Evolutionary classification of tumor- and root-inducing plasmids based on T-DNAs and virulence regions

Nabi, Nesrine; Hafsa, Ahmed Ben; Gaillard, Vincent; Nesme, Xavier; Chaouachi, Maher; Vial, Ludovic

doi:10.1016/j.ympev.2022.107388

Cited by 5 publications

(5 citation statements)

References 56 publications

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“…The tumorigenic properties of oncogenes are mediated by the transfer (T)-DNA region of tumor-inducing (Ti) plasmids, which are approximately 160–240 kb in size, with the T-DNA region being 15–30 kb, and the virulence (vir) gene region being almost 36 kb [ 22 ]. The T-DNA comprises three sets of genes, of which two are referred to as oncogenes and synthesize mitogens (auxin and cytokinin), promoting the unrestricted growth and division of plant wound tissues to form crown gall tumors; the third set is opine (rare amino acids), producing octopine, nopaline, agropine, and succinamopine, which are utilized as carbon and nitrogenous sources by Agrobacterium [ 23 ]. The vir region encodes for proteins that initiate, process, mediate, and integrate T-DNA into the plant nuclear genome [ 24 ].…”

Section: Ways To Deliver Crispr/cas Reagents To Plantsmentioning

confidence: 99%

Plant Virus-Derived Vectors for Plant Genome Engineering

Mahmood

Naqvi

Rahman

et al. 2023

Viruses

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Advances in genome engineering (GE) tools based on sequence-specific programmable nucleases have revolutionized precise genome editing in plants. However, only the traditional approaches are used to deliver these GE reagents, which mostly rely on Agrobacterium-mediated transformation or particle bombardment. These techniques have been successfully used for the past decades for the genetic engineering of plants with some limitations relating to lengthy time-taking protocols and transgenes integration-related regulatory concerns. Nevertheless, in the era of climate change, we require certain faster protocols for developing climate-smart resilient crops through GE to deal with global food security. Therefore, some alternative approaches are needed to robustly deliver the GE reagents. In this case, the plant viral vectors could be an excellent option for the delivery of GE reagents because they are efficient, effective, and precise. Additionally, these are autonomously replicating and considered as natural specialists for transient delivery. In the present review, we have discussed the potential use of these plant viral vectors for the efficient delivery of GE reagents. We have further described the different plant viral vectors, such as DNA and RNA viruses, which have been used as efficient gene targeting systems in model plants, and in other important crops including potato, tomato, wheat, and rice. The achievements gained so far in the use of viral vectors as a carrier for GE reagent delivery are depicted along with the benefits and limitations of each viral vector. Moreover, recent advances have been explored in employing viral vectors for GE and adapting this technology for future research.

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Section: Ways To Deliver Crispr/cas Reagents To Plantsmentioning

confidence: 99%

Plant Virus-Derived Vectors for Plant Genome Engineering

Mahmood

Naqvi

Rahman

et al. 2023

Viruses

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“…Compared to the classical classification scheme based on the opine type (18,91) or an alternative scheme that additionally considers the vir loci structure and T-DNA gene content (84), analyses reported in 2020 employed a more comprehensive classification scheme (120). Multiple features, including k-mer profile, gene content, core gene phylogeny, and plasmid structure, were all examined and found to produce consistent typing results (10,120,121).…”

Section: Classification Of Oncogenic Plasmidsmentioning

confidence: 99%

Virulence and Ecology of Agrobacteria in the Context of Evolutionary Genomics

Weisberg

Chang

et al. 2023

Annu. Rev. Phytopathol.

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Among plant-associated bacteria, agrobacteria occupy a special place. These bacteria are feared in the field as agricultural pathogens. They cause abnormal growth deformations and significant economic damage to a broad range of plant species. However, these bacteria are revered in the laboratory as models and tools. They are studied to discover and understand basic biological phenomena and used in fundamental plant research and biotechnology. Agrobacterial pathogenicity and capability for transformation are one and the same and rely on functions encoded largely on their oncogenic plasmids. Here, we synthesize a substantial body of elegant work that elucidated agrobacterial virulence mechanisms and described their ecology. We review findings in the context of the natural diversity that has been recently unveiled for agrobacteria and emphasize their genomics and plasmids. We also identify areas of research that can capitalize on recent findings to further transform our understanding of agrobacterial virulence and ecology. Expected final online publication date for the Annual Review of Phytopathology, Volume 61 is September 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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“…In this respect, Otten (2021) analyzed T-DNA regions from 350 agrobacterial genomes and classified them into three main groups, which were further divided into a number of subgroups. Nabi et al (2022) investigated the diversity among T-DNAs and vir regions of 56 Ti/Ri plasmid sequences. In recent studies, complete sequences of several Ti/Ri plasmids and their relationship with related plasmids were investigated ( Hooykaas and Hooykaas 2021a , 2021 b ; Shao et al 2018 ; Kuzmanović and Puławska 2019 ; Shao et al 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Diversity and Evolutionary History of Ti Plasmids of “tumorigenes” Clade of Rhizobium spp. and Their Differentiation from Other Ti and Ri Plasmids

Kuzmanović

Wolf

Will

et al. 2023

Genome Biology and Evolution

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Agrobacteria are important plant pathogens responsible for crown/cane gall and hairy root diseases. Crown/cane gall disease is associated with strains carrying tumor-inducing (Ti) plasmids, while hairy root disease is caused by strains harboring root-inducing (Ri) plasmids. In this study, we analyzed the sequences of Ti plasmids of the novel “tumorigenes” clade of the family Rhizobiaceae (“tumorigenes” Ti plasmids), which includes two species, Rhizobium tumorigenes and Rhizobium rhododendri. The sequences of reference Ti/Ri plasmids were also included, which was followed with comparative analysis of their backbone and accessory regions. The “tumorigenes” Ti plasmids have novel opine signatures compared to other Ti/Ri plasmids characterized so far. The first group exemplified by pTi1078 is associated with production of agrocinopine, nopaline and ridéopine in plant tumors, while the second group comprising pTi6.2 is responsible for synthesis of leucinopine. Bioinformatic and chemical analyses, including opine utilization assays, indicated that leucinopine associated with pTi6.2 most likely has D, L stereochemistry, unlike the L, L-leucinopine produced in tumors induced by reference strains Chry5 and Bo542. Most of the “tumorigenes” Ti plasmids have conjugative transfer system genes that are unusual for Ti plasmids, composed of avhD4/avhB and traA/mobC/parA regions. Next, our results suggested that “tumorigenes” Ti plasmids have a common origin, but they diverged through large-scale recombination events, through recombination with single or multiple distinct Ti plasmids. Lastly, we showed that Ti/Ri plasmids could be differentiated based on pairwise Mash or AAI distance clustering, and we supply a script to facilitate application of the former approach by other researchers.

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Evolutionary classification of tumor- and root-inducing plasmids based on T-DNAs and virulence regions

Cited by 5 publications

References 56 publications

Plant Virus-Derived Vectors for Plant Genome Engineering

Plant Virus-Derived Vectors for Plant Genome Engineering

Virulence and Ecology of Agrobacteria in the Context of Evolutionary Genomics

Diversity and Evolutionary History of Ti Plasmids of “tumorigenes” Clade of Rhizobium spp. and Their Differentiation from Other Ti and Ri Plasmids

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