [PubMed:23795293] [DOI]
  41. ↑ Bouuaert CC, Tellier M, Chalmers R . One to rule them all: A highly conserved motif in mariner transposase controls multiple steps of transposition. - Mob Genet Elements: 2014 Jan 1, 4(1);e28807 [PubMed:24812590] [DOI]
  42. ↑ Tellier M, Bouuaert CC, Chalmers R . Mariner and the ITm Superfamily of Transposons. - Microbiol Spectr: 2015 Apr, 3(2);MDNA3-0033-2014. [PubMed:26104691] [DOI]



Retrieved from "https://tnpedia.fcav.unesp.br/index.php?title=General_Information/ClpX,_ClpP,_and_Lon&oldid=1314"