1887

Chapter 2 : Iteron Plasmids

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in
Zoomout

Iteron Plasmids, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818982/9781555818975_Chap02-1.gif /docserver/preview/fulltext/10.1128/9781555818982/9781555818975_Chap02-2.gif

Abstract:

Iteron plasmids are extrachromosomal genetic elements that can be found in all Gram-negative bacteria. Despite the fact that these plasmids bring antibiotic resistance to host bacterium, they can also bring other features, for example, genes for degradation of specific compounds or toxin production. Iteron plasmids possess characteristic directed repeats located within the origin of replication initiation that are called iterons. These plasmids became model systems for investigation of the molecular mechanisms for DNA replication initiation and for the analysis of mechanisms of control of plasmid copy number in bacterial cells. This research has provided our basic understanding of plasmid biology and the relationship between plasmid DNA and host cells. The control mechanisms utilized by iteron plasmids are based on the nucleoprotein complexes formed by the plasmid-encoded replication initiation protein (Rep). The Rep proteins interact with iterons, which initiates the process of plasmid DNA synthesis, but Rep proteins are also able to form complexes with iterons, which inhibits the replication initiation process. This inhibition is called “handcuffing.” Also, Rep protein can interact with inverted repeated sequences, causing transcriptional auto-repression. Finally, various chaperone protein systems and proteases affect the Rep activity and, therefore, overall plasmid DNA metabolism.

Citation: Konieczny I, Bury K, Wawrzycka A, Wegrzyn K. 2015. Iteron Plasmids, p 33-44. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0026-2014
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1
Figure 1

Scheme of the iteron-containing plasmid origin structure. The direct repeats—iterons—and inverted repeats (IR) are depicted as red arrows. The DUE region of each origin is marked, and repeated sequences within the region are depicted as green triangles. DnaA-box sequences are marked in blue. The region rich in guanidine and cytidine residues (GC-rich) is marked within the origins, if identified. The origins are not drawn to scale.

Citation: Konieczny I, Bury K, Wawrzycka A, Wegrzyn K. 2015. Iteron Plasmids, p 33-44. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0026-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

Structure of replication initiators. DnaA of , RepE54 from mini-F plasmid, π from R6K, and the C-terminal part of the TrfA protein (190-382 aa) of plasmid RK2 are depicted. Structure of the DnaA, RepE54, and π are derived from crystallographic data (PDB entry 1L8Q, 1REP, and 2NRA, respectively). The TrfA model was developed based on homology modeling. The AAA+ domain is colored in blue, the DNA binding domain (DBD) is shown in red, and Winged-Helix domains (WH1 and WH2) are colored in yellow and green, respectively. References and detailed information for crystallographic data of the DnaA, RepE54, π, and TrfA model are given in the text.

Citation: Konieczny I, Bury K, Wawrzycka A, Wegrzyn K. 2015. Iteron Plasmids, p 33-44. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0026-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
Figure 3

Model of replication initiation: comparison of the processes occurring on the iteron-containing plasmid origin with the replication initiation of bacterial chromosomes. The iteron-containing plasmid origin is recognized by the plasmid-encoded initiator (Rep), which binds cooperatively to the iterons. The interaction of Rep with iterons results in the formation of an open complex and destabilization of the DNA unwinding element (DUE), which creates ssDNA. In RK2, pPS10, F, R6K, P1, and pSC101 the formation of the open complex requires cooperation of the plasmid Rep and host DnaA proteins, while at the chromosomal origin the DnaA protein is sufficient for this process. During the chromosomal origin opening DnaA forms filament on the ssDNA. Helicase delivery and loading requires interaction with the replication initiators; in addition, in the DnaB helicase delivery at the chromosomal as well as at the plasmid RK2 requires the DnaC accessory protein. During the RK2 replication initiation in the host-encoded DnaBC helicase complex is delivered to the DnaA-box sequence through interaction with DnaA, and subsequently the plasmid initiator TrfA translocates the helicase to the opened plasmid origin. The interactions between DnaB and the R6K π protein, F RepE, and pSC101 RepA have also been established as essential for helicase complex formation at the plasmids’ origins. The helicase unwinds the DNA double helix, and after a short RNA fragment is synthesized by a primase, a polymerase complex is assembled. Single-stranded DNA binding protein (SSB) is required for replication initiation of both chromosomal and iteron-containing plasmid DNA. The HU/IHF proteins’ contribution in DNA replication initiation was omitted in the scheme. For a detailed description see the text.

Citation: Konieczny I, Bury K, Wawrzycka A, Wegrzyn K. 2015. Iteron Plasmids, p 33-44. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0026-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4
Figure 4

Regulation of iteron-containing plasmid replication initiation by the iterons. Rep protein activation occurs by the action of chaperones that convert the Rep dimer to the active monomeric form. Monomers bind to the iteron sequences and perform the initial complex that leads to replication of DNA. Rep protein may also act as a negative regulator of DNA replication by creating “handcuff” structures. Rep proteins couple origins of two separate plasmid particles in a process termed “handcuffing.” In the literature suggestions of chaperone proteins’ participation in the “uncuffing” process can be found, but the mechanism of the handcuff structures’ reversal is still unclear. For details see the text.

Citation: Konieczny I, Bury K, Wawrzycka A, Wegrzyn K. 2015. Iteron Plasmids, p 33-44. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0026-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 5
Figure 5

Regulation of iteron-containing plasmid replication initiation by the auto-repression mechanism. Binding of Rep dimers to inverted repeats inhibits the initiation of transcription starting from the gene promoter. This phenomenon is called auto-repression. An active, monomeric form of Rep protein arises as a result of the action of chaperones. It binds to the iteron sequences that lead to the initiation of DNA replication. Proteases are another factor that may influence the replication process. They limit the amount of both dimer and monomer forms of the Rep protein. For details see the text.

Citation: Konieczny I, Bury K, Wawrzycka A, Wegrzyn K. 2015. Iteron Plasmids, p 33-44. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0026-2014
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555818982.chap2
1. Stalker DM,, Thomas CM,, Helinski DR . 1981. Nucleotide sequence of the region of the origin of replication of the broad host range plasmid RK2. Mol Gen Genet 181 : 8 12.[PubMed] [CrossRef]
2. Murotsu T,, Matsubara K,, Sugisaki H,, Takanami M . 1981. Nine unique repeating sequences in a region essential for replication and incompatibility of the mini-F plasmid. Gene 15 : 257 271.[PubMed] [CrossRef]
3. Abeles AL,, Snyder KM,, Chattoraj DK . 1984. P1 plasmid replication: replicon structure. J Mol Biol 173 : 307 324.[PubMed] [CrossRef]
4. Filutowicz M,, McEachern MJ,, Mukhopadhyay P,, Greener A,, Yang SL,, Helinski DR . 1987. DNA and protein interactions in the regulation of plasmid replication. J Cell Sci Suppl 7 : 15 31.[PubMed] [CrossRef]
5. Nieto C,, Giraldo R,, Fernandez-Tresguerres E,, Diaz R . 1992. Genetic and functional analysis of the basic replicon of pPS10, a plasmid specific for Pseudomonas isolated from Pseudomonas syringae patovar savastanoi . J Mol Biol 223 : 415 426.[PubMed] [CrossRef]
6. Loftie-Eaton W,, Rawlings DE . 2012. Diversity, biology and evolution of IncQ-family plasmids. Plasmid 67 : 15 34.[PubMed] [CrossRef]
7. Wu LT,, Tseng YH . 2000. Characterization of the IncW cryptic plasmid pXV2 from Xanthomonas campestris pv. vesicatoria . Plasmid 44 : 163 172.[PubMed] [CrossRef]
8. Churchward G,, Linder P,, Caro L . 1984. Replication functions encoded by the plasmid pSC101. Adv Exp Med Biol 179 : 209 214.[PubMed] [CrossRef]
9. Page DT,, Whelan KF,, Colleran E . 2001. Characterization of two autoreplicative regions of the IncHI2 plasmid R478: RepHI2A and RepHI1A((R478)). Microbiology 147 : 1591 1598.[PubMed]
10. Wickner S,, Hoskins J,, McKenney K . 1991. Monomerization of RepA dimers by heat shock proteins activates binding to DNA replication origin. Proc Natl Acad Sci USA 88 : 7903 7907.[PubMed] [CrossRef]
11. Ishiai M,, Wada C,, Kawasaki Y,, Yura T . 1994. Replication initiator protein RepE of mini-F plasmid: functional differentiation between monomers (initiator) and dimers (autogenous repressor). Proc Natl Acad Sci USA 91 : 3839 3843.[PubMed] [CrossRef]
12. Toukdarian AE,, Helinski DR,, Perri S . 1996. The plasmid RK2 initiation protein binds to the origin of replication as a monomer. J Biol Chem 271( 12) : 7072 7078.[PubMed] [CrossRef]
13. Kruger R,, Konieczny I,, Filutowicz M . 2001. Monomer/dimer ratios of replication protein modulate the DNA strand-opening in a replication origin. J Mol Biol 306 : 945 955.[PubMed] [CrossRef]
14. Perri S,, Helinski DR . 1993. DNA sequence requirements for interaction of the RK2 replication initiation protein with plasmid origin repeats. J Biol Chem 268 : 3662 3669.[PubMed]
15. Bowers LM,, Kruger R,, Filutowicz M . 2007. Mechanism of origin activation by monomers of R6K-encoded pi protein. J Mol Biol 368 : 928 938.[PubMed] [CrossRef]
16. McEachern MJ,, Filutowicz M,, Helinski DR . 1985. Mutations in direct repeat sequences and in a conserved sequence adjacent to the repeats result in a defective replication origin in plasmid R6K. Proc Natl Acad Sci USA 82 : 1480 1484.[PubMed] [CrossRef]
17. Brendler TG,, Abeles AL,, Reaves LD,, Austin SJ . 1997. The iteron bases and spacers of the P1 replication origin contain information that specifies the formation of a complex structure involved in initiation. Mol Microbiol 23 : 559 567.[PubMed] [CrossRef]
18. Ohkubo S,, Yamaguchi K . 1997. A suppressor of mutations in the region adjacent to iterons of pSC101 ori. J Bacteriol 179 : 2089 2091.[PubMed]
19. Doran KS,, Konieczny I,, Helinski DR . 1998. Replication origin of the broad host range plasmid RK2. Positioning of various motifs is critical for initiation of replication. J Biol Chem 273 : 8447 8453.[PubMed] [CrossRef]
20. Messer W . 2002. The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. FEMS Microbiol Rev 26 : 355 374.[PubMed]
21. Rajewska M,, Wegrzyn K,, Konieczny I . 2012. AT-rich region and repeated sequences: the essential elements of replication origins of bacterial replicons. FEMS Microbiol Rev 36 : 408 434.[PubMed] [CrossRef]
22. Doran KS,, Helinski DR,, Konieczny I . 1999. Host-dependent requirement for specific DnaA boxes for plasmid RK2 replication. Mol Microbiol 33 : 490 498.[PubMed] [CrossRef]
23. Speck C,, Messer W . 2001. Mechanism of origin unwinding: sequential binding of DnaA to double- and single-stranded DNA. EMBO J 20 : 1469 1476.[PubMed] [CrossRef]
24. Konieczny I,, Doran KS,, Helinski DR,, Blasina A . 1997. Role of TrfA and DnaA proteins in origin opening during initiation of DNA replication of the broad host range plasmid RK2. J Biol Chem 272 : 20173 20178.[PubMed] [CrossRef]
25. Wei T,, Bernander R . 1996. Interaction of the IciA protein with AT-rich regions in plasmid replication origins. Nucleic Acids Res 24 : 1865 1872.[PubMed] [CrossRef]
26. Bramhill D,, Kornberg A . 1988. A model for initiation at origins of DNA replication. Cell 54 : 915 918.[PubMed] [CrossRef]
27. Stalker DM,, Kolter R,, Helinski DR . 1979. Nucleotide sequence of the region of an origin of replication of the antibiotic resistance plasmid R6K. Proc Natl Acad Sci USA 76 : 1150 1154.[PubMed] [CrossRef]
28. Chattoraj DK,, Snyder KM,, Abeles AL . 1985. P1 plasmid replication: multiple functions of RepA protein at the origin. Proc Natl Acad Sci USA 82 : 2588 2592.[PubMed] [CrossRef]
29. Abeles AL,, Reaves LD,, Austin SJ . 1990. A single DnaA box is sufficient for initiation from the P1 plasmid origin. J Bacteriol 172 : 4386 4391.[PubMed]
30. Kowalczyk L,, Rajewska M,, Konieczny I . 2005. Positioning and the specific sequence of each 13-mer motif are critical for activity of the plasmid RK2 replication origin. Mol Microbiol 57 : 1439 1449.[PubMed] [CrossRef]
31. Rajewska M,, Kowalczyk L,, Konopa G,, Konieczny I . 2008. Specific mutations within the AT-rich region of a plasmid replication origin affect either origin opening or helicase loading. Proc Natl Acad Sci USA 105 : 11134 11139.[PubMed] [CrossRef]
32. Fekete RA,, Venkova-Canova T,, Park K,, Chattoraj DK . 2006. IHF-dependent activation of P1 plasmid origin by dnaA. Mol Microbiol 62 : 1739 1751.[PubMed] [CrossRef]
33. Stenzel TT,, Patel P,, Bastia D . 1987. The integration host factor of Escherichia coli binds to bent DNA at the origin of replication of the plasmid pSC101. Cell 49 : 709 717.[PubMed] [CrossRef]
34. Filutowicz M,, Appelt K . 1988. The integration host factor of Escherichia coli binds to multiple sites at plasmid R6K gamma origin and is essential for replication. Nucleic Acids Res 16 : 3829 3843.[PubMed] [CrossRef]
35. Shah DS,, Cross MA,, Porter D,, Thomas CM . 1995. Dissection of the core and auxiliary sequences in the vegetative replication origin of promiscuous plasmid RK2. J Mol Biol 254 : 608 622.[PubMed] [CrossRef]
36. Brendler T,, Abeles A,, Austin S . 1991. Critical sequences in the core of the P1 plasmid replication origin. J Bacteriol 173 : 3935 3942.[PubMed]
37. Brendler T,, Abeles A,, Austin S . 1995. A protein that binds to the P1 origin core and the oriC 13mer region in a methylation-specific fashion is the product of the host seqA gene. EMBO J 14 : 4083 4089.[PubMed]
38. Slater S,, Wold S,, Lu M,, Boye E,, Skarstad K,, Kleckner N . 1995. E. coli SeqA protein binds oriC in two different methyl-modulated reactions appropriate to its roles in DNA replication initiation and origin sequestration. Cell 82 : 927 936.[PubMed] [CrossRef]
39. Lu M,, Campbell JL,, Boye E,, Kleckner N . 1994. SeqA: a negative modulator of replication initiation in E. coli . Cell 77 : 413 426.[PubMed] [CrossRef]
40. Hwang DS,, Kornberg A . 1990. A novel protein binds a key origin sequence to block replication of an E. coli minichromosome. Cell 63 : 325 331.[PubMed] [CrossRef]
41. Wu F,, Wu J,, Ehley J,, Filutowicz M . 1996. Preponderance of Fis-binding sites in the R6K gamma origin and the curious effect of the penicillin resistance marker on replication of this origin in the absence of Fis. J Bacteriol 178 : 4965 4974.[PubMed]
42. Giraldo R,, Andreu JM,, Diaz-Orejas R . 1998. Protein domains and conformational changes in the activation of RepA, a DNA replication initiator. EMBO J 17 : 4511 4526.[PubMed] [CrossRef]
43. Komori H,, Matsunaga F,, Higuchi Y,, Ishiai M,, Wada C,, Miki K . 1999. Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6 A resolution. EMBO J 18 : 4597 4607.[PubMed] [CrossRef]
44. Swan MK,, Bastia D,, Davies C . 2006. Crystal structure of pi initiator protein-iteron complex of plasmid R6K: implications for initiation of plasmid DNA replication. Proc Natl Acad Sci USA 103 : 18481 18486.[PubMed] [CrossRef]
45. Giraldo R,, Fernandez-Tornero C,, Evans PR,, Diaz-Orejas R,, Romero A . 2003. A conformational switch between transcriptional repression and replication initiation in the RepA dimerization domain. Nat Struct Biol 10 : 565 571.[PubMed] [CrossRef]
46. Garcia de Viedma D,, Serrano-Lopez A,, Diaz-Orejas R . 1995. Specific binding of the replication protein of plasmid pPS10 to direct and inverted repeats is mediated by an HTH motif. Nucleic Acids Res 23 : 5048 5054.[PubMed] [CrossRef]
47. Matsunaga F,, Kawasaki Y,, Ishiai M,, Nishikawa K,, Yura T,, Wada C . 1995. DNA-binding domain of the RepE initiator protein of mini-F plasmid: involvement of the carboxyl-terminal region. J Bacteriol 177 : 1994 2001.[PubMed]
48. Diaz-Lopez T,, Davila-Fajardo C,, Blaesing F,, Lillo MP,, Giraldo R . 2006. Early events in the binding of the pPS10 replication protein RepA to single iteron and operator DNA sequences. J Mol Biol 364 : 909 920.[PubMed] [CrossRef]
49. Pierechod M,, Nowak A,, Saari A,, Purta E,, Bujnicki JM,, Konieczny I . 2009. Conformation of a plasmid replication initiator protein affects its proteolysis by ClpXP system. Protein Sci 18 : 637 649.[PubMed]
50. Lin J,, Helinski DR . 1992. Analysis of mutations in trfA, the replication initiation gene of the broad-host-range plasmid RK2. J Bacteriol 174 : 4110 4119.[PubMed]
51. Cereghino JL,, Helinski DR,, Toukdarian AE . 1994. Isolation and characterization of DNA-binding mutants of a plasmid replication initiation protein utilizing an in vivo binding assay. Plasmid 31 : 89 99.[PubMed] [CrossRef]
52. Sharma S,, Sathyanarayana BK,, Bird JG,, Hoskins JR,, Lee B,, Wickner S . 2004. Plasmid P1 RepA is homologous to the F plasmid RepE class of initiators. J Biol Chem 279 : 6027 6034.[PubMed] [CrossRef]
53. Giraldo R . 2003. Common domains in the initiators of DNA replication in Bacteria, Archaea and Eukarya: combined structural, functional and phylogenetic perspectives. FEMS Microbiol Rev 26 : 533 554.[PubMed] [CrossRef]
54. Liu J,, Smith CL,, DeRyckere D,, DeAngelis K,, Martin GS,, Berger JM . 2000. Structure and function of Cdc6/Cdc18: implications for origin recognition and checkpoint control. Mol Cell 6 : 637 648.[PubMed] [CrossRef]
55. Giraldo R . 2007. Defined DNA sequences promote the assembly of a bacterial protein into distinct amyloid nanostructures. Proc Natl Acad Sci USA 104 : 17388 17393.[PubMed] [CrossRef]
56. Gasset-Rosa F,, Mate MJ,, Davila-Fajardo C,, Bravo J,, Giraldo R . 2008. Binding of sulphonated indigo derivatives to RepA-WH1 inhibits DNA-induced protein amyloidogenesis. Nucleic Acids Res 36 : 2249 2256.[PubMed] [CrossRef]
57. Fernandez-Tresguerres ME,, de la Espina SM,, Gasset-Rosa F,, Giraldo R . 2010. A DNA-promoted amyloid proteinopathy in Escherichia coli . Mol Microbiol 77 : 1456 1469.[PubMed] [CrossRef]
58. Giraldo R,, Moreno-Diaz de la Espina S,, Fernandez-Tresguerres ME,, Gasset-Rosa F . 2011. RepA-WH1 prionoid: a synthetic amyloid proteinopathy in a minimalist host. Prion 5 : 60 64.[PubMed] [CrossRef]
59. Giraldo R . Amyloid assemblies: protein legos at a crossroads in bottom-up synthetic biology. Chembiochem 11 : 2347 2357.[PubMed] [CrossRef]
60. Kawasaki Y,, Wada C,, Yura T . 1990. Roles of Escherichia coli heat shock proteins DnaK, DnaJ and GrpE in mini-F plasmid replication. Mol Gen Genet 220 : 277 282.[PubMed] [CrossRef]
61. Diaz-Lopez T,, Lages-Gonzalo M,, Serrano-Lopez A,, Alfonso C,, Rivas G,, Diaz-Orejas R,, Giraldo R . 2003. Structural changes in RepA, a plasmid replication initiator, upon binding to origin DNA. J Biol Chem 278 : 18606 18616.[PubMed] [CrossRef]
62. Ingmer H,, Fong EL,, Cohen SN . 1995. Monomer-dimer equilibrium of the pSC101 RepA protein. J Mol Biol 250 : 309 314.[PubMed] [CrossRef]
63. Filutowicz M,, Davis G,, Greener A,, Helinski DR . 1985. Autorepressor properties of the pi-initiation protein encoded by plasmid R6K. Nucleic Acids Res 13 : 103 114.[PubMed] [CrossRef]
64. Landschulz WH,, Johnson PF,, McKnight SL . 1988. The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science 240 : 1759 1764.[PubMed] [CrossRef]
65. Ingmer H,, Cohen SN . 1993. Excess intracellular concentration of the pSC101 RepA protein interferes with both plasmid DNA replication and partitioning. J Bacteriol 175 : 7834 7841.[PubMed]
66. Miron A,, Mukherjee S,, Bastia D . 1992. Activation of distant replication origins in vivo by DNA looping as revealed by a novel mutant form of an initiator protein defective in cooperativity at a distance. EMBO J 11 : 1205 1216.[PubMed]
67. Fernandez-Tresguerres ME,, Martin M,, Garcia de Viedma D,, Giraldo R,, Diaz-Orejas R . 1995. Host growth temperature and a conservative amino acid substitution in the replication protein of pPS10 influence plasmid host range. J Bacteriol 177 : 4377 4384.[PubMed]
68. Shingler V,, Thomas CM . 1984. Analysis of the trfA region of broad host-range plasmid RK2 by transposon mutagenesis and identification of polypeptide products. J Mol Biol 175 : 229 249.[PubMed] [CrossRef]
69. Kornacki JA,, West AH,, Firshein W . 1984. Proteins encoded by the trans-acting replication and maintenance regions of broad host range plasmid RK2. Plasmid 11 : 48 57.[PubMed] [CrossRef]
70. Toukdarian AE,, Helinski DR,, Perri S . 1996. The plasmid RK2 initiation protein binds to the origin of replication as a monomer. J Biol Chem 271 : 7072 7078.[PubMed] [CrossRef]
71. Zhong Z,, Helinski D,, Toukdarian A . 2003. A specific region in the N terminus of a replication initiation protein of plasmid RK2 is required for recruitment of Pseudomonas aeruginosa DnaB helicase to the plasmid origin. J Biol Chem 278 : 45305 45310.[PubMed] [CrossRef]
72. Hughes JM,, Lohman BK,, Deckert GE,, Nichols EP,, Settles M,, Abdo Z,, Top EM . 2012. The role of clonal interference in the evolutionary dynamics of plasmid-host adaptation. MBio 3( 4) : e00077-e00012. [PubMed] [CrossRef]
73. Sota M,, Yano H,, Hughes JM,, Daughdrill GW,, Abdo Z,, Forney LJ,, Top EM . 2010. Shifts in the host range of a promiscuous plasmid through parallel evolution of its replication initiation protein. ISME J 4 : 1568 1580.[PubMed] [CrossRef]
74. Pacek M,, Konopa G,, Konieczny I . 2001. DnaA box sequences as the site for helicase delivery during plasmid RK2 replication initiation in Escherichia coli . J Biol Chem 276 : 23639 23644.[PubMed] [CrossRef]
75. Kim PD,, Banack T,, Lerman DM,, Tracy JC,, Camara JE,, Crooke E,, Oliver D,, Firshein W . 2003. Identification of a novel membrane-associated gene product that suppresses toxicity of a TrfA peptide from plasmid RK2 and its relationship to the DnaA host initiation protein. J Bacteriol 185 : 1817 1824.[PubMed] [CrossRef]
76. Kongsuwan K,, Josh P,, Picault MJ,, Wijffels G,, Dalrymple B . 2006. The plasmid RK2 replication initiator protein (TrfA) binds to the sliding clamp beta subunit of DNA polymerase III: implication for the toxicity of a peptide derived from the amino-terminal portion of 33-kilodalton TrfA. J Bacteriol 188 : 5501 5509.[PubMed] [CrossRef]
77. Sutton MD,, Kaguni JM . 1997. The Escherichia coli dnaA gene: four functional domains. J Mol Biol 274 : 546 561.[PubMed] [CrossRef]
78. Messer W,, Blaesing F,, Majka J,, Nardmann J,, Schaper S,, Schmidt A,, Seitz H,, Speck C,, Tungler D,, Wegrzyn G,, Weigel C,, Welzeck M,, Zakrzewska-Czerwinska J . 1999. Functional domains of DnaA proteins. Biochimie 81 : 819 825.[PubMed] [CrossRef]
79. Erzberger JP,, Pirruccello MM,, Berger JM . 2002. The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation. EMBO J 21 : 4763 4773.[PubMed] [CrossRef]
80. Erzberger JP,, Mott ML,, Berger JM . 2006. Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling. Nat Struct Mol Biol 13 : 676 683.[PubMed] [CrossRef]
81. Duderstadt KE,, Chuang K,, Berger JM . 2011. DNA stretching by bacterial initiators promotes replication origin opening. Nature 478 : 209 213.[PubMed] [CrossRef]
82. Ozaki S,, Kawakami H,, Nakamura K,, Fujikawa N,, Kagawa W,, Park SY,, Yokoyama S,, Kurumizaka H,, Katayama T . 2008. A common mechanism for the ATP-DnaA-dependent formation of open complexes at the replication origin. J Biol Chem 283 : 8351 8362.[PubMed] [CrossRef]
83. DasGupta S,, Mukhopadhyay G,, Papp PP,, Lewis MS,, Chattoraj DK . 1993. Activation of DNA binding by the monomeric form of the P1 replication initiator RepA by heat shock proteins DnaJ and DnaK. J Mol Biol 232 : 23 34.[PubMed] [CrossRef]
84. Wickner S,, Hoskins J,, McKenney K . 1991. Function of DnaJ and DnaK as chaperones in origin-specific DNA binding by RepA. Nature 350 : 165 167.[PubMed] [CrossRef]
85. Kawasaki Y,, Wada C,, Yura T . 1992. Binding of RepE initiator protein to mini-F DNA origin (ori2). Enhancing effects of repE mutations and DnaJ heat shock protein. J Biol Chem 267 : 11520 11524.[PubMed]
86. Manen D,, Upegui-Gonzalez LC,, Caro L . 1992. Monomers and dimers of the RepA protein in plasmid pSC101 replication: domains in RepA. Proc Natl Acad Sci USA 89 : 8923 8927.[PubMed] [CrossRef]
87. Germino J,, Bastia D . 1983. Interaction of the plasmid R6K-encoded replication initiator protein with its binding sites on DNA. Cell 34 : 125 134.[PubMed] [CrossRef]
88. Kelley WL,, Bastia D . 1992. Activation in vivo of the minimal replication origin beta of plasmid R6K requires a small target sequence essential for DNA looping. New Biol 4 : 569 580.[PubMed]
89. Kelley WL,, Patel I,, Bastia D . 1992. Structural and functional analysis of a replication enhancer: separation of the enhancer activity from origin function by mutational dissection of the replication origin gamma of plasmid R6K. Proc Natl Acad Sci USA 89 : 5078 5082.[PubMed] [CrossRef]
90. Lu YB,, Datta HJ,, Bastia D . 1998. Mechanistic studies of initiator-initiator interaction and replication initiation. EMBO J 17 : 5192 5200.[PubMed] [CrossRef]
91. Kruger R,, Filutowicz M . 2000. Dimers of pi protein bind the A+T-rich region of the R6K gamma origin near the leading-strand synthesis start sites: regulatory implications. J Bacteriol 182 : 2461 2467.[PubMed] [CrossRef]
92. Mukherjee S,, Erickson H,, Bastia D . 1988. Enhancer-origin interaction in plasmid R6K involves a DNA loop mediated by initiator protein. Cell 52 : 375 383.[PubMed] [CrossRef]
93. Kawasaki Y,, Matsunaga F,, Kano Y,, Yura T,, Wada C . 1996. The localized melting of mini-F origin by the combined action of the mini-F initiator protein (RepE) and HU and DnaA of Escherichia coli . Mol Gen Genet 253 : 42 49.[PubMed] [CrossRef]
94. Hasunuma K,, Sekiguchi M . 1977. Replication of plasmid pSC101 in Escherichia coli K12: requirement for dnaA function. Mol Gen Genet 154 : 225 230.[PubMed] [CrossRef]
95. Gamas P,, Burger AC,, Churchward G,, Caro L,, Galas D,, Chandler M . 1986. Replication of pSC101: effects of mutations in the E. coli DNA binding protein IHF. Mol Gen Genet 204 : 85 89.[PubMed] [CrossRef]
96. Mukhopadhyay G,, Carr KM,, Kaguni JM,, Chattoraj DK . 1993. Open-complex formation by the host initiator, DnaA, at the origin of P1 plasmid replication. EMBO J 12 : 4547 4554.[PubMed]
97. Durland RH,, Helinski DR . 1987. The sequence encoding the 43-kilodalton trfA protein is required for efficient replication or maintenance of minimal RK2 replicons in Pseudomonas aeruginosa . Plasmid 18 : 164 169.[PubMed] [CrossRef]
98. Fang FC,, Helinski DR . 1991. Broad-host-range properties of plasmid RK2: importance of overlapping genes encoding the plasmid replication initiation protein TrfA. J Bacteriol 173 : 5861 5868.[PubMed]
99. Wegrzyn K,, Witosinska M,, Schweiger P,, Bury K,, Jenal U,, Konieczny I . 2013. RK2 plasmid dynamics in Caulobacter crescentus cells: two modes of DNA replication initiation. Microbiology 159 : 1010 1022.[PubMed] [CrossRef]
100. Maestro B,, Sanz JM,, Faelen M,, Couturier M,, Diaz-Orejas R,, Fernandez-Tresguerres E . 2002. Modulation of pPS10 host range by DnaA. Mol Microbiol 46 : 223 234.[PubMed] [CrossRef]
101. Sharma R,, Kachroo A,, Bastia D . 2001. Mechanistic aspects of DnaA-RepA interaction as revealed by yeast forward and reverse two-hybrid analysis. EMBO J 20 : 4577 4587.[PubMed] [CrossRef]
102. Skarstad K,, Baker TA,, Kornberg A . 1990. Strand separation required for initiation of replication at the chromosomal origin of E. coli is facilitated by a distant RNA-DNA hybrid. EMBO J 9 : 2341 2348.[PubMed]
103. Ryan VT,, Grimwade JE,, Nievera CJ,, Leonard AC . 2002. IHF and HU stimulate assembly of pre-replication complexes at Escherichia coli oriC by two different mechanisms. Mol Microbiol 46 : 113 124.[PubMed] [CrossRef]
104. Hwang DS,, Kornberg A . 1992. Opening of the replication origin of Escherichia coli by DnaA protein with protein HU or IHF. J Biol Chem 267 : 23083 23086.[PubMed]
105. Duderstadt KE,, Mott ML,, Crisona NJ,, Chuang K,, Yang H,, Berger JM . 2010. Origin remodeling and opening in bacteria rely on distinct assembly states of the DnaA initiator. J Biol Chem 285 : 28229 28239.[PubMed] [CrossRef]
106. Schnos M,, Zahn K,, Inman RB,, Blattner FR . 1988. Initiation protein induced helix destabilization at the lambda origin: a prepriming step in DNA replication. Cell 52 : 385 395.[PubMed] [CrossRef]
107. Park K,, Mukhopadhyay S,, Chattoraj DK . 1998. Requirements for and regulation of origin opening of plasmid P1. J Biol Chem 273 : 24906 24911.[PubMed] [CrossRef]
108. Jiang Y,, Pacek M,, Helinski DR,, Konieczny I,, Toukdarian A . 2003. A multifunctional plasmid-encoded replication initiation protein both recruits and positions an active helicase at the replication origin. Proc Natl Acad Sci USA 100 : 8692 8697.[PubMed] [CrossRef]
109. Caspi R,, Pacek M,, Consiglieri G,, Helinski DR,, Toukdarian A,, Konieczny I . 2001. A broad host range replicon with different requirements for replication initiation in three bacterial species. EMBO J 20 : 3262 3271.[PubMed] [CrossRef]
110. Davey MJ,, Fang L,, McInerney P,, Georgescu RE,, O’Donnell M . 2002. The DnaC helicase loader is a dual ATP/ADP switch protein. EMBO J 21 : 3148 3159.[PubMed] [CrossRef]
111. Konieczny I,, Helinski DR . 1997. Helicase delivery and activation by DnaA and TrfA proteins during the initiation of replication of the broad host range plasmid RK2. J Biol Chem 272 : 33312 33318.[PubMed] [CrossRef]
112. Ratnakar PV,, Mohanty BK,, Lobert M,, Bastia D . 1996. The replication initiator protein pi of the plasmid R6K specifically interacts with the host-encoded helicase DnaB. Proc Natl Acad Sci USA 93 : 5522 5526.[PubMed] [CrossRef]
113. Zhong Z,, Helinski D,, Toukdarian A . 2005. Plasmid host-range: restrictions to F replication in Pseudomonas . Plasmid 54 : 48 56.[PubMed] [CrossRef]
114. Datta HJ,, Khatri GS,, Bastia D . 1999. Mechanism of recruitment of DnaB helicase to the replication origin of the plasmid pSC101. Proc Natl Acad Sci USA 96 : 73 78.[PubMed] [CrossRef]
115. Giraldo R,, Diaz R . 1992. Differential binding of wild-type and a mutant RepA protein to oriR sequence suggests a model for the initiation of plasmid R1 replication. J Mol Biol 228 : 787 802.[PubMed] [CrossRef]
116. Wickner SH,, Chattoraj DK . 1987. Replication of mini-P1 plasmid DNA in vitro requires two initiation proteins, encoded by the repA gene of phage P1 and the dnaA gene of Escherichia coli . Proc Natl Acad Sci USA 84 : 3668 3672.[PubMed] [CrossRef]
117. Abhyankar MM,, Zzaman S,, Bastia D . 2003. Reconstitution of R6K DNA replication in vitro using 22 purified proteins. J Biol Chem 278 : 45476 45484.[PubMed] [CrossRef]
118. Zzaman S,, Abhyankar MM,, Bastia D . 2004. Reconstitution of F factor DNA replication in vitro with purified proteins. J Biol Chem 279 : 17404 17410.[PubMed] [CrossRef]
119. Dalrymple BP,, Kongsuwan K,, Wijffels G . 2007. Identification of putative DnaN-binding motifs in plasmid replication initiation proteins. Plasmid 57 : 82 88.[PubMed] [CrossRef]
120. Bloom LB . 2009. Loading clamps for DNA replication and repair. DNA Repair (Amst) 8 : 570 578.[PubMed] [CrossRef]
121. Simonetta KR,, Kazmirski SL,, Goedken ER,, Cantor AJ,, Kelch BA,, McNally R,, Seyedin SN,, Makino DL,, O’Donnell M,, Kuriyan J . 2009. The mechanism of ATP-dependent primer-template recognition by a clamp loader complex. Cell 137 : 659 671.[PubMed] [CrossRef]
122. Park K,, Han E,, Paulsson J,, Chattoraj DK . 2001. Origin pairing (‘handcuffing’) as a mode of negative control of P1 plasmid copy number. EMBO J 20 : 7323 7332.[PubMed] [CrossRef]
123. Zzaman S,, Bastia D . 2005. Oligomeric initiator protein-mediated DNA looping negatively regulates plasmid replication in vitro by preventing origin melting. Mol Cell 20 : 833 843.[PubMed] [CrossRef]
124. Urh M,, Wu J,, Forest K,, Inman RB,, Filutowicz M . 1998. Assemblies of replication initiator protein on symmetric and asymmetric DNA sequences depend on multiple protein oligomerization surfaces. J Mol Biol 283 : 619 631.[PubMed] [CrossRef]
125. Kunnimalaiyaan S,, Inman RB,, Rakowski SA,, Filutowicz M . 2005. Role of pi dimers in coupling (“handcuffing”) of plasmid R6K’s gamma ori iterons. J Bacteriol 187 : 3779 3785.[PubMed] [CrossRef]
126. McEachern MJ,, Bott MA,, Tooker PA,, Helinski DR . 1989. Negative control of plasmid R6K replication: possible role of intermolecular coupling of replication origins. Proc Natl Acad Sci USA 86 : 7942 7946.[PubMed] [CrossRef]
127. Miron A,, Patel I,, Bastia D . 1994. Multiple pathways of copy control of gamma replicon of R6K: mechanisms both dependent on and independent of cooperativity of interaction of tau protein with DNA affect the copy number. Proc Natl Acad Sci USA 91 : 6438 6442.[PubMed] [CrossRef]
128. Das N,, Chattoraj DK . 2004. Origin pairing (‘handcuffing’) and unpairing in the control of P1 plasmid replication. Mol Microbiol 54 : 836 849.[PubMed] [CrossRef]
129. Toukdarian AE,, Helinski DR . 1998. TrfA dimers play a role in copy-number control of RK2 replication. Gene 223 : 205 211.[PubMed] [CrossRef]
130. Paulsson J,, Chattoraj DK . 2006. Origin inactivation in bacterial DNA replication control. Mol Microbiol 61 : 9 15.[PubMed] [CrossRef]
131. Becskei A,, Serrano L . 2000. Engineering stability in gene networks by autoregulation. Nature 405 : 590 593.[PubMed] [CrossRef]
132. Simpson ML,, Cox CD,, Sayler GS . 2003. Frequency domain analysis of noise in autoregulated gene circuits. Proc Natl Acad Sci USA 100 : 4551 4556.[PubMed] [CrossRef]
133. York D,, Filutowicz M . 1993. Autoregulation-deficient mutant of the plasmid R6K-encoded pi protein distinguishes between palindromic and nonpalindromic binding sites. J Biol Chem 268 : 21854 21861.[PubMed]
134. Pabo CO,, Sauer RT . 1992. Transcription factors: structural families and principles of DNA recognition. Annu Rev Biochem 61 : 1053 1095.[PubMed] [CrossRef]
135. Vocke C,, Bastia D . 1985. The replication initiator protein of plasmid pSC101 is a transcriptional repressor of its own cistron. Proc Natl Acad Sci USA 82 : 2252 2256.[PubMed] [CrossRef]
136. Kelley W,, Bastia D . 1985. Replication initiator protein of plasmid R6K autoregulates its own synthesis at the transcriptional step. Proc Natl Acad Sci USA 82 : 2574 2578.[PubMed] [CrossRef]
137. Chattoraj DK,, Ghirlando R,, Park K,, Dibbens JA,, Lewis MS . 1996. Dissociation kinetics of RepA dimers: implications for mechanisms of activation of DNA binding by chaperones. Genes Cells 1 : 189 199.[PubMed] [CrossRef]
138. Nakamura A,, Wada C,, Miki K . 2007. Structural basis for regulation of bifunctional roles in replication initiator protein. Proc Natl Acad Sci USA 104 : 18484 18489.[PubMed] [CrossRef]
139. Konieczny I,, Helinski DR . 1997. The replication initiation protein of the broad-host-range plasmid RK2 is activated by the ClpX chaperone. Proc Natl Acad Sci USA 94 : 14378 14382.[PubMed] [CrossRef]
140. Konieczny I,, Liberek K . 2002. Cooperative action of Escherichia coli ClpB protein and DnaK chaperone in the activation of a replication initiation protein. J Biol Chem 277 : 18483 18488.[PubMed] [CrossRef]
141. Kruklitis R,, Welty DJ,, Nakai H . 1996. ClpX protein of Escherichia coli activates bacteriophage Mu transposase in the strand transfer complex for initiation of Mu DNA synthesis. EMBO J 15 : 935 944.[PubMed]
142. Zzaman S,, Reddy JM,, Bastia D . 2004. The DnaK-DnaJ-GrpE chaperone system activates inert wild type pi initiator protein of R6K into a form active in replication initiation. J Biol Chem 279 : 50886 50894.[PubMed] [CrossRef]
143. Sozhamannan S,, Chattoraj DK . 1993. Heat shock proteins DnaJ, DnaK, and GrpE stimulate P1 plasmid replication by promoting initiator binding to the origin. J Bacteriol 175 : 3546 3555.[PubMed]
144. Wickner S,, Gottesman S,, Skowyra D,, Hoskins J,, McKenney K,, Maurizi MR . 1994. A molecular chaperone, ClpA, functions like DnaK and DnaJ. Proc Natl Acad Sci USA 91 : 12218 12222.[PubMed] [CrossRef]
145. Pak M,, Wickner S . 1997. Mechanism of protein remodeling by ClpA chaperone. Proc Natl Acad Sci USA 94 : 4901 4906.[PubMed] [CrossRef]
146. Dougan DA,, Mogk A,, Bukau B . 2002. Protein folding and degradation in bacteria: to degrade or not to degrade? That is the question. Cell Mol Life Sci 59 : 1607 1616.[PubMed] [CrossRef]
147. Levchenko I,, Luo L,, Baker TA . 1995. Disassembly of the Mu transposase tetramer by the ClpX chaperone. Genes Dev 9 : 2399 2408.[PubMed] [CrossRef]
148. Wojtkowiak D,, Georgopoulos C,, Zylicz M . 1993. Isolation and characterization of ClpX, a new ATP-dependent specificity component of the Clp protease of Escherichia coli . J Biol Chem 268 : 22609 22617.[PubMed]
149. Kubik S,, Wegrzyn K,, Pierechod M,, Konieczny I . 2012. Opposing effects of DNA on proteolysis of a replication initiator. Nucleic Acids Res 40 : 1148 1159.[PubMed] [CrossRef]
150. Tsutsui H,, Fujiyama A,, Murotsu T,, Matsubara K . 1983. Role of nine repeating sequences of the mini-F genome for expression of F-specific incompatibility phenotype and copy number control. J Bacteriol 155 : 337 344.[PubMed]
151. Pal SK,, Chattoraj DK . 1988. P1 plasmid replication: initiator sequestration is inadequate to explain control by initiator-binding sites. J Bacteriol 170 : 3554 3560.[PubMed]
152. Durland RH,, Helinski DR . 1990. Replication of the broad-host-range plasmid RK2: direct measurement of intracellular concentrations of the essential TrfA replication proteins and their effect on plasmid copy number. J Bacteriol 172 : 3849 3858.[PubMed]

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error