Bradyrhizobium japonicum USDA 110

Bradyrhizobium_japonicum
Names Bradyrhizobium japonicum USDA 110
Accession numbers NC_004463
Background Rhizobium, Bradyrhizobium, Mesorhizobium, Sinorhizobium, and Azorhizobium - known as rhizobia - are symbiotic nitrogen fixers that can be found in the roots of plants and especially in legume plants. They are responsible for the worlds largest portion of fixed atmospheric nitrogen. (Nitrogen-fixation by organisms provides about 65% of the the biosphere's available nitrogen (Lodwig et al. 2003).) Bradyrhizobium japonicum has been used since 1957 in molecular genetics, physiology, and ecology due to its exellent ability in symbiotic nitrogen fixation.The genome of Rhizobium sp. NGR234 has a genome structure much like Agrobacterium tumefaciens, which comes in three parts. However, while Agrobacterium tumefaciens has a circular chromosome, a linear chromosome, and a megaplasmid, Rhizobium sp. NGR234 has a chromosome 3.5 Mb in length, a megaplasmid of more than 2 Mb (pNGR234b), and a smaller plasmid 536,165 bp in length (pNGR234a) that carries most of the genes used for symbioses with legumes. The average G-C content of the entire genome is about 61.2 mol %. Most of the assumed coding sequences in the Rhizobium sp. NGR234 genome can be "distributed into functional classes similar to those in Bacillus subtilis, [however,] functions related to transposable elements are more abundant in NGR234" (Viprey et al. 2000).The genome of Bradyrhizobium japonicum is a single chromosome 9,105,828 bp in length. The average G-C content of the genome is 64.1 mol %. Fifty-two percent of the 8317 potential protein-coding genes are like genes of known function, 30% of the genes are hypothetical, and 18% have no similarity to any reported genes. In addition, 34% of the genes were like genes in Mesorhizobium loti and Sinorhizobium meliloti, and 23% of the genes were unique to Bradyrhizobium japonicum (Kaneko et al.).The genome of Sinorhizobium meliloti is similar to Rhizobium sp. NGR234; it has a 3.65 Mb chromosome, a 1.35 Mb megaplasmid (pSymA), and a 1.68 Mb megaplasmid (pSymB). All three genomic elements contribute in some way to plant symbiosis (Galibert et al. 2001).Mesorhizobium and Azorhizobium have not been genetically sequenced but are known to carry out similar processes to other rhizobia.Rhizobium, Bradyrhizobium, Mesorhizobium, Sinorhizobium, and Azorhizobium - collectively known as rhizobia - are Gram-negative, nitrogen-fixing bacteria that form nodules on host plants. They also have symbiotic relationships with legume plants, which can't live without these bacteria's essential nitrogen-fixing processes. In nodules, the rhizobia bacteriods use carbon and energy from the plant in the form of dicarboxylic acids. Recent studies have suggested that the bacteroids do more than just provide the plant with ammonium (through nitrogen fixation). It was shown that a more complex amino-acid cycle is needed for Rhizobium to successfully fix nitrogen in pea nodules. Rhizobium can use the amino acids from the plant to shut down their ammonium assimilation; however, the bacteria must provide the plant with ammonium in order to obtain the amino acids. This alone would mean that the plant could regulate the amount of dicarboxylate that the bacteroids use by amino acid supply and dominate the relationship. This is not the case, however, because the bacteroids "act like plant organelles to cycle amino acids back to the plant for asparagine synthesis," making the plant dependent on them (Lodwig et al. 2003). This system creates mutualism between the bacteria and the plant.However, nitrogen fixation is an energy expensive process that requires up to 22% of the plants net photosynthate. In addition, at least 25% of the electron flux through the nitrogenase goes towards reducing protons into hydrogen gas. This process of nitrogenase-dependent hydrogen production is a major factor in the efficiency of symbiotic nitrogen fixation. To have more efficient energy use, some Rhizobium and many Bradyrhizobium strains recycle the hydrogen produced by nitrogenase in nodule bacteroids that have a hydrogen uptake system (Hup). However, Sinorhizobium meliloti, M. ciceri, and R. leguminosarum by. viciae UML2 strains have poor expression of the hup system (Palacios et al. 2000).Rhizobia can be found in the roots, or rhizosphere, of other types of plants where they cause the formation of nodules. For example, Bradyrhizobium japonicum was first isolated from a soybean nodule in Florida in 1957. Rhizobium sp. NGR234 has a host range of more than 112 genera of legumes (Viprey et al. 2000). These symbiotic relationships occur when rhizobia penetrate their hosts with centripetally-developing infection threads. The bacterium induces the a meristem at the cortex of the plant roots where nodules then develop. Meanwhile, the infection threads make their way into the nodule cells and release rhizobia into the cytoplasm of infected cells. The rhizobia, which act as symbiosomes, enlarge and differentiate into nitrogen-fixing bacteroids, which have low free-oxygen levels. The symbiotic development comes from an exchange of chemical signals between the plant and the bacteria. One of the first signals in this continuous exchange are called flavonoids and are released by the legume roots. They actually activate the expression of nodulation genes (nod, noe, and nol) by interacting with rhizobial regulators of the NodD family. Most of these nodulations genes then help synthesis and secrete a family of lipochito-oligosaccharide molecules that help the bacteria get into the root hairs (Viprey et al. 2000). (From http://microbewiki.kenyon.edu/index.php/Bradyrhizobium) (MicrobeWiki: Bradyrhizobium)
Taxonomy
Kingdom:Bacteria
Phylum:Proteobacteria
Class:Alphaproteobacteria
Order:Rhizobiales
Family:Bradyrhizobiaceae
Genus:Bradyrhizobium
Species:japonicum
Strain USDA 110
Complete Yes
Sequencing centre (20-NOV-2002) Kazusa DNA Research Institute, The First Laboratory for Plant Gene Research, 2-6-7 Kazusa-kamatari,
(27-DEC-2002) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA
Sequencing quality Level 6: Finished
Sequencing depth NA
Sequencing method Sanger
Isolation site Soybean nodule in 1957 in Florida USA
Isolation country USA
Number of replicons 1
Gram staining properties Negative
Shape Bacilli
Mobility Yes
Flagellar presence Yes
Number of membranes 2
Oxygen requirements Aerobic
Optimal temperature 25.0
Temperature range Mesophilic
Habitat HostAssociated
Biotic relationship Symbiotic
Host name Soybean
Cell arrangement NA
Sporulation NA
Metabolism Nitrogen fixation
Stores polyhydroxybutyrate
Energy source Photosynthetic
Diseases NA
Pathogenicity No
Glycolysis / Gluconeogenesis
Citrate cycle (TCA cycle)
Pentose phosphate pathway
Pentose and glucuronate interconversions
Fructose and mannose metabolism
Fatty acid metabolism
Synthesis and degradation of ketone bodies
Purine metabolism
Pyrimidine metabolism
Alanine, aspartate and glutamate metabolism
Glycine, serine and threonine metabolism
Cysteine and methionine metabolism
Valine, leucine and isoleucine degradation
Geraniol degradation
Valine, leucine and isoleucine biosynthesis
Lysine biosynthesis
Arginine and proline metabolism
Histidine metabolism
Tyrosine metabolism
Phenylalanine metabolism
Chlorocyclohexane and chlorobenzene degradation
Benzoate degradation
Bisphenol degradation
Fluorobenzoate degradation
Tryptophan metabolism
Phenylalanine, tyrosine and tryptophan biosynthesis
beta-Alanine metabolism
Taurine and hypotaurine metabolism
Selenocompound metabolism
Cyanoamino acid metabolism
D-Glutamine and D-glutamate metabolism
D-Arginine and D-ornithine metabolism
D-Alanine metabolism
Starch and sucrose metabolism
Lipopolysaccharide biosynthesis
Peptidoglycan biosynthesis
Pyruvate metabolism
Toluene degradation
Polycyclic aromatic hydrocarbon degradation
Chloroalkane and chloroalkene degradation
Naphthalene degradation
Aminobenzoate degradation
Glyoxylate and dicarboxylate metabolism
Nitrotoluene degradation
Propanoate metabolism
Styrene degradation
Butanoate metabolism
C5-Branched dibasic acid metabolism
One carbon pool by folate
Carbon fixation in photosynthetic organisms
Thiamine metabolism
Riboflavin metabolism
Vitamin B6 metabolism
Nicotinate and nicotinamide metabolism
Pantothenate and CoA biosynthesis
Biotin metabolism
Lipoic acid metabolism
Folate biosynthesis
Atrazine degradation
Porphyrin and chlorophyll metabolism
Terpenoid backbone biosynthesis
Limonene and pinene degradation
Nitrogen metabolism
Sulfur metabolism
Caprolactam degradation
Aminoacyl-tRNA biosynthesis