Agrobacterium

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Agrobacterium
Agrobacterium-tumefaciens.png
Scientific classification OOjs UI icon edit-ltr.svg
Domain: Bacteria
Phylum: Pseudomonadota
Class: Alphaproteobacteria
Order: Hyphomicrobiales
Family: Rhizobiaceae
Genus: Agrobacterium
Conn 1942 (Approved Lists 1980)
Type species
Agrobacterium radiobacter
(Smith and Townsend 1907) Conn 1942 (Approved Lists 1980)
Species
Synonyms [1]
  • PolymonasLieske 1928

Agrobacterium is a genus of Gram-negative bacteria established by H. J. Conn that uses horizontal gene transfer to cause tumors in plants. Agrobacterium tumefaciens is the most commonly studied species in this genus. Agrobacterium is well known for its ability to transfer DNA between itself and plants, and for this reason it has become an important tool for genetic engineering.

Contents

Nomenclatural history

Leading up to the 1990s, the genus Agrobacterium was used as a wastebasket taxon. With the advent of 16S sequencing, many Agrobacterium species (especially the marine species) were reassigned to genera such as Ahrensia , Pseudorhodobacter , Ruegeria , and Stappia . [2] [3] The remaining Agrobacterium species were assigned to three biovars: biovar 1 ( Agrobacterium tumefaciens ), biovar 2 (Agrobacterium rhizogenes), and biovar 3 (Agrobacterium vitis). In the early 2000s, Agrobacterium was synonymized with the genus Rhizobium . [4] This move proved to be controversial. [5] [6] The debate was finally resolved when the genus Agrobacterium was reinstated [7] after it was demonstrated that it was phylogenetically distinct from Rhizobium [8] [9] and that Agrobacterium species were unified by a unique synapomorphy: the presence of the protelomerase gene, telA, which causes all members of the genus to have a linear chromid. [10] By this time, however, the three Agrobacterium biovars had become defunct; biovar 1 remained with Agrobacterium, biovar 2 was renamed Rhizobium rhizogenes , and biovar 3 was renamed Allorhizobium vitis .

Plant pathogen

The large growths on these roots are galls induced by Agrobacterium sp. Agrobacteriumgall.jpg
The large growths on these roots are galls induced by Agrobacterium sp.

Agrobacterium tumefaciens causes crown-gall disease in plants. The disease is characterised by a tumour-like growth or gall on the infected plant, often at the junction between the root and the shoot. Tumors are incited by the conjugative transfer of a DNA segment (T-DNA) from the bacterial tumour-inducing (Ti) plasmid. The closely related species, Agrobacterium rhizogenes, induces root tumors, and carries the distinct Ri (root-inducing) plasmid. Although the taxonomy of Agrobacterium is currently under revision it can be generalised that 3 biovars exist within the genus, Agrobacterium tumefaciens, Agrobacterium rhizogenes, and Agrobacterium vitis. Strains within Agrobacterium tumefaciens and Agrobacterium rhizogenes are known to be able to harbour either a Ti or Ri-plasmid, whilst strains of Agrobacterium vitis, generally restricted to grapevines, can harbour a Ti-plasmid. Non-Agrobacterium strains have been isolated from environmental samples which harbour a Ri-plasmid whilst laboratory studies have shown that non-Agrobacterium strains can also harbour a Ti-plasmid. Some environmental strains of Agrobacterium possess neither a Ti nor Ri-plasmid. These strains are avirulent. [11]

The plasmid T-DNA is integrated semi-randomly into the genome of the host cell, [12] and the tumor morphology genes on the T-DNA are expressed, causing the formation of a gall. The T-DNA carries genes for the biosynthetic enzymes for the production of unusual amino acids, typically octopine or nopaline. It also carries genes for the biosynthesis of the plant hormones, auxin and cytokinins, and for the biosynthesis of opines, providing a carbon and nitrogen source for the bacteria that most other micro-organisms can't use, giving Agrobacterium a selective advantage. [13] By altering the hormone balance in the plant cell, the division of those cells cannot be controlled by the plant, and tumors form. The ratio of auxin to cytokinin produced by the tumor genes determines the morphology of the tumor (root-like, disorganized or shoot-like).

In humans

Although generally seen as an infection in plants, Agrobacterium can be responsible for opportunistic infections in humans with weakened immune systems, [14] [15] but has not been shown to be a primary pathogen in otherwise healthy individuals. One of the earliest associations of human disease caused by Agrobacterium radiobacter was reported by Dr. J. R. Cain in Scotland (1988). [16] A later study suggested that Agrobacterium attaches to and genetically transforms several types of human cells by integrating its T-DNA into the human cell genome. The study was conducted using cultured human tissue and did not draw any conclusions regarding related biological activity in nature. [17]

Uses in biotechnology

The ability of Agrobacterium to transfer genes to plants and fungi is used in biotechnology, in particular, genetic engineering for plant improvement. Genomes of plants and fungi can be engineered by use of Agrobacterium for the delivery of sequences hosted in T-DNA binary vectors. A modified Ti or Ri plasmid can be used. The plasmid is 'disarmed' by deletion of the tumor inducing genes; the only essential parts of the T-DNA are its two small (25 base pair) border repeats, at least one of which is needed for plant transformation. [18] [19] The genes to be introduced into the plant are cloned into a plant binary vector that contains the T-DNA region of the disarmed plasmid, together with a selectable marker (such as antibiotic resistance) to enable selection for plants that have been successfully transformed. Plants are grown on media containing antibiotic following transformation, and those that do not have the T-DNA integrated into their genome will die. An alternative method is agroinfiltration. [20] [21]

Plant (S. chacoense) transformed using Agrobacterium. Transformed cells start forming calluses on the side of the leaf pieces Transformation with Agrobacterium.JPG
Plant ( S. chacoense ) transformed using Agrobacterium. Transformed cells start forming calluses on the side of the leaf pieces

Transformation with Agrobacterium can be achieved in multiple ways. Protoplasts or alternatively leaf-discs can be incubated with the Agrobacterium and whole plants regenerated using plant tissue culture. In agroinfiltration the Agrobacterium may be injected directly into the leaf tissue of a plant. This method transforms only cells in immediate contact with the bacteria, and results in transient expression of plasmid DNA. [22]

Agroinfiltration is commonly used to transform tobacco ( Nicotiana ). A common transformation protocol for Arabidopsis is the floral dip method: [23] An inflorescence is dipped in a suspension of Agrobacterium, and the bacterium transforms the germline cells that make the female gametes. The seeds can then be screened for antibiotic resistance (or another marker of interest). Plants that have not integrated the plasmid DNA will die when exposed to the antibiotic. [20]

Agrobacterium is listed as being the vector of genetic material that was transferred to these USA GMOs: [24]

The transformation of fungi using Agrobacterium is used primarily for research purposes, [25] [26] and follows similar approaches as for plant transformation. The Ti plasmid system is modified to include DNA elements to select for transformed fungal strains, after co-incubation of Agrobacterium strains carrying these plasmids with fungal species.

Genomics

The Agrobacterium genome consists of three parts: a circular chromosome, a linear chromosome/chromid, and (in some species) a Ti plasmid. [27]

The sequencing of the genomes of several species of Agrobacterium has permitted the study of the evolutionary history of these organisms and has provided information on the genes and systems involved in pathogenesis, biological control and symbiosis. One important finding is the possibility that chromosomes are evolving from plasmids in many of these bacteria. Another discovery is that the diverse chromosomal structures in this group appear to be capable of supporting both symbiotic and pathogenic lifestyles. The availability of the genome sequences of Agrobacterium species will continue to increase, resulting in substantial insights into the function and evolutionary history of this group of plant-associated microbes. [28]

History

Marc Van Montagu and Jozef Schell at the University of Ghent (Belgium) discovered the gene transfer mechanism between Agrobacterium and plants, which resulted in the development of methods to alter Agrobacterium into an efficient delivery system for gene engineering in plants. [18] [19] A team of researchers led by Mary-Dell Chilton were the first to demonstrate that the virulence genes could be removed without adversely affecting the ability of Agrobacterium to insert its own DNA into the plant genome (1983). [29]

See also

Related Research Articles

<span class="mw-page-title-main">Bacterial conjugation</span> Method of bacterial gene transfer

Bacterial conjugation is the transfer of genetic material between bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells. This takes place through a pilus. It is a parasexual mode of reproduction in bacteria.

<span class="mw-page-title-main">Genetic transformation</span> Genetic alteration of a cell by uptake of genetic material from the environment

In molecular biology and genetics, transformation is the genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from its surroundings through the cell membrane(s). For transformation to take place, the recipient bacterium must be in a state of competence, which might occur in nature as a time-limited response to environmental conditions such as starvation and cell density, and may also be induced in a laboratory.

<i>Agrobacterium tumefaciens</i> Bacterium, genetic engineering tool

Agrobacterium tumefaciens is the causal agent of crown gall disease in over 140 species of eudicots. It is a rod-shaped, Gram-negative soil bacterium. Symptoms are caused by the insertion of a small segment of DNA, from a plasmid into the plant cell, which is incorporated at a semi-random location into the plant genome. Plant genomes can be engineered by use of Agrobacterium for the delivery of sequences hosted in T-DNA binary vectors.

<span class="mw-page-title-main">Transfer DNA</span> Type of DNA in bacterial genomes

The transfer DNA is the transferred DNA of the tumor-inducing (Ti) plasmid of some species of bacteria such as Agrobacterium tumefaciens and Agrobacterium rhizogenes . The T-DNA is transferred from bacterium into the host plant's nuclear DNA genome. The capability of this specialized tumor-inducing (Ti) plasmid is attributed to two essential regions required for DNA transfer to the host cell. The T-DNA is bordered by 25-base-pair repeats on each end. Transfer is initiated at the right border and terminated at the left border and requires the vir genes of the Ti plasmid.

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<span class="mw-page-title-main">Ti plasmid</span> Circular plasmid used in creation of transgenic plants

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Rhizobium rhizogenes is a Gram-negative soil bacterium that produces hairy root disease in dicotyledonous plants. R. rhizogenes induces the formation of proliferative multiple-branched adventitious roots at the site of infection, so-called 'hairy roots'. It also induces galls.

<span class="mw-page-title-main">Alphaproteobacteria</span> Class of bacteria

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<span class="mw-page-title-main">Gene delivery</span> Introduction of foreign genetic material into host cells

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<span class="mw-page-title-main">Jozef Schell</span> Belgian molecular biologist

Jozef Stefaan "Jeff", Baron Schell was a Belgian molecular biologist.

Plant transformation vectors are plasmids that have been specifically designed to facilitate the generation of transgenic plants. The most commonly used plant transformation vectors are T-DNA binary vectors and are often replicated in both E. coli, a common lab bacterium, and Agrobacterium tumefaciens, a plant-virulent bacterium used to insert the recombinant DNA into plants.

A transfer DNA (T-DNA) binary system is a pair of plasmids consisting of a T-DNA binary vector and a virhelper plasmid. The two plasmids are used together to produce genetically modified plants. They are artificial vectors that have been derived from the naturally occurring Ti plasmid found in bacterial species of the genus Agrobacterium, such as A. tumefaciens. The binary vector is a shuttle vector, so-called because it is able to replicate in multiple hosts.

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αr7 is a family of bacterial small non-coding RNAs with representatives in a broad group of Alphaproteobacterial species from the order Hyphomicrobiales. The first member of this family was found in a Sinorhizobium meliloti 1021 locus located in the chromosome (C). Further homology and structure conservation analysis identified full-length homologs in several nitrogen-fixing symbiotic rhizobia, in the plant pathogens belonging to Agrobacterium species as well as in a broad spectrum of Brucella species. αr7 RNA species are 134-159 nucleotides (nt) long and share a well defined common secondary structure. αr7 transcripts can be catalogued as trans-acting sRNAs expressed from well-defined promoter regions of independent transcription units within intergenic regions (IGRs) of the Alphaproteobacterial genomes.

αr15 is a family of bacterial small non-coding RNAs with representatives in a broad group of α-proteobacteria from the order Rhizobiales. The first members of this family were found tandemly arranged in the same intergenic region (IGR) of the Sinorhizobium meliloti 1021 chromosome (C). Further homology and structure conservation analysis have identified full-length Smr15C1 and Smr15C2 homologs in several nitrogen-fixing symbiotic rhizobia, in the plant pathogens belonging to Agrobacterium species as well as in a broad spectrum of Brucella species. The Smr15C1 and Smr15C2 homologs are also encoded in tandem within the same IGR region of Rhizobium and Agrobacterium species, whereas in Brucella species the αr15C loci are spread in the IGRs of Chromosome I. Moreover, this analysis also identified a third αr15 loci in extrachromosomal replicons of the mentioned nitrogen-fixing α-proteobacteria and in the Chromosome II of Brucella species. αr15 RNA species are 99-121 nt long and share a well defined common secondary structure consisting of three stem loops. The transcripts of the αr15 family can be catalogued as trans-acting sRNAs encoded by independent transcription units with recognizable promoter and transcription termination signatures within intergenic regions (IGRs) of the α-proteobacterial genomes.

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EHA101 was one of the first and most widely used Agrobacterium helper plasmid for plant gene transfer. Created in 1985 in the laboratory of Mary-Dell Chilton at Washington University in St. Louis, it was named after the graduate student who constructed it. The EH stands for "Elizabeth Hood" and A for "Agrobacterium". The EHA101 helper strain is a derivative of A281, the hypervirulent A. tumefaciens strain that causes large, fast-growing tumors on solanaceous plants. This strain is used for moving genes of interest into many hundreds of species of plants all over the world.

Allorhizobium vitis is a plant pathogen that infects grapevines. The species is best known for causing a tumor known as crown gall disease. One of the virulent strains, A. vitis S4, is responsible both for crown gall on grapevines and for inducing a hypersensitive response in other plant species. Grapevines that have been affected by crown gall disease produce fewer grapes than unaffected plants. Though not all strains of A. vitis are tumorigenic, most strains can damage plant hosts.

Agrobacterium radiobacter is the type species of the genus Agrobacterium. It was formerly incorrectly synonymized with Agrobacterium tumefaciens. Unlike other members of its genus, it does not harbor a tumor-inducing (Ti) plasmid, and is hence not pathogenic to plants. This species is widely found in soil, in plant rhizospheres, and in human clinical specimens.

The root inducing (Ri) -plasmid of Rhizobium rhizogenes is a plasmid capable of undergoing horizontal gene transfer of its transfer DNA (T-DNA), upon contact with a plant host. The T-DNA of the Ri-plasmid affects the plant host in such a way, that gene expression is altered, especially in regard to phytohormonal balances, metabolism and certain phenotypical characteristics.

References

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  24. ↑ The FDA List of Completed Consultations on Bioengineered Foods Archived May 13, 2008, at the Wayback Machine
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  29. ↑ Chilton, Mary-Dell (2001). "Agrobacterium. A Memoir". Plant Physiology. 125 (1): 9–14. doi: 10.1104/pp.125.1.9 . ISSN   0032-0889. PMC   1539314 . PMID   11154285.

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