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Otten L. T-DNA regions from 350 Agrobacterium genomes: maps and phylogeny. PLANT MOLECULAR BIOLOGY 2021; 106:239-258. [PMID: 33826062 DOI: 10.1007/s11103-021-01140-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/12/2021] [Indexed: 05/27/2023]
Abstract
Analysis of 350 Agrobacterium wgs sequences reveals complex evolutionary history of T-DNA regions Virulent Agrobacterium strains transfer one or more plasmid DNA fragments to plant cells during a well-characterized transformation process. The transferred DNA sequences (T-DNA regions) are delimited by 25 nucleotide long conserved border sequences. Until recently, relatively few T-DNA regions were known. However, due to increased whole genome sequencing efforts, about 400 Agrobacterium sequences have now become available, 350 of which contain T-DNA regions. Detailed analysis identified 92 different T-DNA regions and several new T-DNA genes. T-DNA regions can be divided into three groups. I. Typical Agrobacterium rhizogenes T-DNA regions with rol genes. II. A large group of T-DNA regions with iaa and ipt genes, which can be further subdivided into seven subgroups. III. A small group of unusual T-DNA regions. The evolutionary relation between the T-DNA regions could not be completely elucidated, because of the lack of evolutionary intermediates. Several clusters of highly related structures suggest that evolution of T-DNA regions proceeds by slow, progressive evolution of gene sequences, accompanied by rapid changes in overall structure, due to recombination between T-DNA regions of different origins, and insertion of bacterial insertion sequences (IS). Divergence values for T-DNA genes suggest that they were recruited at different times in evolution. An attempt was made to link T-DNA region evolution to plasmid evolution. The present study provides a solid basis for further studies on T-DNA region diversity and evolution.
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Affiliation(s)
- Léon Otten
- Institut de Biologie Moléculaire des Plantes, 12 Rue du Général Zimmer, 67084, Strasbourg, France.
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Complete Genome Sequence of Allorhizobium vitis Strain K306, the Causal Agent of Grapevine Crown Gall. Microbiol Resour Announc 2020; 9:9/29/e00565-20. [PMID: 32675186 PMCID: PMC7365797 DOI: 10.1128/mra.00565-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Here, we present the annotated complete genome sequence of Allorhizobium vitis K306, a phytopathogenic strain causing crown gall of grapevine. The A. vitis K306 genome is 5.79 Mb long with 5,199 predicted protein-coding genes and contains 2 circular chromosomes of 3.8 Mb and 1.1 Mb and 2 plasmids, namely, pTiK306 and pTrK306, that are 262 kb and 581 kb, respectively. Here, we present the annotated complete genome sequence of Allorhizobium vitis K306, a phytopathogenic strain causing crown gall of grapevine. The A. vitis K306 genome is 5.79 Mb long with 5,199 predicted protein-coding genes and contains 2 circular chromosomes of 3.8 Mb and 1.1 Mb and 2 plasmids, namely, pTiK306 and pTrK306, that are 262 kb and 581 kb, respectively.
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The Ecology of Agrobacterium vitis and Management of Crown Gall Disease in Vineyards. Curr Top Microbiol Immunol 2019; 418:15-53. [PMID: 29556824 DOI: 10.1007/82_2018_85] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Agrobacterium vitis is the primary causal agent of grapevine crown gall worldwide. Symptoms of grapevine crown gall disease include tumor formation on the aerial plant parts, whereas both tumorigenic and nontumorigenic strains of A. vitis cause root necrosis. Genetic and genomic analyses indicated that A. vitis is distinguishable from the members of the Agrobacterium genus and its transfer to the genus Allorhizobium was suggested. A. vitis is genetically diverse, with respect to both chromosomal and plasmid DNA. Its pathogenicity is mainly determined by a large conjugal tumor-inducing (Ti) plasmid characterized by a mosaic structure with conserved and variable regions. Traditionally, A. vitis Ti plasmids and host strains were differentiated into octopine/cucumopine, nopaline, and vitopine groups, based on opine markers. However, tumorigenic and nontumorigenic strains of A. vitis may carry other ecologically important plasmids, such as tartrate- and opine-catabolic plasmids. A. vitis colonizes vines endophytically. It is also able to survive epiphytically on grapevine plants and is detected in soil exclusively in association with grapevine plants. Because A. vitis persists systemically in symptomless grapevine plants, it can be efficiently disseminated to distant geographical areas via international trade of propagation material. The use of healthy planting material in areas with no history of the crown gall represents the crucial measure of disease management. Moreover, biological control and production of resistant grape varieties are encouraging as future control measures.
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Jung SM, Hur YY, Preece JE, Fiehn O, Kim YH. Profiling of Disease-Related Metabolites in Grapevine Internode Tissues Infected with Agrobacterium vitis. THE PLANT PATHOLOGY JOURNAL 2016; 32:489-499. [PMID: 27904455 PMCID: PMC5117857 DOI: 10.5423/ppj.ft.08.2016.0163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/04/2016] [Accepted: 10/05/2016] [Indexed: 06/06/2023]
Abstract
Green shoot cuttings of 10 different grapevine species were inoculated with Agrobacterium vitis to find disease-related metabolites in the grapevine. Crown galls formed 60 days after inoculation varied in gall severity (GS) evaluated by gall incidence (GI) and gall diameter (GD), which were classified into three response types as RR (low GI and small GD), SR (high GI and small GD), and SS (high GI and large GD), corresponding to resistant, moderately resistant, and susceptible responses, respectively. In this, 4, 4, and 2 Vitis species were classified into RR, SR, and SS, respectively. Gas chromatography mass spectrometry (GC-MS) analysis of the grapevine stem metabolites with A. vitis infection showed 134 metabolites in various compound classes critically occurred, which were differentially clustered with the response types by the principal component analysis. Multivariate analysis of the metabolite profile revealed that 11 metabolites increased significantly in relation to the response types, mostly at post-inoculation stages, more prevalently (8 metabolites) at two days after inoculation than other stages, and more related to SS (7 metabolites) than RR (3 metabolites) or SR (one metabolite). This suggests most of the disease-related metabolites may be rarely pre-existing but mostly induced by pathogen infection largely for facilitating gall development except stilbene compound resveratrol, a phytoalexin that may be involved in the resistance response. All of these aspects may be used for the selection of resistant grapevine cultivars and their rootstocks for the control of the crown gall disease of the grapevine.
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Affiliation(s)
- Sung-Min Jung
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365,
Korea
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Youn-Young Hur
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365,
Korea
| | - John E. Preece
- National Clonal Germplasm Repository, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Davis, CA 95616,
USA
| | - Oliver Fiehn
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, CA 95616,
USA
| | - Young-Ho Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
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Zheng D, Burr TJ. Inhibition of Grape Crown Gall by Agrobacterium vitis F2/5 Requires Two Nonribosomal Peptide Synthetases and One Polyketide Synthase. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:109-118. [PMID: 26575143 DOI: 10.1094/mpmi-07-15-0153-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Agrobacterium vitis nontumorigenic strain F2/5 is able to inhibit crown gall disease on grapevines. The mechanism of grape tumor inhibition (GTI) by F2/5 has not been fully determined. In this study, we demonstrate that two nonribosomal peptide synthetase (NRPS) genes (F-avi3342 and F-avi5730) and one polyketide synthase gene (F-avi4330) are required for GTI. Knockout of any one of them resulted in F/25 losing GTI capacity. We previously reported that F-avi3342 and F-avi4330 but not F-avi5730 are required for induction of grape tissue necrosis and tobacco hypersensitive response. F-avi5730 is predicted to encode a single modular NRPS. It is located in a cluster that is homologous to the siderophore vicibactin biosynthesis locus in Rhizobium species. Individual disruption of F-avi5730 and two immediate downstream genes, F-avi5731 and F-avi5732, all resulted in reduced siderophore production; however, only F-avi5730 was found to be required for GTI. Complemented F-avi5730 mutant (ΔF-avi5730(+)) restored a wild-type level of GTI activity. It was determined that, over time, populations of ΔF-avi4330, ΔF-avi3342, and ΔF-avi5730 at inoculated wound sites on grapevine did not differ from those of ΔF-avi5730(+) indicating that loss of GTI was not due to reduced colonization of wound sites by mutants.
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Affiliation(s)
- Desen Zheng
- Department of Plant Pathology and Plant-Microbe Biology, New York State Agricultural Experimental Station, Cornell University, 630 W. North Street Geneva, NY 14456, U.S.A
| | - Thomas J Burr
- Department of Plant Pathology and Plant-Microbe Biology, New York State Agricultural Experimental Station, Cornell University, 630 W. North Street Geneva, NY 14456, U.S.A
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Creasap JE, Reid CL, Goffinet MC, Aloni R, Ullrich C, Burr TJ. Effect of Wound Position, Auxin, and Agrobacterium vitis Strain F2/5 on Wound Healing and Crown Gall in Grapevine. PHYTOPATHOLOGY 2005; 95:362-367. [PMID: 18943037 DOI: 10.1094/phyto-95-0362] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
ABSTRACT Agrobacterium vitis is the causal agent of crown gall disease in grapevine, which can be severe in many regions worldwide. Vitis vinifera cultivars are highly susceptible to freeze injury, providing the wounds necessary for infection by A. vitis. Wound position in relation to the uppermost bud of cuttings was determined to be important in tumor development. Inoculated wounds below buds developed tumors, whereas wounds opposite the bud did not, implying that indole-3-aectic acid flow contributes to tumor formation. If auxin was applied to wounds prior to inoculation with a tumorigenic A. vitis strain, all sites of inoculation developed tumors, accompanied by an increased amount of callus in the cambium. Wounds inoculated with an A. vitis biological control strain F2/5 prior to application of the pathogen did not develop galls. A closer examination of these wounds determined that callus cells formed in the cambium during wound healing are susceptible to transformation by the pathogen. Although the mechanism by which F2/5 prevents transformation is unknown, our observations suggest that F2/5 inhibits normal wound healing by inducing necrosis in the cambium.
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Argun N, Momol MT, Maden S, Momol EA, Reid CL, Çelek H, Burr TJ. Characterization of Agrobacterium vitis Strains Isolated from Turkish Grape Cultivars in the Central Anatolia Region. PLANT DISEASE 2002; 86:162-166. [PMID: 30823314 DOI: 10.1094/pdis.2002.86.2.162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Crown gall was detected in several vineyards in the Central Anatolia region of Turkey. Vineyards were planted to cultivars of grape that originated in Turkey and that were not grafted. The predominant species isolated from galls consisted of tumorigenic strains of Agrobacterium vitis. They were identified based on reactions to standard biochemical and physiological tests, by polymerase chain reaction amplification of specific Ti plasmid and chromosomal sequences, and by reaction to a species-specific monoclonal antibody. All strains utilized octopine, suggesting that they may carry similar types of Ti plasmids. Some of the strains exhibited a differential host range compared with others and were less virulent based on the numbers of galls that they induced on grape. When grapevines were treated with nontumorigenic A. vitis strain F2/5 prior to inoculation with the Turkish A. vitis strains, crown gall was effectively controlled. The genetic diversity of strains was evaluated by comparing DNA fingerprints that were generated by restriction enzyme digestion of the intergenic spacer region that lies between 16S and 23S rRNA genes. They segregated into two main groups, one that is similar to previously identified A. vitis strains carrying octopine type Ti plasmids and one that was more similar to strains carrying nopaline and vitopine Ti plasmids. The strains of A. vitis from Turkey may represent ancestral forms of the pathogen that will provide insight into the evolution of the bacterium.
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Affiliation(s)
- N Argun
- Department of Plant Protection, Agricultural Faculty of Ankara, 06110, Ankara, Turkey
| | - M T Momol
- Department of Plant Pathology, NFREC, IFAS, University of Florida, Quincy 32351
| | - S Maden
- Department of Plant Protection, Agricultural Faculty of Ankara
| | - E A Momol
- Department of Plant Protection, NYSAES, Cornell University, Geneva NY 14456
| | - C L Reid
- Department of Plant Protection, NYSAES, Cornell University, Geneva NY 14456
| | - H Çelek
- Department of Horticulture, Agricultural Faculty of Ankara
| | - T J Burr
- Department of Plant Pathology, NYSAES, Cornell University
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Herlache TC, Zhang HS, Ried CL, Carle SA, Zheng D, Basaran P, Thaker M, Burr AT, Burr TJ. Mutations that Affect Agrobacterium vitis-Induced Grape Necrosis also Alter Its Ability to Cause a Hypersensitive Response on Tobacco. PHYTOPATHOLOGY 2001; 91:966-972. [PMID: 18944123 DOI: 10.1094/phyto.2001.91.10.966] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
ABSTRACT Tn5-induced mutations in Agrobacterium vitis F2/5 resulted in both altered grape necrosis and tobacco leaf panel collapse phenotypes, suggesting that the underlying mechanisms of the reactions are related. The reaction on tobacco resembles the classical hypersensitive response (HR) caused by several plant pathogenic bacteria in that it is observable within 14 h, is inhibited by treatment of plants with metabolic inhibitors, and results in the inability to recover the pathogen from the necrotic zone. Strains of A. vitis differ with regard to their efficiency of causing the reaction on tobacco. An EcoRI fragment from one mutant, M6, which is necrosis-altered and HR-minus, was cloned and sequenced. Sequence analysis revealed that the Tn5 insertion occurred in a region that shares significant homology with genes involved in long chain fatty acid production by the marine bacteria Shewanella spp. and Moritella marina. Complementation of M6 with a cosmid clone from an F2/5 DNA library restored the tobacco HR and grape necrosis phenotypes.
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Burr TJ, Otten L. CROWN GALL OF GRAPE: Biology and Disease Management. ANNUAL REVIEW OF PHYTOPATHOLOGY 1999; 37:53-80. [PMID: 11701817 DOI: 10.1146/annurev.phyto.37.1.53] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Not until 1973 was it reported that strains of Agrobacterium that cause crown gall disease of grape form a specific group (later characterized as Agrobacterium vitis). Tumorigenic and nontumorigenic A. vitis have since been isolated from infected and symptomless grapes worldwide. Research on the genetic makeup of A. vitis has led to an improved understanding of pathogen biology and bacterial evolution. In addition, the identification of significant gene sequences has facilitated the development of PCR and RFLP-based identification procedures that continue to improve the detection of A. vitis in plants and soil. Current control practices rely on the use of disease-resistant cultivars, cultural practices that minimize plant injury, and the production of pathogen-free vines. Promising future controls include employment of biological control agents and development of crown gall-resistant transgenic grapevines.
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Affiliation(s)
- Thomas J. Burr
- Department of Plant Pathology, New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
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