A Microbial Biorealm page on the genus Agrobacterium tumefaciens
Higher order taxa
Bacteria; Proteobacteria; Alpha Proteobacteria; Rhizobiales; Agrobacterium [Others may be used. Use NCBI link to find]
Description and significance
Describe the appearance, habitat, etc. of the organism, and why it is important enough to have its genome sequenced. Describe how and where it was isolated.
Include a picture or two (with sources) if you can find them. Agrobacterium tumefaciens is a gram negative rod-shaped bacteria closely related to nitrogen-fixing bacteria which dwell at root nodules in legumes. Unlike most other soil-dwelling bacteria, it infects the roots of plants to cause Crown Gall disease. In the wild Agrobacterium tumefaciens targets dicots, and causes economic damage to both plants with agricultural and horicultural importance. Various remediation methods, including utilization of a strain closely related bacteria (Agrobacterium radiobacter) to control and limit its damage, but due to a peculiarity in its method of infecting its host it is also a useful genetic engineering tool in plants. It is famous for taking advantage of its host by injecting DNA derived from its Ti (tumor inducing) plasmid into its host, causing the plant to create galls which excrete opines which the bacteria utilize as an energy source. However, scientists have exploited this ability of this bacteria to put DNA into its host to create transgenic plants, and Agrobacterium tumefaciens have emerged as an important molecular tool for manipulating plants and creating genetically modified crops for research and agriculture. Because of its importance in the laboratory, a complete genome of Agrobacterium tumefaciens strain C58 was published in 2001.
Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence? Does it have any plasmids? Are they important to the organism's lifestyle? Agrobacterium tumefaciens is unusual for bacteria in that it is one of the few to have both a linear and a circular chromosome. Of its total of 5.7 million base-pairs, 2.8 million reside on its circular chromosome and 2.1 million reside on its linear chromosome. Most of the genes essential for its survival is located on the circular chromosome, although through evolution some essential genes have migrated to the linear chromosome. Based on sequence analysis, it was determined that the linear chromosome was derived from a plasmid that was transformed into the bacteria a long time ago. The ends of the linear chromosomes are protected by a telomere that is a covalently closed hairpin, like in other bacteria which contain a linear chromosome. In addition to the two chromosome, strain C58 also contain two plasmids, pTiC58 (generically called Ti) and pAtC58 (also called the "cryptic plasmid"). pTiC58 contains genes necessary for its pathogenicity against plants, including the T-DNA which is injected into the plant and causes it to produce opines, along with accessory proteins which helps the T-DNA enter and transform the plant cell into a gall cell. It is believed that pAtC58 contains genes essential for opine catabolism, or its ability to use opines as an energy source, which is important for its lifestyle as a pathogen.
Cell structure and metabolism
Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces. Agrobacterium tumefaciens contain flagella, which are important in their life cycle as it helps them swim through the soil to find their plant hosts. The membrane-bound receptor VirA senses concentration of phenolic compounds and directs the flagella to swim in the direction of plants which produce these compounds.
Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc. Inside their hosts, they create a special environment for themselves. The "Opine Hypothesis" is the primary theory behind the pathology and ecology of Agrobacterium tumefaciens in the natural world. Agrobacterium tumefaciens is one of the few organism that can utilize opines as an energy source, and therefore inducing its host to produce opines creates a special niche which it has few competition. However, the natural situation might be more complex than what the opine hypothesis suggests, since various species of Pseudomonas which also have the capability of using opines as an energy source have been discovered in opine-producing galls along with Agrobacterium tumefaciens, so the opine niche which the bacteria creates also supports the growth of other organisms.
A. tumefaciens also competes with other bacteria in the soil, along closely related bacteria. Agrobacterium radiobacter strain K84, a non-pathogenic species of the same genus, also has an unusual ability to use opines as an energy source. Being able to grow on the same opine-producing galls as A. tumefaciens, it secretes a substance called Agrocin 84, which is taken up by A. tumefaciens. Agrocin 84, a nucleotide analogue, blocks DNA replication in A. tumefaciens and eventually kills it. A. radiobacter is immune from Agrocin 84 since it contains natural pathways for detoxifying the substance. The ability for A. radiobacter to kill A. tumefaciens have been exploited by horticulturalists to control the damage done by A. tumefaciens.
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.
Agrobacterium tumefaciens infects plants usually through an open wound. It seeks out phenolic compounds which spills from a plant wound and chemotactically moves toward its source. Once it enters its plant host, it injects a section of its DNA called the T-DNA which is derived from its Ti (tumor inducing) plasmid into its host. The T-DNA is then integrated into the plant's genome, and has two effects on the plant host. The T-DNA first directs the plant cells to become irregularly shaped cells which forms a visible tumor which is called a gall. The T-DNA then directs the plant cell to start making opines (usually nopaline or agropine) which Agrobacterium tumefaciens could use as an energy source. Since few other organisms (including the plant cell which it infects) can use the opines as an energy source, Agrobacterium tumefaciens creates a special niche for itself inside the gall which it has an energy source only available to itself.
Although it is clear that Agrobacterium tumefaciens integrates its own DNA into that of its hosts and induces them to make opine-producing tumor cells, the details of this process is just being unraveled. It is known that all of the required virulence factors resides on the Ti plasmid, and Agrobacterium tumefaciens that have lost this plasmid becomes no longer pathogenic. The bacteria uses a Type IV secretion system to inject the T-DNA and virulence protein into its host. It has been discovered that an entire suite of proteins, in addition to the T-DNA, is necessary in inducing the host plant to make gall cells. When the T-DNA is copied from the Ti plasmid a protein called VirD2 complexes with it to protect it for nucleases of its host cell and help its transport into the nucleus where it can act. In order for the T-DNA to cross from the bacteria into the plant cell, a protein called VirE2 forms a channel between the membrane of the plant and bacterial cell. Another protein, VirE3, has been discovered to be injected into the plant cell. It has been showned that VirE3 is translocated into the plant nucleus which it interacts with native transcription factors to cause a deregulation of plant cell proliferation and cause the growth of galls. Other virulence factors are not necessary for the process of tumor induction but extends the host range of Agrobacterium tumefaciens. The process which Agrobacterium tumefaciens causes disease has not fully been elucidated, future research still promises to shed light on the process.
Application to Biotechnology
Does this organism produce any useful compounds or enzymes? What are they and how are they used? Due to its ability to integrate DNA into its plant hosts, A. tumefaciens have been used to make transgenic plants since the 1980's. Even though other methods such as biolistic has developed to put genes inside plants, A. tumefaciens has remained popular for genetic manipulation of plants due to the low copy number of genes in plants created and stability of the transgene. The trick is that A. tumefaciens will inject whatever DNA is flanked by a specific 25 bp border repeat sequence. In normal A. tumefaciens this DNA is the T-DNA, so the first step is to create an artificial plasmid with the T-DNA excised, then insert the desired gene construct with the flanking border repeats into the plasmid. The gene construct will usually contain a selection marker (usually kanamycin resistance) along with the desired gene(s) to be expressed in the plant. This artificial plasmid is then transformed into A. tumefaciens, presumably one that lacks a normal Ti plasmid. Plant tissue is then infected with this engineered A. tumefaciens, placed on a selection media (such as one containing kanamycin), and using plant tissue culture methods, the selection media will have killed the cells that have not been transformed, and the shoots which have successfully grown will contain the desired gene which was inserted.
Modern methods for creating transgenic plants using A. tumefaciens is usually a variation of the method described above. In order to simplify the process of plasmid construction, a binary vector is sometimes used. Since the T-DNA does not have to be on the Ti plasmid in order for it to be integrated into the host genome, it can be put on a separate plasmid as long as it as the flanking border repeats. A previous limitation of using A. tumefaciens to create transgenic plants is that A. tumefaciens only infects dicots and gymnosperms in nature. However, additional virulence factors have been discovered which extend A. tumefaciens' host range to monocots, so this method is now useful for creating transgenic plants for all flowering plants.
A. agrobacterium continues to be one of the oldest and most commonly used technique for transfecting genes into plants. Recent research to produce cellulase has used to express a bacterial cellulase gene in Lemna minor (duckweed) using A. agrobacterium. As the interest in producing cellulosic ethanol has increase, a method for breaking down cellulose into sugars is being seeked by scientists. A gene for cellulase was isolated from a thermophilic bacteria and transformed into duckweed using A. tumefaciens as the vector. Duckweed expressing this bacterial cellulase is in no danger of destroying its cell wall since the bacterial cellulase in question is only active at 60 - 80 degrees Celsius. Because Duckweed is a plant with high protein content (up to 40% of its dry weight) it is expected that it could be turned into an efficient bioreactor for proteins such as cellulase. However, extraction of cellulase from genetically engineered duckweed has been complicated by the fact that a subunit of the cellulase complexes with the cellulose of the duckweed in a form that is hard to remove. Further engineering of the cellulase to rid the subunit which binds to cellulose will hopefully result in a higher yield of cellulase.
Of great interest to scientists is the molecular machinery which A. tumefaciens uses to inject DNA into its host, which has only been characterized in the last decade or so. One protein of interest is VirE2. VirE2 appears to bind to single-stranded T-DNA and appears to protect it from the external environment, but in recent years it was discovered it had another function. It appears to form a voltage-gated channel in the plant cell's plasma membrane through which single-stranded T-DNA could pass through into the plant. VirE2 therefore has two different forms with two different functions, first in its monomeric form it is freely soluble and could bind to and protect single-stranded T-DNA, while in its multimeric form it is membrane-bound and acts as a channel for which ssDNA and other soluble components could pass through.
Enter summaries of the most recent research here--at least three required
[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.
Valérie Vaudequin-Dransart, Annik Petit W. Scott Chilton and Yves Dessaux "The Cryptic Plasmid of Agrobacterium tumefaciens Cointegrates with the Ti Plasmid and Cooperates for Opine Degradation". Molecular Plant-Microbe Interactions. 1998. Vol. 11, No. 7, pp. 583–591.
Goodner B, Hinkle G, Gattung S, Miller N, Blanchard M, Qurollo B, Goldman BS, Cao Y, Askenazi M, Halling C, Mullin L, Houmiel K, Gordon J, Vaudin M, Iartchouk O, Epp A, Liu F, Wollam C, Allinger M, Doughty D, Scott C, Lappas C, Markelz B, Flanagan C, Crowell C, Gurson J, Lomo C, Sear C, Strub G, Cielo C, Slater S. "Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58.". Science. 2000. Volume 50. p. 489-500.
Jesús Escudero, Amke den Dulk-Ras, Tonny J. G. Regensburg-Tuïnk and Paul J. J. Hooykaas "VirD4-independent transformation by CloDF13 evidences an unknown factor required for the genetic colonization of plants via Agrobacterium". Molecular Microbiology. 2003. 47(4), 891–901.
Ye Sun, Jay J. Cheng, Michael E. Himmel, Christopher D. Skory, William S. Adney, Steven R. Thomas, Brent Tisserat, Yufuko Nishimura, Yuri T. Yamamoto, "Expression and characterization of Acidothermus cellulolyticus E1 endoglucanase in transgenic duckweed Lemna minor 8627". Bioresource Technology. 2006 Nov 24.
Edited by student of Rachel Larsen