Skip to main content

Ti and Ri Plasmids

  • Chapter
Microbial Megaplasmids

Part of the book series: Microbiology Monographs ((MICROMONO,volume 11))

Abstract

Agrobacterium species harboring tumor-inducing (Ti) or hairy root-inducing (Ri) plasmids cause crown gall or hairy root diseases, respectively. These natural plasmids provide the basis for vectors to construct transgenic plants. The plasmids are approximately 200 kbp in size. Complete sequence analysis indicates that the pathogenic plasmids contain gene clusters for DNA replication, virulence, T-DNA, opine utilization, and conjugation. T-DNA genes have lower G + C content, which is presumably suitable for expression in host plant cells. Besides these genes, each plasmid contains a large number of unique genes. Even plasmids of the same opine type differ considerably in gene content and have highly chimeric structures. The plasmids seem to interact with each other and with plasmids of other members of the Rhizobiaceae and are likely to shuffle genes for infection between Ti and Ri plasmids. Plasmid stability genes are discussed, which are important for plasmid evolution and construction of useful strains.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Anand A, Krichevsky A, Schornack S, Lahaye T, Tzfira T et-al. (2007) Arabidopsis VIRE2 INTERACTING PROTEIN2 is required for Agrobacterium T-DNA integration in plants. Plant Cell 19:1695–1708

    Article  CAS  PubMed  Google Scholar 

  • Aoyama T, Takanami M, Oka A (1989) Signal structure for transcriptional activation in the upstream regions of virulence genes on the hairy-root-inducing plasmid A4. Nucleic Acids Res 17:8711–8725

    Article  CAS  PubMed  Google Scholar 

  • Bautista-Zapanta J, Arafat HH, Tanaka K, Samala H, Suzuki K (2007) Variation of 16S-23S internally transcribed spacer sequence and intervening sequence in rDNA among the three major Agrobacterium species. Microbiol Res (doi:10.1016)

    Google Scholar 

  • Cangelosi GA, Ankenbauer RG, Nester EW (1990) Sugars induce the Agrobacterium virulence genes through a periplasmic binding protein and a transmembrane signal protein. Proc Natl Acad Sci USA 87:6708–6712

    Article  CAS  PubMed  Google Scholar 

  • Christie PJ (2004a) The Agrobacterium Ti plasmids. In: Funnell BE, Phillips GJ (eds) Plasmid biology, ASM Press, Washington, DC, pp 455–472

    Google Scholar 

  • Christie PJ (2004b) Type IV secretion: the Agrobacterium VirB/D4 and related conjugation systems. Biochim Biophys Acta 1694:219–234

    Article  CAS  Google Scholar 

  • Citovsky V, Zupan J, Warnick D, Zambryski P (1992) Nuclear localization of Agrobacterium VirE2 protein in plant cells. Science 256:1802–1805

    Article  CAS  PubMed  Google Scholar 

  • Deng W, Chen L, Peng WT, Liang X, Sekiguchi S et-al. (1999) VirE1 is a specific molecular chaperone for the exported single-stranded-DNA-binding protein VirE2 in Agrobacterium Mol Microbiol 31:1795–1807

    Article  CAS  Google Scholar 

  • Dessaux Y, Petit A, Teme J (1992) Opines in Agrobacterium biology. In: Verma DPS (ed) Molecular signals in plant-microbe communications, CRC Press, Boca Raton, FL, pp 109–136

    Google Scholar 

  • Dunoyer P, Himber C, Voinnet O (2006) Induction, suppression and requirement of RNA silencing pathways in virulent Agrobacterium tumefaciens infections. Nat Genet 38:258–263

    Article  CAS  PubMed  Google Scholar 

  • Fullner KJ, Lara JC, Nester EW (1996) Pilus assembly by Agrobacterium T-DNA transfer genes. Science 273:1107–1109

    Article  CAS  PubMed  Google Scholar 

  • Gelvin SB (2003) Agrobacterium-mediated plant transformation: the biology behind the “gene-jockeying” tool. Microbiol Mol Biol Rev 67:16–37

    Article  CAS  PubMed  Google Scholar 

  • González V, Santamaría RI, Bustos P, Hernández-González I, Medrano-Soto A et-al. (2006) The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons. Proc Natl Acad Sci USA 103:3834–3839

    Article  PubMed  Google Scholar 

  • Goodner B, Hinkle G, Gattung S, Miller N, Blanchard M et-al. (2001) Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 294:2323–2328

    Article  CAS  PubMed  Google Scholar 

  • Hansen G, Tempé J, Brevet J (1992) A T-DNA transfer stimulator sequence in the vicinity of the right border of pRi8196. Plant Mol Biol 20:113–122

    Article  CAS  PubMed  Google Scholar 

  • Hattori Y, Iwata K, Suzuki K, Uraji M, Ohta Net-al. (2001) Sequence characterization of the vir region of a nopaline type Ti plasmid, pTi-SAKURA. Genes Genet Syst 76:121–130

    Article  CAS  PubMed  Google Scholar 

  • Hattori Y, Uraji M, Suzuki, K, Ohta N, Iwata K et-al. (2000) Gene list on a plant tumor-inducing plasmid, pTi-SAKURA in Agrobacterium tumefaciens MAFF301001. DNA Res 7:371–380

    Article  CAS  PubMed  Google Scholar 

  • Hodges LD, Cuperus J, Ream W (2004) Agrobacterium rhizogenes GALLS protein substitutes for Agrobacterium tumefaciens single-stranded DNA-binding protein VirE2. J Bacteriol 186:3065–3077

    Article  CAS  PubMed  Google Scholar 

  • Hodges LD, Vergunst AC, Neal-McKinney J, den Dulk-Ras A, Moyer DM et-al. (2006) Agrobacterium rhizogenes GALLS protein contains domains for ATP binding, nuclear localization, and type IV secretion. J Bacteriol 188:8222–8230

    Article  CAS  PubMed  Google Scholar 

  • Hooykaas PJJ, den Dulk-Ras H, Ooms G, Schilperoort RA (1980) Interactions between octopine and nopaline plasmids in Agrobacterium tumefaciens J Bacteriol 143:1295–1306

    CAS  Google Scholar 

  • Hooykaas, PJJ, den Dulk-Ras H, Schilperoort RA (1988) The Agrobacterium tumefaciens T-DNA gene 6b is an onc gene. Plant Mol Biol 11:791–794

    Article  CAS  Google Scholar 

  • Hooykaas PJJ, Klapwijk PM, Nuti MP, Schilperoort RA, Rorsch A (1977) Transfer of the Agrobacterium tumefaciens Ti plasmid to avirulent Agrobacteria and to Rhizobium ex planta. J Gen Microbiol 98:477–484

    Google Scholar 

  • Howard EA, Zupan JR, Citovsky V, Zambryski PC (1992) The VirD2 protein of A. tumefaciens contains a C-terminal bipartite nuclear localization signal: implications for nuclear uptake of DNA in plant cells. Cell 68:109–118

    Article  CAS  PubMed  Google Scholar 

  • Kado CI (2002) Negative transcriptional regulation of virulence and oncogenes of the Ti plasmid by bearing a conserved C2H2-zinc finger motif. Plasmid 48:179–185

    Article  CAS  PubMed  Google Scholar 

  • Kalogeraki VS, Zhu J, Eberhard A, Madsen EL, Winans SC (1999) The phenolic vir gene inducer ferulic acid is O-demethylated by the VirH2 protein of an Agrobacterium tumefaciens Ti plas-mid. Mol Microbiol 34:512–522

    Article  CAS  PubMed  Google Scholar 

  • Kaneko T, Nakamura Y, Sato S, Asamizu E, Kato T et-al. (2000) Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti DNA Res 7:331–338

    Article  CAS  Google Scholar 

  • Kaneko T, Nakamura Y, Sato S, Minamisawa K, Uchiumi T et-al. (2002) Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res 9:189–197

    Article  PubMed  Google Scholar 

  • Kitakura S, Fujita T, Ueno Y, Terakura S, Wabiko H, Machida Y (2002) The protein encoded by oncogene 6b from Agrobacterium tumefaciens interacts with a nuclear protein of tobacco. Plant Cell 14:451–463

    Article  CAS  PubMed  Google Scholar 

  • Klein DT, Klein RM (1953) Transmittance of tumor-inducing ability to avirulent crown-gall and related bacteria. J Bacteriol 66:220–228

    CAS  PubMed  Google Scholar 

  • Lacroix B, Tzfira T, Vainstein A, Citovsky V (2006) A case of promiscuity: Agrobacterium's endless hunt for new partners. Trends Genet 22:29–37

    Article  CAS  PubMed  Google Scholar 

  • Li PL, Farrand SK (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 182:179–188

    Article  CAS  PubMed  Google Scholar 

  • Mankin SL, Hill DS, Olhoft PM, Toren E, Wenck AR et-al. (2007) Disarming and sequencing of Agrobacterium rhizogenes strain K599 (NCPPB2659) plasmid pRi2659. In Vitro Cell Dev Biol Plant 43:521–535

    Article  CAS  Google Scholar 

  • McCullen CA, Binns AN (2006) Agrobacterium tumefaciens and plant cell interactions and activities required for interkingdom macromolecular transfer. Annu Rev Cell Dev Biol 22:101–127

    Article  CAS  PubMed  Google Scholar 

  • Moriguchi K, Maeda Y, Satou M, Handayani NSN, Kataoka M et-al. (2001) The complete nucle-otide 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 307:771–784

    Article  CAS  Google Scholar 

  • Moriguchi K, Maeda Y, Satou M, Kataoka M, Tanaka N, Yoshida K (2000) Analysis of unique variable region of a plant root inducing plasmid, pRi1724, by the construction of its physical map and library. DNA Res 7:157–163

    Article  CAS  PubMed  Google Scholar 

  • Moriuchi H, Okamoto C, Nishihama R, Yamashita I, Machida Y, Tanaka N (2004) Nuclear localization and interaction of RolB with plant 14–3–3 proteins correlates with induction of adventitious roots by the oncogene rolB Plant J 38:260–275

    Article  CAS  Google Scholar 

  • Nair GR, Liu Z, Binns AN (2003) Reexamining the role of the accessory plasmid pAtC58 in the virulence of Agrobacterium tumefaciens strain C58. Plant Physiol 133:989–999

    Article  CAS  PubMed  Google Scholar 

  • Pan SQ, Jin S, Boulton MI, Hawes M, Gordon MP, Nester EW (1995) An Agrobacterium virulence factor encoded by a Ti plasmid gene or a chromosomal gene is required for T-DNA transfer into plants. Mol Microbiol 17:259–269

    Article  CAS  PubMed  Google Scholar 

  • Paulus F, Otten L (1993) Functional and mutated agrocinopine synthase genes on octopine T-DNAs. Mol Plant Microbe Interact 6:393–402

    CAS  PubMed  Google Scholar 

  • Peralta EG, Hellmiss R, Ream W (1986) Overdrive, a T-DNA transmission enhancer on the A. tumefaciens tumour-inducing plasmid. EMBO J 5:1137–1142

    CAS  PubMed  Google Scholar 

  • Roitsch T, Wang H, Jin SG, Nester EW (1990) Mutational analysis of the VirG protein, a tran-scriptional activator of Agrobacterium tumefaciens virulence genes. J Bacteriol 172:6054–6060

    CAS  PubMed  Google Scholar 

  • Scheiffele P, Pansegrau W, Lanka E (1995) Initiation of Agrobacterium tumefaciens T-DNA processing. Purified proteins VirD1 and VirD2 catalyze site- and strand-specific cleavage of superhelical T-border DNA in vitro J Biol Chem 270:1269–1276

    CAS  Google Scholar 

  • Schrammeijer B, Hemelaar J, Hooykaas PJJ (1998) The presence and characterization of a virF gene on Agrobacterium vitis Ti plasmids. Mol Plant Microb Interact 11:429–433

    Article  CAS  Google Scholar 

  • Schröder G, Lanka E (2005) The mating pair formation system of conjugative plasmids — A versatile secretion machinery for transfer of proteins and DNA. Plasmid 54:1–25

    Article  PubMed  Google Scholar 

  • Shimoda N, Toyoda-Yamamoto A, Aoki S, Machida Y (1993) Genetic evidence for an interaction between the VirA sensor protein and the ChvE sugar-binding protein of Agrobacterium J Biol Chem 268:26552–26558

    CAS  Google Scholar 

  • Stachel SE, Zambryski PC (1986) virA and virG control the plant-induced activation of the T-DNA transfer process of A tumefaciens. Cell 46:325–333

    Article  CAS  PubMed  Google Scholar 

  • Sundberg C, Meek L, Carroll K, Das A, Ream W (1996) VirE1 protein mediates export of the single-stranded DNA-binding protein VirE2 from Agrobacterium tumefaciens into plant cells. J Bacteriol 178:1207–1212

    CAS  PubMed  Google Scholar 

  • Suzuki K, Hattori Y, Uraji M, Ohta N, Iwata K et-al. (2000) Complete nucleotide sequence of a plant tumor-inducing Ti plasmid. Gene 242:331–336

    Article  CAS  PubMed  Google Scholar 

  • Suzuki K, Iwata K, Yoshida K (2001) Genome analysis of Agrobacterium tumefaciens: construction of physical maps for linear and circular chromosomal DNAs, determination of copy number ratio and mapping of chromosomal virulence genes. DNA Res 8:141–152

    Article  CAS  PubMed  Google Scholar 

  • Suzuki K, Uraji M, De Costa D, Hattori Y, Ohta N et-al. (2004) An overview of the agrobacterial genome. Endocytobiosis Cell Res 15:143–150

    Google Scholar 

  • Szegedi E, Czako M, Otten L (1996) Further evidence that vitopine-type pTis of Agrobacterium vitis represent a novel group of Ti plasmids. Mol Plant-Microbe Interact 9:139–143

    CAS  Google Scholar 

  • Tabata S, Hooykaas PJ, Oka A (1989) Sequence determination and characterization of the replicator region in the tumor-inducing plasmid pTiB6S3. J Bacteriol 171:1665–1672

    CAS  PubMed  Google Scholar 

  • Tanaka K, Urbanczyk H, Matsui H, Sawada H, Suzuki K (2006) Construction of physical map and mapping of chromosomal virulence genes of the biovar 3 Agrobacterium (Rhizobium vitis) strain K-Ag-1. Genes Genet Syst 81:373–380

    Article  CAS  PubMed  Google Scholar 

  • Terakura S, Ueno Y, Tagami H, Kitakura S, Machida C et-al. (2007) An oncoprotein from the plant pathogen Agrobacterium has histone chaperone-like activity. Plant Cell 19:2855–2865

    Article  CAS  PubMed  Google Scholar 

  • Toro N, Datta A, Carmi OA, Young C, Prusti RK, Nester EW (1989) The Agrobacterium tumefa-ciens virC1 gene product binds to overdrive, a T-DNA transfer enhancer. J Bacteriol 171:6845–6849

    CAS  PubMed  Google Scholar 

  • Tzfira T, Vaidya M, Citovsky V (2001) VIP1, an Arabidopsis protein that interacts with Agrobacterium VirE2, is involved in VirE2 nuclear import and Agrobacterium infectivity. EMBO J 20:3596–3607

    Article  CAS  PubMed  Google Scholar 

  • Tzfira T, Vaidya M, Citovsky V (2004) Involvement of targeted proteolysis in plant genetic transformation by Agrobacterium Nature 431:87–92

    Article  CAS  Google Scholar 

  • Uraji M, Suzuki K, Yoshida K (2002) A novel plasmid curing method using incompatibility of plant pathogenic Ti plasmids in Agrobacterium tumefaciens Genes Genet Syst 77:1–9

    Article  CAS  Google Scholar 

  • Urbanczyk H, Suzuki K, Yoshida K, Kondo K (2003) Physical and gene maps of Agrobacterium biovar 2 strains and their relationship to biovar 1 chromosomes. Microbiology 149:3035–3042

    Article  CAS  PubMed  Google Scholar 

  • Velázquez E, Peix A, Zurdo-Piñeiro JL, Palomo JL, Mateos PF et-al. (2005) The coexistence of symbiosis and pathogenicity-determining genes in Rhizobium rhizogenes strains enables them to induce nodules and tumors or hairy roots in plants. Mol Plant Microbe Interact 18:1325–1332

    Article  PubMed  Google Scholar 

  • van Haaren MJ, Sedee NJ, Schilperoort RA, Hooykaas PJ (1987) Overdrive is a T-region transfer enhancer which stimulates T-strand production in Agrobacterium tumefaciens Nucleic Acids Res 15:8983–8997

    Article  Google Scholar 

  • Wabiko H, Minemura M (1996) Exogenous phytohormone-independent growth and regeneration of tobacco plants transgenic for the 6b gene of Agrobacterium tumefaciens AKE10. Plant Physiol 112:939–951

    Article  CAS  PubMed  Google Scholar 

  • White CE, Winans SC (2007) Cell-cell communication in the plant pathogen Agrobacterium tumefaciens Philos Trans R Soc Lond B Biol Sci 362:1135–1148

    Article  CAS  Google Scholar 

  • Wirawan IG, Kang HW, Kojima M (1993) Isolation and characterization of a new chromosomal virulence gene of Agrobacterium tumefaciens J Bacteriol 175:3208–3212

    CAS  Google Scholar 

  • Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP et-al. (2001) The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294:2317–2323

    Article  CAS  PubMed  Google Scholar 

  • Yadav NS, Vanderlayden J, Bennett DR, Barnes WM, Chilton MD (1982) Short direct repeats flank the T-DNA on a nopaline Ti plasmid. Proc Natl Acad Sci USA 79:6322–6326

    Article  CAS  PubMed  Google Scholar 

  • Yamamoto S, Uraji M, Tanaka K, Moriguchi K, Suzuki K (2007) Identification of pTi-SAKURA DNA region conferring enhancement of plasmid incompatibility and stability. Genes Genet Syst 82:197–206

    Article  CAS  PubMed  Google Scholar 

  • Yoshida K, Uraji M, Hattori Y, Moriguchi K, Suzuki K et-al. (2003) The first complete sequencing analyses of plant tumor-inducing plasmid Ti and root-inducing plasmid Ri indicate their chi-meric structures and unique evolutional relationships. Recent Res Devel Plant Cell Physiol 1:53–61

    CAS  Google Scholar 

  • Yoshida K, Uraji M, Hattori Y, Moriguchi K, Suzuki K et-al. (2004) Genome structure and evolution of giant plant pathogenic plasmids in Agrobacterium tumefaciens and Agrobacterium rhizogenes Endocytobiosis Cell Res 15:371–378

    Google Scholar 

  • Young JM, Kuykendall LD, Martínez-Romero E, Kerr A, Sawada H (2003) Classification and nomenclature of Agrobacterium and Rhizobium Int J Syst Evol Microbiol 53:1689–1695

    Article  CAS  Google Scholar 

  • Zambryski P, Tempe J, Schell J (1989) Transfer and function of T-DNA genes from Agrobacterium Ti and Ri plasmids in plants. Cell 56:193–201

    Article  CAS  PubMed  Google Scholar 

  • Zhu JP, Oger PM, Schrammeijer B, Hooykaas PJJ, Farrand SK, Winans SC (2000) The basis of crown gall tumorigenesis. J Bacteriol 182:3885–3895

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Suzuki, K., Tanaka, K., Yamamoto, S., Kiyokawa, K., Moriguchi, K., Yoshida, K. (2009). Ti and Ri Plasmids. In: Schwartz, E. (eds) Microbial Megaplasmids. Microbiology Monographs, vol 11. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-85467-8_6

Download citation

Publish with us

Policies and ethics