T-DNA regions from 350 Agrobacterium genomes: maps and phylogeny

Otten, Léon

doi:10.1007/s11103-021-01140-0

Cited by 19 publications

(22 citation statements)

References 60 publications

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“…The presence of T-DNA2 in pTiAB2/73 also explains the previously reported presence of agrocinopines in tumors induced by AB2/73 [18] as T-DNA2 contains the gene for agrocinopine synthase. T-DNA2 is unique to AB2/73, but T-DNA1 can also be found in the A. vitis pTiS4 plasmid ( [30], our results), where it is present as the fourth T-DNA in addition to the three T-DNAs previously described [28].…”

Section: Discussionsupporting

confidence: 59%

“…Between border repeat 4 and 5 genes are present including a gene annotated as an octopine/nopaline dehydrogenase, which may encode an opine synthase expressed in transformed plant cells. During the preparation of our manuscript the presence of putative border repeat 4 and an ocs-like gene in p42a was reported by Otten [30]. Therefore, it seems that a Ti plasmid transferred into this R. etli strain may have been inactivated over time by deletion of much of its T-DNAs suggesting that this bacterium may not be adapted well enough to compete with agrobacteria in the tumor niche.…”

Section: Discussionmentioning

confidence: 77%

“…6. The composition of T-DNA2 is unique to AB2/73 and differs from all the T-DNAs so far identified [30]. The acs gene most closely resembles the acs genes present in agropine-type pTiBo542 and chrysopinetype pTiChry5, while the 6b gene is most similar to that Fig.…”

Section: Plasmid Patab2/73d: the Mega-ti Plasmid Of Ab2/73mentioning

confidence: 78%

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Complete genomic sequence and phylogenomics analysis of Agrobacterium strain AB2/73: a new Rhizobium species with a unique mega-Ti plasmid

Hooykaas

2021

BMC Microbiol

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Background The Agrobacterium strain AB2/73 has a unique host range for the induction of crown gall tumors, and contains an exceptionally large, over 500 kbp mega Ti plasmid. We used whole genome sequencing to fully characterize and comparatively analyze the complex genome of strain AB2/73, including its Ti plasmid and virulence factors. Results We obtained a high-quality, full genomic sequence of AB2/73 by a combination of short-read Illumina sequencing and long-read Nanopore sequencing. The AB2/73 genome has a total size of 7,266,754 bp with 59.5% GC for which 7012 genes (6948 protein coding sequences) are predicted. Phylogenetic and comparative genomics analysis revealed that strain AB2/73 does not belong to the genus Agrobacterium, but to a new species in the genus Rhizobium, which is most related to Rhizobium tropici. In addition to the chromosome, the genome consists of 6 plasmids of which the largest two, of more than 1 Mbp, have chromid-like properties. The mega Ti plasmid is 605 kbp in size and contains two, one of which is incomplete, repABC replication units and thus appears to be a cointegrate consisting of about 175 kbp derived from an unknown Ti plasmid linked to 430 kbp from another large plasmid. In pTiAB2/73 we identified a complete set of virulence genes and two T-DNAs. Besides the previously described T-DNA we found a larger, second T-DNA containing a 6b-like onc gene and the acs gene for agrocinopine synthase. Also we identified two clusters of genes responsible for opine catabolism, including an acc-operon for agrocinopine degradation, and genes putatively involved in ridéopine catabolism. The plasmid also harbours tzs, iaaM and iaaH genes for the biosynthesis of the plant growth regulators cytokinin and auxin. Conclusions The comparative genomics analysis of the high quality genome of strain AB2/73 provided insight into the unusual phylogeny and genetic composition of the limited host range Agrobacterium strain AB2/73. The description of its unique genomic composition and of all the virulence determinants in pTiAB2/73 will be an invaluable tool for further studies into the special host range properties of this bacterium.

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Section: Discussionsupporting

confidence: 59%

Section: Discussionmentioning

confidence: 77%

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Complete genomic sequence and phylogenomics analysis of Agrobacterium strain AB2/73: a new Rhizobium species with a unique mega-Ti plasmid

Hooykaas

2021

BMC Microbiol

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“…Prior studies failed to identify a T-DNA on p42a, suggesting it is 'unarmed'. Though we also could not identify homologues of known oncogenes, we and others have identified a single T-DNA border sequence and genes encoding an opine synthase [59]. We also identified additional T-DNA border sequences and a gene encoding trehalose-6-synthase on p42a.…”

Section: (C) Virulence Plasmid Evolutionmentioning

confidence: 62%

Diversification of plasmids in a genus of pathogenic and nitrogen-fixing bacteria

Weisberg

Miller

Ream

et al. 2021

Phil. Trans. R. Soc. B

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Members of the agrobacteria–rhizobia complex (ARC) have multiple and diverse plasmids. The extent to which these plasmids are shared and the consequences of their interactions are not well understood. We extracted over 4000 plasmid sequences from 1251 genome sequences and constructed a network to reveal interactions that have shaped the evolutionary histories of oncogenic virulence plasmids. One newly discovered type of oncogenic plasmid is a mosaic with three incomplete, but complementary and partially redundant virulence loci. Some types of oncogenic plasmids recombined with accessory plasmids or acquired large regions not known to be associated with pathogenicity. We also identified two classes of partial virulence plasmids. One class is potentially capable of transforming plants, but not inciting disease symptoms. Another class is inferred to be incomplete and non-functional but can be found as coresidents of the same strain and together are predicted to confer pathogenicity. The modularity and capacity for some plasmids to be transmitted broadly allow them to diversify, convergently evolve adaptive plasmids and shape the evolution of genomes across much of the ARC. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

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“…This can be especially useful for exploring novel Agrobacterium strains for wider host ranges, as diverse Agrobacterium strains have been sequenced. Comparative genomic and transcriptomic studies can provide new tools for understanding Agrobacterium ‐plant interactions (Otten, 2021; Weisberg et al ., 2020).…”

Section: Discussionmentioning

confidence: 99%

CRISPR RNA‐guided integrase enables high‐efficiency targeted genome engineering in Agrobacterium tumefaciens

Aliu

Lee

Wang

2022

Plant Biotechnology Journal

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Summary Agrobacterium tumefaciens, the causal agent of plant crown gall disease, has been widely used to genetically transform many plant species. The inter‐kingdom gene transfer capability made Agrobacterium an essential tool and model system to study the mechanism of exporting and integrating a segment of bacterial DNA into the plant genome. However, many biological processes such as Agrobacterium‐host recognition and interaction are still elusive. To accelerate the understanding of this important plant pathogen and further improve its capacity in plant genetic engineering, we adopted a CRISPR RNA‐guided integrase system for Agrobacterium genome engineering. In this work, we demonstrate that INsertion of Transposable Elements by Guide RNA–Assisted TargEting (INTEGRATE) can efficiently generate DNA insertions to enable targeted gene knockouts. In addition, in conjunction with Cre‐loxP recombination system, we achieved precise deletions of large DNA fragments. This work provides new genetic engineering strategies for Agrobacterium species and their gene functional analyses.

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T-DNA regions from 350 Agrobacterium genomes: maps and phylogeny

Cited by 19 publications

References 60 publications

Complete genomic sequence and phylogenomics analysis of Agrobacterium strain AB2/73: a new Rhizobium species with a unique mega-Ti plasmid

Complete genomic sequence and phylogenomics analysis of Agrobacterium strain AB2/73: a new Rhizobium species with a unique mega-Ti plasmid

Diversification of plasmids in a genus of pathogenic and nitrogen-fixing bacteria

CRISPR RNA‐guided integrase enables high‐efficiency targeted genome engineering in Agrobacterium tumefaciens

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