Bradyrhizobium japonicum

Classification

Gram-negative nitrogen fixing bacteria

Higher order taxa

Domain: Bacteria, Phylum: Proteobacteria, Class: Alphaproteobacteria, Order: Rhizobiales, Family: Bradyrhizobiaceae

Strains: Bradyrhizobium japonicum strain USDA 110. Bradyrhizobium japonicum bv. genistearum. Bradyrhizobium japonicum bv. glycinearum.

Edited by Erik Low, student of Rachel Larsen at UCSD.

Genus

Genus species: Bradyrhizobium japonicum

NCBI: Taxonomy

Edited by Erik Low, student of Rachel Larsen at UCSD.

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.

Bradyrhizobium japonicum is gram negative, rod shaped, nitrogen fixing bacteria that forms a symbiotic relationship with the soybean plant Glycean Max. It is located on the root tips of the soy bean plant Glycine Max and eventually begins to colonize in the root nodules of the plant itself. Within these root nodules, Bradyrhizobium japonicum is located in symbiosomes derived from the plant membrane. One to several of these bacteria can inhabit a single symbiosome. In the symbiotic relationship, the plant provides a safe environment with a constant supply of carbon for growth and energy. Such carbon sources come in the form of dicarboxylic acids, succinate, fumarate, and malate. The bacteria in turn, provides the plant with fixed nitrogen, which is nitrogen gas that has been reduced and is readily usable by the plant. This allows the plant to grow significantly in the absence of external fertilizer. It is important to have the Bradyrhizobium japonicum's genome sequenced because manipulation of its genome can produce benefitial and desirable traits, which can improve soy bean crop production. It was originally isolated from a soybean nodule in Florida, USA in 1957 through whole genome shotgun sequencing combined with bridging shotgun method.

Edited by Erik Low, student of Rachel Larsen at UCSD.

Genome structure

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?

Bradyrhizobium japonicum has a complete genome. It is made up of a single circular chromosome with 9,105,828 base pairs in length and has no plasmids. The average GC content was 64.1%. It has 8317 potential protein coding genes, 1 set of rRNA genes, and 50 sets of tRNA genes. A total of 167 genes for transposases/104 copies of insertion sequences were identified in the genome. It was remarkable that 100 out of 167 transposase genes are located in the presumptive symbiotic island. DNA segments of 4 to 97 kb inserted into tRNA genes were found at 14 locations in the genome, which generates partial duplication of the target tRNA genes. These observations suggest plasticity of the B. japonicum genome, which is probably due to complex genome rearrangements such as horizontal transfer and insertion of various DNA elements, and to homologous recombination. Replicon Type: chromosome.

Edited by Erik Low, student of Rachel Larsen at UCSD.

Cell structure and metabolism

Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.

The genome reveals factors mediating coaggregation, cell signaling, and stress protection. It has a spiral shape and is arranged in singles. It is a mobile organism but does not contain any endospores. Motility is by rapid rotation around the long axis, flexation of the cell and locomotion along a helical path. The most distinctive property is the presence of periplasmic flagella wound around the helical protoplasmic cylinder and encased in an outer sheath.

Edited by Neena Patel, student of Rachel Larsen at UCSD.

Ecology

Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.

Pathology

Treponema denticola is a bacterial pathogen and plant plastid. It causes periodontal disease and gum inflammation.

How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.

Edited by Neena Patel, student of Rachel Larsen at UCSD.

Application to Biotechnology

Does this organism produce any useful compounds or enzymes? What are they and how are they used?

Current Research

Enter summaries of the most recent research here--at least three required

References

[http://expasy.org/sprot/hamap/BRAJA.html, Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S., Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M., Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S. ; "Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110."; DNA Res. 9:189-197(2002)] Joe Bischoff, Mikhail Domrachev, Scott Federhen, Carol Hotton, Detlef Leipe, Vladimir Soussov, Richard Sternberg, Sean Turner. David J. Westenberg

example: Glockner, F. O., M. Kube, M. Bauer, H. Teeling, T. Lombardot, W. Ludwig, D. Gade, A. Beck, K Borzym, K Heitmann, R. Rabus, H. Schlesner, R. Amann, and R. Reinhardt. 2003. "Complete genome sequence of the marine planctomycete Pirellula sp. strain 1." Proceedings of the National Acedemy of Sciences, vol. 100, no. 14. (8298-8303)

Edited by student of Rachel Larsen and Kit Pogliano