Abstract
The Ti plasmid of the Agrobacterium vitis nopaline-type strain AB4 was subcloned and mapped. Several regions of the 157 kb Ti plasmid are similar or identical to parts of the A. vitis octopine/cucumopine (o/c)-type Ti plasmids, and other regions are homologous to the nopaline-type Ti plasmid pTiC58. The T-DNA of pTiAB4 is a chimaeric structure of recent origin: the left part is 99.2% homologous to the left part of the TA-DNA of the o/c-type Ti plasmids, while the right part is 97.1 % homologous to the right part of an unusual nopaline T-DNA recently identified in strain 82.139, a biotype Il strain from wild cherry. The 3′ non-coding regions of the ipt genes from pTiAB4 and pTi82.139 are different from those of other ipt genes and contain a 62 by fragment derived from the coding sequence of an ipt gene of unknown origin. A comparison of different ipt gene sequences indicates that the corresponding 62 by sequence within the coding region of the AB4 ipt gene has been modified during the course of its evolution, apparently by sequence transfer from the 62 by sequence in the 3′ non-coding region. In pTi82.139 the original coding region of the ipt gene has remained largely unmodified. The pTiAB4 6b gene differs from its pTi82.139 counterpart by the lack of a 12 by repeat in the 3′ part of the coding sequence. This leads to the loss of four glutamic acid residues from a series of ten. In spite of these differences, the ipt and 6b genes of pTiAB4 are functional. Our results provide new insight into the evolution of Agrobacterium Ti plasmids and confirm the remarkable plasticity of these genetic elements. Possible implications for the study of bacterial phylogeny are discussed.
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Barker RF, Idler KB, Thompson DV, Kemp JD (1983) Nucleotide sequence of the T-region from Agrobacterium tumefaciens octopine Ti plasmid pTi15955. Plant Mol Biol 2:335–350
Bevan M (1985) Binary Agrobacterium vectors for plant transformation. Nucleic Acids Res 84:8711–8721
Blundy KS, White J, Firmin JL, Hepburn AG (1986) Characterisation of the T-region of the SAP-type Ti-plasmid pTiAT181: identification of a gene involved in SAP synthesis. Mol Gen Genet 202:62–67
Bonnard G, Vincent F, Otten L (1989a) Sequence and distribution of IS866, a novel T-region associated insertion sequence from Agrobacterium tumefaciens. Plasmid 22:70–81
Bonnard G, Tinland B, Paulus F, Szegedi E, Otten L (1989b) Nucleotide sequence, evolutionary origin and biological role of a rearranged cytokinin gene isolated from a wide host range biotype III Agrobacterium strain. Mol Gen Genet 216:428–438
Bonnard G, Vincent F, Otten L (1991) Sequence of Agrobacterium tumefaciens biotype III auxin genes. Plant Mol Biol 16:733–738
Burr TJ, Katz BH (1983) Isolation of biovar 3 from grapevine galls and sap and from vineyard soil. Phytopathology 73:163–165
Burr TJ, Katz BH, Bishop AL (1987) Populations of Agrobacterium in vineyard and nonvineyard soils and grape roots in vineyards and nurseries. Plant Dis 71:617–620
Canaday J, Gérard J-C, Crouzet P, Otten L (1992) Organization and functional analysis of three T-DNAs from the vitopine Ti plasmid pTiS4. Mol Gen Genet 235:292–303
Currier TC, Nester EW (1976) Isolation of covalently closed circular DNA of high molecular weight from bacteria. Anal Biochem 76:431–441
Dahl GA, Gyon P, Petit A, Tempé J (1983) Silver nitrate-positive opines in Crown Gall tumors. Plant Sci Lett 32:193–203
Depicker A, de Wilde M, de Vos G, de Vos R, van Montagu M, Schell J (1980) Molecular cloning of overlapping segments of the nopaline Ti-plasmid pTiC58 as a means to restriction endonuclease mapping. Plasmid 3:193–211
Dessaux Y, Petit A, Tempé J (1992) Opines in Agrobacterium biology. In: Verma DPS (ed) Molecular signals in plant-microbe communications. CRC Press, Boca Raton, Fla., p 109–136
Devereux J, Haeberli P, Marquess P (1987) The program manual for the sequence analysis software package of the genetics computer group. Nucleic Acids Res 12:387–395
Drevet C, Brasileiro ACM, Jouanin L (1994) Oncogene arrangement in a shooty strain of Agrobacterium tumefaciens. Plant Mol Biol 25:83–90
Engler G, Depicker A, Maenhaut R, Villarroel R, van Montagu M, Schell J (1981) Physical mapping of DNA base sequence homologies between an octopine and a nopaline Ti plasmid of Agrobacterium tumefaciens. J Mol Biol 152:183–208
Fournier P, de Ruffray P, Otten L (1994) Natural instability of Agrobacterium vitis Ti plasmid due to unusual duplication of a 2.3 kb DNA fragment. Mol Plant-Microb Interact 7:164–172
Gérard J-C, Canaday J, Szegedi E, Delasalle H, Otten L (1992) Physical map of the vitopine Ti plasmid pTiS4. Plasmid 28:146–156
Gielen J, De Beuckeleer M, Seurinck J, Deboeck F, De Greve H, Lemmers M, van Montagu M, Schell J (1984) The complete nucleotide sequence of the TL DNA of the Agrobacterium tumefaciens plasmid pTiAch5. EMBO J 3:835–846
Goldberg SB, Flick JS, Rogers SG (1984) Nucleotide sequence of the tmr locus of the Agrobacterium tumefaciens pTiT37 T-DNA. Nucleic Acids Res 12:4665–4677
Hayman GT, Farrand SK (1990) Agrobacterium plasmids encode structurally and functionally different loci for catabolism of agrocinopine-type opines. Mol Gen Genet 223:465–473
Hooykaas P, Schilperoort R (1992) Agrobacterium and plant genetic engineering. Plant Mol Biol 19:15–38
Huss B, Bonnard G, Otten L (1989) Isolation and functional analysis of a set of auxin genes with low root-inducing activity from an Agrobacterium tumefaciens biotype III strain. Plant Mol Biol 12:271–283
Hynes MF, Simon R, Puhler A (1985) The development of plasmid-free strains of Agrobacterium tumefaciens by using incompatibility with a Rhizobium meliloti plasmid to eliminate pAtC58. Plasmid 13:99–105
Janssens D, Kersters K, De Ley J (1983) The catabolism of 3-ketolactose in Agrobacterium. Sys Appl Microbiol 4:155–168
Kado CI (1991) Molecular mechanisms of Crown Gall tumorigenesis. Crit Rev Plant Sci 10:1–32
Kerr A, Panagopoulos CG (1977) Biotypes of Agrobacterium radiobacter var. tumefaciens and their biological control. Z Phytopathol 90:172–179
Knauf VC, Panagopoulos CG, Nester EW (1982) Genetic factors controlling the host range of Agrobacterium tumefaciens. Phytopathology 72:1545–1549
Knauf VC, Panagopoulos CG, Nester EW (1983) Comparison of Ti plasmids from three different biotypes of Agrobacterium tumefaciens isolated from grapevines. J Bacteriol 153:1535–1542
Knauf VC, Yanofsky M, Montoya A, Nester EW (1984) Physical and functional map of an Agrobacterium tumefaciens plasmid that confers a narrow host range. J Bacteriol 160:564–568
Michel MF, Brasileiro ACM, Depierreux C, Otten L, Delmotte F, Jouanin L (1990) Identification of different Agrobacterium strains isolated from the same forest nursery. Appl Environ Microbiol 56:3537–3545
Ooms G, Hooykaas PJJ, van Veen RJM, van Beelen P, Regensburg-Tuïnk AJG, Schilperoort RA (1982) Octopine Ti-plasmid deletion mutants of Agrobacterium tumefaciens with emphasis on the right side of the T-region. Plasmid 7:15–29
Ophel K, Kerr A (1990) Agrobacterium vitis sp. nov. Strains of Agrobacterium biovar 3 from grapevines. Int J Syst Bacteriol 40:236–241
Otten L, Schilperoort R (1978) A rapid micro scale method for the detection of lysopine and nopaline dehydrogenase activities. Biochim Biophys Acta 527:497–500
Otten L, van Nuenen M (1993) Natural instability of o/c Ti plasmids of clonal origin. Microb Releases 2:91–96
Otten L, Canaday J, Gerard J-C, Crouzet P, Paulus F (1992) Evolution of Agrobacteria and their Ti plasmids. A review. Mol Plant-Microb Interact 5:279–287
Otten L, Gérard J-C, de Ruffray P (1993) The Ti plasmid from the wide host range Agrobacterium vitis strain Tm4: map and homology with other Ti plasmids. Plasmid 29:154–159
Panagopoulos CG, Psallidas PG (1973) Characteristics of Greek isolates of Agrobacterium tumefaciens (EF Smith and Townsend). Conn J Appl Bacteriol 36:233–240
Paulus F, Otten L (1993) Functional and mutated agrocinopine synthase genes on octopine T-DNAs. Mol Plant-Microb Interact 6:393–402
Paulus F, Huss B, Bonnard G, Ridé M, Szegedi E, Tempé J, Petit A, Otten L (1989a) Molecular systematics of biotype III Ti plasmids of Agrobacterium tumefaciens. Mol Plant-Microb Interact 2:64–74
Paulus F, Ridé M, Otten L (1989b) Distribution of two Agrobacterium tumefaciens insertion elements in natural isolates: evidence for stable association between Ti plasmids and their bacterial hosts. Mol Gen Genet 219:145–152
Paulus F, Canaday J, Vincent F, Bonnard G, Kares C, Otten L (1991) Sequence of the iaa and ipt region of different Agrobacterium tumefaciens biotype III octopine strains: reconstruction of octopine Ti plasmid evolution. Plant Mol Biol 16:601–614
Perry KL, Kado CI (1982) Characteristics of Ti plasmids from broad-host range and ecologically specific biotype 2 and 3 strains of Agrobacterium tumefaciens. J Bacteriol 151:343–350
Petit A, Tempé J, Kerr A, Holsters M, van Montagu M, Schell J (1978) Substrate induction of conjugative activity of Agrobacterium tumefaciens Ti plasmids. Nature 271:570–571
Rao RN, Rogers SG (1979) Plasmid pKC7: a vector containing ten restriction endonuclease sites suitable for cloning DNA segments. Gene 7:79–82
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, second edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
Schulz T (1992) Untersuchungen zur Epidemiologie und Phylogenie van Agrobacterium vitis sp. nov., dem Erreger der Mauke an Weinreben. Ph. D. Thesis, University of Kaiserslautern, Germany
Schulz T, Lorenz D, Eichhorn KW, Otten L (1993) Amplification of different marker sequences for identification of Agrobacterium vitis strains. Vitis 32:179–182
Strabala TJ, Bednarek SY, Bertoni G, Amasino RM (1989) Isolation and characterization of an ipt gene from the Ti plasmid Bo542. Mol Gen Genet 216:388–394
Szegedi E (1985) Host range and specific L(+)-tartrate utilization of biotype 3 Agrobacterium tumefaciens. Acta Phytopathol Acad Sci Hung 20:17–22
Szegedi E, Csako M, Otten L, Koncz Cs (1988) Opines in crown gall tumours induced by biotype 3 isolates of Agrobacterium tumefaciens. Physiol Mol Plant Pathol 32:237–247
Szegedi E, Otten L, Czako M (1992) Diverse types of tartrate plasmids in Agrobacterium tumefaciens biotype III strains. Mol Plant-Microb Interact 5:435–438
Thomashow MF, Knauf VC, Nester EW (1981) Relationship between the limited and wide host range octopine-type Ti plasmids of Agrobacterium tumefaciens. J Bacteriol 146:484–493
Tinland B, Huss B, Paulus F, Bonnard G, Otten L (1989) Agrobacterium tumefaciens 6b genes are strain-specific and affect the activity of auxin as well as cytokinin genes. Mol Gen Genet 219:217–224
Vanderleyden J, Desair J, De Meirsman C, Michiels K, van Gool A, Jen G, Chilton M-D (1986) Nucleotide sequence of the T-DNA region encoding transcripts 6a and 6b of the pTiT37 nopaline Ti plasmid. Plant Mol Biol 7:33–41
Van Nuenen M, de Ruffray P, Otten L (1993) Rapid divergence of Agrobacterium vitis octopine-cucumopine Ti plasmids from a recent common ancestor. Mol Gen Genet 240:49–57
Velten J, Willmitzer L, Leemans J, Ellis J, Deblaere R, van Montagu M, Schell J (1983) TR genes involved in agropine production; In: Pühler A (ed) Molecular genetics of the bacteria-plant interaction. Springer-Verlag, Berlin-Heidelberg, pp 303–312
Von Lintig J, Zanker H, Schröder J (1991) Positive regulators of the opine-inducible promoters in the nopaline and octopine catabolism regions of Ti plasmids. Mol Plant Microb Interact 4:370–378
Wabiko H, Kagaya M, Kodama I, Masuda K, Kodama Y, Yamamoto H, Shibano Y, Sano H (1989) Isolation and characterization of diverse nopaline type Ti plasmids of Agrobacterium tumefaciens from Japan. Arch Microbiol 152:119–124
Willmitzer L, Dhaese P, Schreier PH, Schmalenbach W, van Montagu M, Schell J (1983) Size, location and polarity of T-DNA-encoded transcripts in nopaline crown gall tumors; common transcripts in octopine and nopaline tumors. Cell 32:1045–1056
Winans SC (1992) Two-way chemical signaling in Agrobacterium-plant interactions. Microbiol Rev 56:12–31
Yamamoto K, Kusano K, Takahashi NK, Yoshikura H, Kobayashi I (1992) Gene conversion in the Escherichia coli RecF pathway: a successive half crossing-over model. Mol Gen Genet 234:1–13
Yanisch-Perron C, Vieira J, Messing J (1985) Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103–119
Yanofsky M, Lowe B, Montoya A, Rubin R, Krul W, Gordon M, Nester E (1985a) Molecular and genetic factors controlling host range in Agrobacterium tumefaciens. Mol Gen Genet 201:237–246
Yanofsky M, Montoya A, Knauf VC, Lowe B, Gordon M, Nester EW (1985b) Limited-host-range plasmids of Agrobacterium tumefaciens: molecular and genetic analysis of transferred DNA. J Bacteriol 163:341–348
Zambryski P (1992) Chronicles from the Agrobacterium-plant cell DNA transfer story. Annu Rev Plant Mol Biol 43:465–490
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Communicated by A. Kondorosi
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Otten, L., De Ruffray, P. Agrobacterium vitis nopaline Ti plasmid pTiAB4: relationship to other Ti plasmids and T-DNA structure. Molec. Gen. Genet. 245, 493–505 (1994). https://doi.org/10.1007/BF00302262
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DOI: https://doi.org/10.1007/BF00302262