Bradyrhizobium japonicum

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A Microbial Biorealm page on the genus Bradyrhizobium japonicum

Classification

Gram-negative nitrogen fixing bacteria

Higher order taxa

Domain: Bacteria, Phylum: Proteobacteria, Class: Alphaproteobacteria, Order: Rhizobiales, Family: Bradyrhizobiaceae*1


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


Genus

Genus species: Bradyrhizobium japonicum


NCBI: Taxonomy


Description and significance

Bradyrhizobium japonicum is gram-negative, rod shaped, nitrogen fixing bacteria that forms a symbiotic relationship with Glycine max, a soybean plant. It is located on the root tips of the soy bean plant Glycine Max and eventually colonizes 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 this symbiotic relationship, the plant provides a safe environment and a constant food supply such as carbon, which is used for growth and energy. Such carbon sources come in the form of dicarboxylic acids, succinate, fumarate, and malate. The bacteria in turn, provide 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 beneficial and desirable traits, which can improve soy bean crop production. The bacterium was originally isolated from a soybean nodule in Florida, USA in 1957. The genome was sequenced by whole genome shotgun sequencing in 2002.*4

Genome structure

Bradyrhizobium japonicum genome has been completely sequenced. It is made up of a single circular chromosome of 9,105,828 base pairs and has no plasmids. The average GC content is 64.1%. It has 8317 potential protein coding genes, 1 set of rRNA genes, and 50 sets of tRNA genes. There is a total of 167 genes coding for transposases with 104 insertion sequences in the genome. DNA insertions of 4 kb to 97 kb in tRNA genes were found at 14 different locations in the genome. This produced variant copies of the target tRNA genes. These observations support the idea of B. japonicum genome's plasticity. Its plasticity is probably due to homologous recombination and horizontal transfer and insertion of different DNA elements.*4

Replicon Type: chromosome.


Cell structure and metabolism

Gram-negative soil bacteria of the family Rhizobiaceae such as Bradyrhizobium japonicum, synthesize a variety of cell-surface carbohydrates. These carbohydrates include lipopolysaccharides, capsular polysaccharides, exopolysaccharides (EPS), nodule polysaccharides, lipo chitin oligosaccharides, and cyclic -glucans, some of which may provide functions important to symbiosis. It uses these carbohydrate structures to obtain the carbon energy sources from the soybean plant as well as gain entry. Bradyrhizobium japonicum uptakes the sugar trehalose the most rapidly and converts it to CO2. Another energy source is UDP-Glucose which was taken up in large amounts but was very slowly metabolized. Sucrose and glucose are also alternative energy sources, but they are metabolized at very low rates as well.*9


Ecology

Bradyrhizobium japonicum has a symbiotic relationship with legumes, or more specifically soybean plants. These bacteria are very beneficial to the environment as they promote the growth of the soybean plants. It carries out a process called nitrogen fixation in the plant, so that the plant has a usable form of nitrogen. This in turn causes the plant to grow rapidly since it has an abundance of readily usable nitrogen. Promotion of plant growth causes more oxygen to be released into the environment, which is a crucial element for survival for most organisms. *4,5


Pathology

Bradyrhizobium japonicum uses its extracellular carbohydrate structures to gain entry into the host root cell. It produces polysaccharide degrading enzymes in order to hydrolyze the cell wall. Specifically polyalacturonase and variants of carboxymethylcellulase cleave glycosidic bonds of the host cell wall polymers. These create erosion pits in the epidermal cells of the root, which allow for entry into the host root cells. These enzymes are only secreted in highly localized areas where the bacteria are concentrated. The reason for localization of these degradative enzymes is that it prevents excessive cell wall hydrolysis to the point where it either kills the host cells or causes a host cell immune reaction, which would ultimately hurt the bacteria. In this way, it can back up away from the root cell if it senses that root cell degradation is proceeding too quickly. However, it should be noted that the entry of Bradyrhizobium japonicum into root cells does not cause disease or damage because it has symbiotic relationship. It has a symbiotic relationship where it fixes nitrogen for the plant, while the plant provides a safe environment and steady carbon source for it.*5


Application to Biotechnology

This organism does not produce compounds or enzymes currently used in biotechnology, but it does carry out proccesses that are applicable to biotechnology. It carries out the nitrogen fixation providing plants with a usable source of nitrogen. This allows the soybean plants to grow in the absence of external fertilizers. Therefore if we can engineer or culture these microorganisms and incorporate it into plants, agriculture will flourish. This will benefit the entire environment by providing bigger and better plants that will in turn give off oxygen.*4


Current Research

1. Bradyrhizobium japonicum produces haloalkane dehalogenase, which degrades halogenated aliphatic pollutants. The haloalkane dehalogenase that it produces has high catalytic activity for beta methylated haloalkanes and researchers are trying to discover the mechanism of its substrate specificity.*6

2. Analysis of the diversity of rhizobia in different parts of China. It was found that certain species of rhizobia were specific to certain geographic areas of China. It was discovered that Bradyrhizobium japonicum was predominant in the nodules of Trifolium, which suggests that the bacteria is selected by both geographic features and legume hosts. *7

3. Using rational genome mining, a mandelonitrile hydrolase was discovered in Bradyrhizobium japonicum. It was then transformed into E. coli where it was discovered to have a molecular mass of 37kDA. It was also discovered that the mandelonitrile hydrolase was very effective in hydrolyzing mandelonitrile derivatives and converting mandelonitrile to mandelic acid.*8

References

1. 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. 2002. "Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110.". DNA Res. 9:189-197

2. Joe Bischoff, Mikhail Domrachev, Scott Federhen, Carol Hotton, Detlef Leipe, Vladimir Soussov, Richard Sternberg, Sean Turner. 2007. "Taxonomy Browser".

3. Heather A. Louch, and Karen J. Miller. 2000. "Synthesis of a Low-Molecular-Weight Form of Exopolysaccharide by Bradyrhizobium japonicum USDA 110". Applied and Environmental Microbiology. p. 1011-1014, Vol. 67, No. 2

4. 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. 2002. "Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110.". DNA Res. 9:189-197

5. Pedro F. Mateos, David L. Baker, Maureen Petersen, Encarna Velázquez,José I. Jiménez-Zurdo, Eustoquio Martínez-Molina, Andrea Squartini,Guy Orgambide, David H. Hubbell, and Frank B. Dazzo. 2001. "Erosion of root epidermal cell walls by Rhizobium polysaccharide-degrading enzymes as related to primary host infection in the Rhizobium–legume symbiosis". Can. J. Microbiol. 47: 475–487

6. Sato Y, Natsume R, Tsuda M, Damborsky J, Nagata Y, Senda T. 2007. "Crystallization and preliminary crystallographic analysis of a haloalkane dehalogenase, DbjA, from Bradyrhizobium japonicum USDA110.". PMID: 17401198.

7. Liu XY, Wang ET, Li Y, Chen WX. 2007. "Diverse bacteria isolated from root nodules of Trifolium, Crotalaria and Mimosa grown in the subtropical regions of China.". PMID: 17497134

8. Zhu D, Mukherjee C, Biehl ER, Hua L. 2007. "Discovery of a mandelonitrile hydrolase from Bradyrhizobium japonicum USDA110 by rational genome mining.". PMID: 17350705

9. SEPPO 0. SALMINEN, JOHN G. STREETER. 1986. "Uptake and Metabolism of Carbohydrates by Bradyrhizobium japonicum Bacteroids". Plant Physiol. 83, 535-540


Edited by Erik Low student of Rachel Larsen and Kit Pogliano KMG