Chapter 25 : Evolution and Population Genetics of Bacterial Plasmids

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

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in

Evolution and Population Genetics of Bacterial Plasmids, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817732/9781555812652_Chap25-1.gif /docserver/preview/fulltext/10.1128/9781555817732/9781555812652_Chap25-2.gif


The distinction between plasmids and chromosomes has been blurred by the discovery of megaplasmids and small chromosomes through the use of pulsed-field gel electrophoresis. This chapter considers why plasmids have survived at all if they are not essential to their host and how they have evolved. Population genetics seeks to explain the evolution of species by considering the competition between individuals in a population and the effect that genetic differences have on this competition. An insight into the process can be gained from comparison of so-called operons of many self-transmissible bacterial plasmids of gram-negative bacteria. The function may be inserted diametrically opposite or it may occur close to the replicon. It may be, for example, that a location close to the region allows the genes to function better because partitioning of early replicated DNA is easier than for late replicated DNA. The selective pressure that promotes plasmid evolution does not work just at the level of competition between bacteria. It is widely accepted that to allow drift to occur requires gene duplication. However, for any other than an absolutely unit copy number plasmid, effective gene duplication is a way of life. The circumstances that place a premium on such evolution involve constantly changing physical/chemical and biological environments inherent to most microbial communities.

Citation: Thomas C. 2004. Evolution and Population Genetics of Bacterial Plasmids, p 509-528. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch25

Key Concept Ranking

Mobile Genetic Elements
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of Figure 1
Figure 1

Evolution of microbial genomes. A number of authors have speculated on how bacterial genomes have evolved, for example, references 87, 106. The idea that the original genome may have consisted of multiple, relatively small, self-replicating molecules propagating beneficial traits fits with the diversity being discovered within the sequences of bacterial genomes. Integration would initially generate hybrids. Resolution to leave the bulk of the genes joined to the lower-copy-number and more stable replicon would be favored, the higher-copy-number replicon becoming free to develop as a plasmid. The process would repeat itself to increase the efficient transmission of genetic information

Citation: Thomas C. 2004. Evolution and Population Genetics of Bacterial Plasmids, p 509-528. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch25
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

The benefits of plasmid transfer. Conjugative transfer genes could benefit the host particularly when integrated into the chromosome. However, the genes themselves would not evolve so fast as if they spread to new hosts, which would be much more likely to occur if they were joined to a plasmid.

Citation: Thomas C. 2004. Evolution and Population Genetics of Bacterial Plasmids, p 509-528. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch25
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
Figure 3

Variations in niche properties in space and time. A niche is often defined by more than one parameter. For example, the presence of an inhibitory substance may be constant while a second one, such as carbon source, may vary, perhaps in a cyclic way. Initially bacterium BI is well adapted, being both resistant (gene Rl) and able to utilize the carbon source due to catabolic genes CI. If resistance to the inhibitory substance is on a mobile element, then this can transfer to a new host (B2) that may be better able to use the second carbon source due to genes C2. Thus the mobile element provides the constant genetic trait in the niche.

Citation: Thomas C. 2004. Evolution and Population Genetics of Bacterial Plasmids, p 509-528. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch25
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4
Figure 4

Rearrangement of genes by excision and integration. (A) Examples of related operons are shown indicating related genes. The examples are selected to show how the same set of genes can appear in different, circular permutations of the same basic order. (B) A proposed explanation for the circular permutation, based on illegitimate excision to form a circle, followed by reintegration in a new location by a similar process, but with the site of integration lying between a different pair of genes. Each step is known to be possible, and the comparative order of genes in the operons provides the evidence that they have occurred.

Citation: Thomas C. 2004. Evolution and Population Genetics of Bacterial Plasmids, p 509-528. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch25
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 5
Figure 5

Clustering of maintenance functions. A plasmid acquires a new stability function that provides an advantage in its present context. Once a plasmid has acquired a new beneficial trait, derivatives that have lost that trait will be disfavored relative to ones that retain it. Random deletions will tend to bring these maintenance functions closer together, and once the plasmid sectors are unequal, insertions will tend to occur in the longer arm. Occasionally the replicon will loop out on a small circle as in Fig. 1 , but only if it is able to carry with it the additional stability functions of the parent plasmid will it outcompete its larger parent.

Citation: Thomas C. 2004. Evolution and Population Genetics of Bacterial Plasmids, p 509-528. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch25
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 6
Figure 6

Interplasmid competition driving plasmid evolution. (A) Cointegrate plasmids and evolution. Pairs of incompatible plasmids A1/A2 and B1/B2 compete equally between themselves. However, any cointegrate plasmid between an A and a B plasmid will immediately have an advantage over either parent, because it will have a backup replication system. (B) The drive to acquire multiple postsegregational killing systems. Two plasmids carrying the same postsegregational killing system will effectively neutralize the advantage of carrying such a system for the other plasmid, because loss of one plasmid will not result in loss of the antidote for the killer. Any plasmid that acquires a second postsegregational killing system will regain the advantage.

Citation: Thomas C. 2004. Evolution and Population Genetics of Bacterial Plasmids, p 509-528. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch25
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Alt-Morbe, J.,, J. L. Stryker,, C. Fuqua,, P. L. Li,, S. K. Farrand,, and S. C. Winans. 1996. The conjugal transfer system of Agrobacterium tumefaciens octopine-type Ti plasmids is closely related to the transfer system of an IncP plasmid and distantly related to Ti plasmid vir genes. J. Bacteriol. 178:42484257.
2. Archdeacon, J.,, N. Bouhouche,, F. O'Connell,, and C. I. Kado. 2000. A single amino acid substitution beyond the C2H2-zinc finger in Ros derepresses virulence and T-DNA genes in Agrobacterium tumefaciens. FEMS Microbiol. Lett. 187:175178.
3. Berger, B. R.,, and P. J. Christie. 1993. The Agrobacterium tumefaciens virB4 gene product is an essential virulence protein requiring an intact nucleoside triphosphate-binding domain. J. Bacteriol. 175:17231734.
4. Berger, B. R.,, and P. J. Christie. 1994. Genetic complementation analysis of the Agrobacterium tumefaciens virB operon: virB2 through virB11 are essential virulence genes. J . Bacteriol. 176:36463660.
5. Binns, A.,, C. Beaupre,, and E. Dale. 1995. Inhibition of VirB-mediated transfer of diverse substrates from Agrobacterium tumefaciens by the IncQ plasmid RSF1010. J. Bacteriol. 177:48904899.
6. Binns, A. N. 2002. T-DNA of Agrobacterium tumefaciens: 25 years and counting. Trends Plant Sci. 7:231233.
7. Binns, A. N.,, and P. Castantino,. 1998. The Agrobacterium oncogenes, p. 251266. In H. P. Spaink,, A. Kondorosi,, and P. J. J. Hooykaas (ed.), The Rhizobiaceae. Kluwer Academic Publishers, Dordrecht, The Netherlands.
8. Binns, A. N.,, and V. R. Howitz. 1994. The genetic and chemical basis of recognition in the Agrobacterium: plant interaction. Curr. Top. Microbiol. Immunol. 192:119138.
9. Bohne, J.,, A. Yim,, and A. N. Binns. 1998. The Ti plasmid increases the efficiency of Agrobacterium tumefaciens as a recipient in virB-mediated conjugal transfer of an IncQ plasmid. Proc. Natl. Acad. Sci. USA 95:80578062.
10. Braun, A. C. 1947. Thermal studies on tumor inception in the crown gall disease. Am. J. Bot. 30:674677.
11. Bundock, P.,, H. van Attikum,, A. den Dulk-Ras,, and P. J. Hooykaas. 2002. Insertional mutagenesis in yeasts using T-DNA from Agrobacterium tumefaciens. Yeast 19:529536.
12. Burns, D. L. 1999. Biochemistry of type IV secretion. Curr. Opin. Microbiol. 2:2529.
13. Cabezon, E.,, J. I. Sastre,, and F. de la Cruz. 1997. Genetic evidence of a coupling role for the TraG protein family in bacterial conjugation. Mol. Gen. Genet. 254:400406.
14. Cangelosi, G. A.,, R. G. Ankenbauer,, and E. W. Nester. 1990. Sugars induce the Agrobacterium virulence genes through a periplasmic binding protein and a transmembrane signal protein. Proc. Natl. Acad. Sci. USA 87:67086712.
15. Censini, S.,, M. Stein,, and A. Covacci. 2001. Cellular responses induced after contact with Helicobacter pylori Curr. Opin. Microbiol. 4:4146.
16. Chen, L.,, C. M. Li,, and E. W. Nester. 2000. Transferred DNA (T-DNA)-associated proteins of Agrobacterium tumefaciens are exported independently of virB. Proc. Natl. Acad. Sci. USA 97:75457550.
17. Chilton, M. D.,, M. H. Drummond,, D. J. Merio,, D. Sciaky,, A. L. Montoya,, M. P. Gordon,, and E. W. Nester. 1977. Stable incorporation of plasmid DNA into higher plant cells: the molecular basis of crown gall tumorigenesis. Cell 11:263271.
18. Christie, P. J., 2000. Agrobacterium and plant cell transformation, p. 86103. In J. Lederberg (ed.), Encyclopedia of Microbiology, 2nd ed., vol. 1. Academic Press, San Diego, Calif..
19. Christie, P. J. 1997. The Agrobacterium tumefaciens T-complex transport apparatus: a paradigm for a new family of multifunctional transporters in eubacteria. J. Bacteriol. 179:30853094.
20. Christie, P. J. 2001. Type IV secretion: intercellular transfer of macromolecules by systems ancestrally-related to conjugation machines. Mol. Microbiol. 40:294305.
21. Christie, P. J.,, J. E. Ward,, S. C Winans,, and E. W. Nester. 1988. The Agrobacterium tumefaciens virE2 gene product is a single-stranded-DNA-binding protein that associates with T-DNA. J. Bacteriol. 170:26592667.
22. Christie, P. J.,, J. E. Ward,, S. C. Winans,, and E. W. Nester. 1989. A gene required for transfer of T-DNA to plants encodes an ATPase with autophosphorylating activity. Proc. Natl. Acad. Sci. USA 86:96779681.
23. Citovsky, V.,, and P. Zambryski. 1993. Transport of nucleic acids through membrane channels: snaking through small holes. Annu. Rev. Microbiol. 47:167197.
24. Covacci, A.,, J. L. Telford,, G. Del Giudice,, J. Parsonnet,, and R. Rappuoli. 1999. Helicobacter pylori virulence and genetic geography. Science 284:13281333.
25. Das, A.,, and Y.-H. Xie. 2000. The Agrobacterium T-DNA transport pore proteins VirB8, VirB9, and VirB10 interact with one another. J. Bacteriol. 182:758763.
26. Deng, W.,, L. Chen,, W.-T. Peng,, X. Liang,, S. Sekiguchi,, M. P. Gordon,, and E. W. Nester. 1999. VirE1 is a specific molecular chaperone for the exported single-stranded-DNA-binding protein VirE2 in Agrobacterium. Mol. Microbiol. 31:17951807.
27. Dessaux, Y.,, A. Petit,, S. K. Farrand,, and P. J. Murphy,. 1998. Opines and opine-like molecules involved in plant-Rhizobiaceae interactions, p. 173197. In H. P. Spaink,, A. Kondorosi,, and P. J. J. Hooykaas (ed.), The Rhizobiaceae. Kluwer Academic Publishers, Dordrecht, The Netherlands.
28. Ding, Z.,, Z. Zhao,, S. Jakubowski,, A. Krishnamohan,, W. Margolin,, and P. J. Christie. 2001. A novel cytology-based, two-hybrid screen for bacteria applied to protein-protein interaction studies of a type IV secretion system. J. Bacteriol. 184:55725582.
29. Eisenbrandt, R.,, M. Kalkum,, E. M. Lai,, R. Lurz,, C. I. Kado,, and E. Lanka. 1999. Conjugative pili of IncP plasmids, and the Ti plasmid T pilus are composed of cyclic subunits. J. Biol. Chem. 274:2254822555.
30. Eisenbrandt, R.,, M. Kalkum,, R. Lurz,, and E. Lanka. 2000. Maturation of IncP pilin precursors resembles the catalytic dyad-like mechanism of leader peptidases J. Bacteriol. 182:67516761.
31. Farrand, S. K.,, I. Hwang,, and D. M. Cook. 1996. The tra region of the nopaline-type Ti plasmid is a chimera with elements related to the transfer systems of RSF1010, RP4, and F. J. Bacteriol. 178:42334247.
32. Fullner, K. J.,, J. C. Lara,, and E. W. Nester. 1996. Pilus assembly by Agrobacterium T-DNA transfer genes. Science 273:11071109.
33. Fuqua, C.,, M. Burbea,, and S. C. Winans. 1995. Activity of the Agrobacterium Ti plasmid conjugal transfer regulator TraR is inhibited by the product of the traM gene. J. Bacteriol. 177:13671373.
34. Fuqua, W. C., S. C. Winans,, and E. P. Grccnbcrg. 1996. Census and consensus in bacterial ecosystems: the LuxR-LuxI family of quorum-sensing transcriptional regulators. Ann. Rev. Microbiol. 50:727751.
35. Gomis-Ruth, F. X.,, G. Moncalian,, R. Perez-Luque,, A. Gonzalez,, E. Cabezon,, F. de la Cruz,, and M. Coll. 2001. The bacterial conjugation protein TrwB resembles ring helicases and F1-ATPase. Nature 409:637641.
36. Goodncr, B.,, G. Hinkle,, S. Gattung,, N. Miller,, M. Blanchard,, B. Qurollo,, B. S. Goldman,, Y. Cao,, M. Askenazi,, C. Halling,, L. Mullin,, K. Houmiel,, J . Gordon,, M. Vaudin,, O. lartchouk,, A. Epp,, F. Liu,, C. Wollam,, M. Allinger,, D. Doughty,, C. Scott,, C. Lappas,, B. Markelz,, C. Flanagan,, C. Crowell,, J. Gurson,, C. Lomo,, C. Sear,, G. Strub,, C. Cielo,, and S. Slater. 2001. Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 294:23232328.
37. Gray, J.,, J. Wang,, and S. B. Gelvin. 1992. Mutation of the miaA gene of Agrobacterium tumefaciens results in reduced vir gene expression. J. Bacteriol. 174:10861098.
38. Hamilton, C. M.,, H. Lee,, P.-L. Li,, D. M. Cook,, K. R. Piper,, S. Beck von Bodman,, E. Lanka,, W. Ream,, and S. K. Farrand. 2000. TraG from RIM and TraG and VirD4 from Ti plasmids confer relaxosome specificity to the conjugal transfer system of pTiC58. J. Bacteriol. 182:15411548.
39. Hapfelmeier, S.,, N. Domke,, P. C. Zambryski,, and C. Baron. 2000. VirB6 is required for stabilization of VirB5 and VirB3 and formation of VirB7 homodimers in Agrobacterium tumefaciens. J. Bacteriol. 182:45054511.
40. Hwang, I.,, D. M. Cook,, and S. K. Farrand. 1995. A new regulatory element modulates homoserine lactone-mediated autoinduction of Ti plasmid conjugal transfer. J. Bacteriol. 177:449458.
41. Hwang, I.,, A. J . Smyth,, Z. Q. Luo,, and S. K. Farrand. 1999. Modulating quorum sensing by antiactivation: TraM interacts with TraR to inhibit activation of Ti plasmid conjugal transfer genes. Mol. Microbiol 34:282294.
41a.. Jakubowski, S. J.,, V. Krishnamoorthy,, and P. J. Christie. 2003. Agrobacterium tumefaciens VirB6 protein participates in formation of VirB7 and VirB9 complexes required for type IV secretion. J. Bacteriol. 185:28672878.
42. Jones, A. L.,, K. Shirasu,, and C. I. Kado. 1994. The product of virB4 gene of Agrobacterium tumefaciens promotes accumulation of VirB3 protein. J. Bacteriol. 176:52255261.
43. Kalogeraki, V. S.,, and S. C. Winans. 1995. The octopine-type Ti plasmid pTiA6 of Agrobacterium tumefaciens contains a gene homologous to the chromosomal virulence gene acvB. J. Bacteriol. 177:892897.
44. Kalogeraki, V. S.,, and S. C. Winans. 1998. Wound-released chemical signals may elicit multiple responses from an Agrobacterium tumefaciens strain containing an octopine-type Ti plasmid. J. Bacteriol. 180:56605667.
45. Kalogeraki, V. S.,, J. Zhu,, A. Eberhard,, E. L. Madsen,, and S. C. Winans. 1999. The phenolic Wr gene inducer ferulic acid is O-demethylated by the VirH2 protein of an Agrobacterium tumefaciens Ti plasmid. Mol Microbiol. 34:512522.
46. Kalogeraki, V. S.,, J. Zhu,, J. L. Stryker,, and S. C. Winans. 2000. The right end of the vir region of an octopine-type Ti plasmid contains four new members of the vir regulon that are not essential for pathogenesis. J. Bacteriol. 182:17741778.
47. Krall, L.,, U. Wiedemann,, G. Unsin,, S. Weiss,, N. Domke,, and C. Baron. 2002. Detergent extraction identifies different VirB protein subassemblies of the type IV secretion machinery in the membranes of Agrobacterium tumefaciens. Proc. Natl. Acad. Sci. USA 99:1140511410.
48. Krause, S.,, M. Barcena,, W. Panseqrau,, R. Lurz,, J. Carazo,, and E. Lanka. 2000. Sequence related protein export NTPases encoded by the conjugative transfer region of RP4 and by the cag pathogenicity island of Helicobacter pylori share similar hexameric ring structures. Proc. Natl. Acad. Sci. USA 97:30673072.
49. Kumar, R. B.,, and A. Das. 2002. Polar location and functional domains of the Agrobacterium tumefaciens DNA transfer protein VirD4. Mol. Microbiol. 43:15231532.
50. Kumar, R. B.,, Y. H. Xie,, and A. Das. 2000. Subcellular localization of the Agrobacterium tumefaciens T-DNA transport pore proteins: VirB8 is essential for the assembly of the transport pore. Mol. Microbiol. 36:608617.
51. Kunik, T.,, T. Tzfira,, Y. Kapulnik,, Y. Gafni,, C. Dingwall,, and V. Citovsky. 2001. Genetic transformation of HeLa cells by Agrobacterium. Proc. Natl. Acad. Sci. USA 98:18711876.
52. Lai, E. M., and C. I. Kado. 1998. Processed VirB2 is the major subunit of the promiscuous pilus of Agrobacterium tumefaciens.J. Bacteriol. 180:27112717.
53. Lai, E. M.,, O. Chesnokova,, L. M. Banta,, and C. I. Kado. 2000. Genetic and environmental factors affecting T-pilin export and T-pilus biogenesis in relation to flagellation of Agrobacterium tumefaciens. J. Bacteriol. 182:37053716.
54. Lai, E. M.,, and C. I. Kado. 2000. The T-pilus of Agrobacterium tumefaciens. Trends Microbiol. 8:361369,
55. Lee, K.,, M. W. Dudley,, K. M. Hess,, D. G. Lynn,, R. D. Joerger,, and A. N. Binns. 1992. Mechanism of activation of Agrobacterium virulence genes: identification of phenol-binding proteins. Proc. Natl. Acad. Sci. USA 89:86668670.
56. Lee, Y. W.,, S. Jin,, W. S. Sim,, and E. W. Nester. 1996. The sensing of plant signal molecules by Agrobacterium: genetic evidence for direct recognition of phenolic inducers by the VirA protein. Gene 179:8388.
57. Lessl, M.,, and E. Lanka. 1994. Common mechanisms in bacterial conjugation and Ti-mediated T-DNA transfer to plant cells. Cell 77:321324.
58. Li, P.,, I. Hwang,, H. Miyagi,, H. True,, and S. Farrand. 1999. Essential components of the Ti plasmid trb system, a type IV macromolecular transporter. J. Bacteriol. 181:50335041.
59. Li, P. L.,, and S. K. Farrand. 2000. The replicator of the nopaline-type Ti plasmid pTiC58 is a member of the repABC family and is influenced by the TraR-dependent quorum-sensing regulatory system. J. Bacteriol. 182:179188.
60. Llosa, M.,, F. X . Gomis-Ruth,, M. Coll,, and F. de la Cruz. 2002. Bacterial conjugation: a two-step mechanism for DNA transport. Mol. Microbiol. 45:18.
61. Lohrke, S. M.,, H. Yang,, and S. Jin. 2001. Reconsritution of acetosyringone-mediated Agrobacterium tumefaciens virulence gene expression in the heterologous host Escherichia coli. J. Bacteriol. 183:37043711.
62. Luo, Z. Q.,, Y. Qin,, and S. K. Farrand. 2000. The antiactivator TraM interferes with the autoinducer-dependent binding of TraR to DNA by interacting with the C-terminal region of the quorum-sensing activator. J. Biol. Chem. 275:77137722.
63. Moriguchi, K.,, Y. Maeda,, M. Satou,, N. S. Hardayani,, M. Kataoka,, N. Tanaka,, and K. Yoshida. 2001. The complete nucleotide sequence of a plant root-inducing (Ri) plasmid indicates its chimeric structure and evolutionary relationship between tumor-inducing (Ti) and symbiotic (Sym) plasmids in Rhizobiaceae. J. Mol. Biol. 307:771784.
64. Oger, P.,, K. S. Kim,, R. L. Sackett,, K. R. Piper,, and S. K. Farrand. 1998. Octopine-type Ti plasmids code for a mannopine-inducible dominant-negative allele of traR. the quorum-sensing activator that regulates Ti plasmid conjugal transfer. Mol. Microbiol. 27:277288.
65. Otten, L.,, J. Canaday,, J. C. Gerard,, P. Fournier,, P. Crouzet,, and F. Paulus. 1992. Evolution of agrobacteria and their Ti plasmids—a review. Mol. Plant Microbe Interact. 5:279287.
66. Otten, L.,, J. Y. Salomone,, A. Helfer,, J. Schmidt,, P. Hammann,, and P. De Ruffray, 1999. Sequence and functional analysis of the left-hand part of the T-region from the nopaline-type Ti plasmid, pTiC58. Plant Mol. Biol. 41:765776.
67. Pansegrau, W.,, F. Schoumacher,, B. Hohn,, and E. Lanka. 1993. Site-specific cleavage and joining of single-stranded DNA by VirD2 protein of Agrobacterium tumefaciens Ti plasmids: analogy to bacterial conjugation. Proc. Natl. Acad. Sci. USA 90:1153811542.
68. Pantoja, M.,, L. Chen,, Y. Chen,, and E. W. Nester. 2002. Agrobacterium type IV secretion is a two step process in which export substrates associate with the virulence protein VirJ in the periplasm. Mol. Microbiol. 45:13251335.
69. Peng, W. T.,, L. M. Banta,, T. C. Charles,, and E. W. Nester. 2001. The cbvH locus of Agrobacterium encodes a homologue of an elongation factor involved in protein synthesis. J. Bacteriol. 183:3645.
70. Piper, K. R.,, S. Beck Von Bodman,, I. Hwang,, and S. K. Farrand. 1999. Hierarchical gene regulatory systems arising from fortuitous gene associations: controlling quorum sensing by the opine regulon in Agrobacterium. Mol. Microbiol. 32:10771089.
71. Planet, P. J.,, S. C. Kachlany,, R. DeSalle,, and D. H. Figurski. 2001. Phylogeny of genes for secretion NTPases: identification of the widespread tadA subfamily and development of a diagnostic key for gene classification. Proc. Natl. Acad. Sci. USA 98:25032508.
72. Potrykus, I. 2001. Golden rice and beyond. Plant Physiol. 125:11571161.
73. Qin, Y.,, Z. Q. Luo,, A. J. Smyth,, P. Gao,, S. Beck von Bodman,, and S. K. Farrand. 2000. Quorum-sensing signal binding results in dimerization of TraR and its release from membranes into the cytoplasm. EMBO J. 19:52125221.
74. Regensburg, T. A.,, and P. J . Hooykaas. 1993. Transgenic N. glauca plants expressing bacterial virulence gene virF are converted into hosts for nopaline strains of A. tumefaciens. Nature 363:6971.
75. Sagulenko, V.,, E. Sagulenko,, S. Jakubowski,, E. Spudich,, and P. J. Christie. 2001. VirB7 lipoprotein is exocellular and associates with the Agrobacterium tumefaciens T-pilus. J. Bacteriol. 183:36423651.
76. Sagulenko, Y.,, V. Sagulenko,, J. Chen,, and P. J. Christie. 2001. Role of Agrobacterium VirB11 ATPase in T-pilus assembly and substrate selection. J. Bacteriol. 183:58135825.
77. Schmidt-Eisenlohr, H.,, D. N.,, A. C.,, G. Wanner,, P. C. Zambryski,, and C. Baron. 1999. Vir proteins stabilize VirB5 and mediate its association with the T pilus of Agrobacterium tumefaciens. J. Bacteriol. 181:74857492.
78. Schrammeijer, B.,, E. Risseeuw,, W. Pansegrau,, T. J. Regensburg-Tuink,, W. L. Crosby,, and P. J. Hooykaas. 2001. Interaction of the virulence protein VirF of Agrobacterium tumefaciens with plant homologs of the yeast Skp1 protein. Curr. Biol. 11:258262.
79. Schroder, G.,, S. Krause,, E., L, Zechner,, B. Traxler,, H. J. Yeo,, R. Lurz,, G. Waksman,, and E. Lanka. 2002. TraG-like proteins of DNA transfer systems and of the Helicobacter pylori type IV secretion system: inner membrane gate for exported substrates? J. Bacteriol. 184:27672779.
80. Sexton, J. A.,, and J. P. Vogel. 2002. Type IVB secretion by intracellular pathogens. Traffic 3:178185.
81. Shirasu, K.,, N. Z. Koukolikova,, B. Hohn,, and C. I. Kado. 1994. An inner-membrane-associated virulence protein essential for T-DNA transfer from Agrobacterium tumefaciens to plants exhibits ATPase activity and similarities to conjugative transfer genes. Mol. Microbiol. 11:581588.
82. Shurvinton, C. E.,, and W. Ream. 1991. Stimulation of Agrobacterium tumefaciens T-DNA transfer by overdrive depends on a flanking sequence but not on helical position with respect to the border repeat. J. Bacteriol. 173:55585563.
83. Simone, M.,, C. A. McCullen,, L. E. Stahl,, and A. N. Binns. 2001. The carboxy-terminus of VirE2 from Agrobacterium tumefaciens is required for its transport to host cells by the virB-encoded type IV transport system. Mol. Microbiol. 41:12831293.
84. Smeets, L. C.,, and J. G. Kusters. 2002. Natural transformation in Helicobacter pylori: DNA transport in an unexpected way. Trends Microbiol. 10:159162.
85. Spudich, G. M.,, D. Fernandez,, X.-R. Zhou,, and P.J. Christie. 1996. Intermolecular disulfide bonds stabilize VirB7 homodimers and VirB7/VirB9 heterodimers during biogenesis of the Agrobacterium tumefaciens T-complex transport apparatus. Proc. Natl. Acad. Sci. USA 93:75127517.
86. Stahl, L. E.,, A. Jacobs,, and A. N. Binns. 1998. The conjugal intermediate of plasmid RSF1010 inhibits Agrobacterium tumefaciens virulence and VirB-dependent export of VirE2. J. Bacteriol. 180:39333939.
87. Stein, M.,, R. Rappuoli,, and A. Covacci. 2000. Tyrosine phosphorylation of the Helicobacter pylori CagA antigen after cag-driven host cell translocation. Proc. Natl. Acad. Sci. USA 97:12631268.
88. Sundberg, C. D.,, and W. Ream. 1999. The Agrobacterium tumefaciens chaperone-like protein, VirE1, interacts with VirE2 at domains required for single-stranded DNA binding and cooperative interaction. J. Bacteriol. 181:68506855.
89. Suzuki, K.,, Y. Hattori,, M. Uraji,, N. Ohta,, K. Iwata,, K. Murata,, A. Kato,, and K. Yoshida. 2000. Complete nucleotide sequence of a plant tumor-inducing Ti plasmid. Gene 242:331336.
90. Toro, N.,, A. Datta,, O. A. Carmi,, C. Young,, R. K. Prusti,, and E. W. Nester. 1989. The Agrobacterium tumefaciens virCl gene product binds to overdrive, a T-DNA transfer enhancer. J. Bacteriol. 171:68456849.
91. Tzfira, T.,, and V. Citovsky. 2002. Partners-in-infection: host proteins involved in the transformation of plant cells by Agrobacterium. Trends Cell Biol. 12:121129.
92. van Haaren, M. J.,, N. J. Sedee,, R. A. Schilperoort,, and P. J. Hooykaas. 1987. Overdrive is a T-region transfer enhancer which stimulates T-strand production in Agrobacterium tumefaciens. Nucleic Acids Res. 15:89838997.
93. Vergunst, A. C.,, B. Schrammeijer,, A. den Dulk-Ras,, C. M. de Vlaam,, T. J. Regensburg-Tuink,, and P. J. Hooykaas. 2000. VirB/D4-dependent protein translocation from Agrobacterium into plant cells. Science 290:979982.
94. Wang, L.,, J. D. Helmann,, and S. C. Winans. 1992. The A. tumefaciens transcriptional activator OccR causes a bend at a target promoter, which is partially relaxed by a plant tumor metabolite. Cell 69:659667.
95. Wang, Y.,, R. Gao,, and D. G. Lynn. 2002. Ratcheting up vir gene expression in Agrobacterium tumefaciens: coiled coils in histidtne kinase signal transduction. Chembiochem. 3:311317.
96. Ward, D. V.,, and P. C Zambryski. 2001. The six functions of Agrobacterium VirE2. Proc. Natl. Acad. Sci. USA 98:385386.
97. Ward, D. V.,, O. Draper,, J ., R, Zupan,, and P. C. Zambryski. 2002. Inaugural article: Peptide linkage mapping of the Agrobacterium tumefaciens vir-encoded type IV secretion system reveals protein subassemblies. Proc. Natl. Acad. Sci. USA 99:11493114500.
98. Wilkins, B. M.,, and A. T. Thomas. 2000. DNA-independent transport of plasmid primase protein between bacteria by the 11 conjugation system. Mol. Microbiol. 38:650657.
99. Winans, S. C, 1992. Two-way chemical signalling in Agrobacterium-plant interactions. Microbiol. Rev. 56:1231.
100. Winans, S. C.,, D. L. Burns,, and P. J. Christie. 1996. Adaptation of a conjugal transfer system for the export of pathogenic macromolecules. Trends Microbiol. 4:6468.
101. Wood, D. W.,, J. C Setubal,, R. Kaul,, D. E. Monks,, J. P. Kitajima,, V. K. Okura,, Y. Zhou,, L. Chen,, G. E. Wood,, N. F. AlmeidaJr.,, L. Woo,, Y. Chen,, I. T. Paulsen,, J. A. Eisen,, P. D. Karp,, D. BoveeSr.,, P. Chapman,, J. Clendenning,, G. Deatherage,, W. Gillet,, C. Grant,, T. Kutyavin,, R. Levy,, M. J. Li,, E. McClelland,, A. Palmieri,, C. Raymond,, G. Rouse,, C. Saenphimmachak,, Z. Wu,, P. Romero,, D. Gordon,, S. Zhang,, H. Yoo,, Y. Tao,, P. Biddle,, M. Jung,, W. Krespan,, M. Perry,, B. Gordon-Kamm,, L. Liao,, S. Kim,, C. Hendrick,, Z. Y. Zhao,, M. Dolan,, F. Chumley,, S. V. Tingey,, J. F. Tomb,, M. P. Gordon,, M. V. Olson,, and E. W. Nester. 2001. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294:23172323.
102. Yeo, H.-J.,, S. N. Savvidcs,, A. B. Herr,, E. Lanka,, and G. Waksman. 2000. Crystal structure of the hexameric traffic ATPase of the Helicobacter pylori type IV system. Mol. Cell. 6:14611472.
103. Zhang, H. B.,, L. H. Wang,, and L. H. Zhang. 2002. Genetic control of quorum-sensing signal turnover in Agrobacterium tumefaciens. Proc. Natl. Acad. Sci. USA 99:46384643.
104. Zhang, L.,, P. J. Murphy,, A. Kerr,, and M. E. Tate. 1993. Agrobacterium conjugation and gene regulation by N-acyl-L-homoserine lactones. Nature 362:446448.
105. Zhang, R. G.,, T. Pappas,, J. L. Brace,, P. C. Miller,, T. Oulmassov,, J. M. Molyneaux,, J. C. Anderson,, J. K. Bashkin,, S. C. Winans,, and A. Joachimiak. 2002. Structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA. Nature 417:971974.
106. Zhao, Z.,, E. Sagulenko,, Z. Ding,, and P. J . Christie. 2001. Activities of virE1 and the VirE1 secretion chaperone in export of the multifunctional VirE2 effector via an Agrobacterium type IVsecretion pathway. J. Bacteriol. 183:38553865.
107. Zhou, X.-R.,, and P. J. Christie. 1999. Mutagenesis of Agrobacterium VirE2 single-stranded DNA-binding protein identifies regions required for self-association and interaction with VirE1 and a permissive site for hybrid protein construction. J. Bacteriol. 181:43424352.
108. Zhu, J.,, P. M. Oger,, B. Schrammeijer,, P. J. Hooykaas,, S. K. Farrand,, and S. C. Winans. 2000. The bases of crown gall tumorigenesis. J. Bacteriol. 182:38853895.
109. Zhu, J.,, and S. C. Winans. 1998. Activity of the quorum-sensing regulator TraR of Agrobacterium tumefaciens is inhibited by a truncated, dominant defective TraR-like protein. Mol. Microbiol. 27:289297.
110. Zhu, J .,,and S. C. Winans. 1999. Autoinducer binding by the quorum-sensing regulator TraR increases affinity for target promoters in vitro and decreases TraR turnover rates in whole cells. Proc. Natl. Acad. Sci. USA 96:48324837.

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