The Rhizobium leguminosarum genome project

We have determined the complete genome sequence of Rhizobium leguminosarum biovar viciae strain 3841. The sequencing and annotation were carried out at the Sanger Institute, with funding provided by the Biotechnology and Biological Science Research Council (BBSRC). The award holders were:

The annotated sequence is available from the  R. leguminosarum web page of the Sanger Institute, as GenBank entries from NCBI, and from Rhizobase.

We have published a description of the genome:
Young JPW, Crossman L, Johnston A, Thomson N, Ghazoui Z, Hull K, Wexler M, Curson A, Todd J, Poole P, Mauchline T, East A, Quail M, Churcher C, Arrowsmith C, Cherevach I, Chillingworth T, Clarke K, Cronin A, Davis P, Fraser A, Hance Z, Hauser H, Jagels K, Moule S, Mungall K, Norbertczak H, Rabbinowitsch E, Sanders M, Simmonds M, Whitehead S, Parkhill J (2006) The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biology 7, R34. [Open Access] **Highly Accessed **

Here are a few of the analyses extracted from that paper.

Genome statistics for Rhizobium leguminosarum biovar viciae 3841
Base pairs
Protein-coding genes
Mean protein length (a. a.)
rRNA operons
tRNA genes

Key to gene colours in the circular maps
0 - white - Pathogenicity/Adaptation/Chaperones (shown here in dark blue)
1 - dark grey - energy metabolism (glycolysis, electron transport etc.)
2 - red - Information transfer (transcription/translation + DNA/RNA modification)
3 - bright green - Surface (IM, OM, secreted, surface structures[LPS etc])
4 - not used
5 - turquoise - Degradation of large molecules
6 - pink/purple - Degradation of small molecules
7 - yellow - Central/intermediary/misc metabolism
8 - pale green - Unknown
9 - pale blue - Regulators
10 - orange/brown - Conserved hypo
11 - dark brown - Pseudogenes and partial genes (remnants)
12 - light pink - Phage/IS elements
13 - light grey - Some misc. infomation e.g. Prosite, but no function

gene functions The distribution of functional classes of genes is fairly similar in the chromosome and larger plasmids, but pRL7 is very different.

phylogeny A phylogeny based on 648 orthologous protein sequences shared among seven alpha-proteobacterial genomes is similar to that based on small subunit ribosomal RNA

All protein-coding genes on the chromosome and six plasmids of R. leguminosarum 3841, showing their nucleotide composition (GC3s: G+C content of silent third positions of codons).Symbols indicate whether each gene encodes a protein with orthologs in A. tumefaciens, S. meliloti and M. loti, and, if so, which phylogenetic topology it supports*.In addition, the nodulation genes nodOTNMLEFDABCIJ are identified on pRL10.
*RA-SM indicates a phylogeny that places Agrobacterium closest to Rhizobium, and so on

dinucleotide composition Dinucleotide compositional analysis of 100 kb regions of the genomes of R. leguminosarum 3841 and Agrobacterium tumefaciens C58, displaying the first two axes of a principal components analysis of the abundance of dinucleotides.  Each chromosome (chr) and plasmid is identified by a distinct symbol.  It is evident that the chromosome of each species has a different but consistent composition, while the smaller plasmids are more similar to each other.

The organism

Rhizobia are bacterial symbionts of legumes (plants in the family Fabaceae). They trigger the formation of root nodules, within which they convert atmospheric nitrogen into ammonia that is utilised by the plant. This symbiotic nitrogen fixation is of global ecological significance in the nitrogen cycle, and of great importance in agriculture.

Almost all known rhizobia belong to the alpha-2 group of the Proteobacteria. Rhizobium leguminosarum is the type species of the type genus. It has three biovars - viciae, trifolii, phaseoli - that differ in their host specificity. Biovar viciae nodulates legumes in the Tribe Viciae - Vicia, Pisum, Lathyrus, Lens. The host-specificity genes are carried on large plasmids that also carry the genes for nitrogen fixation.

R. leguminosarum biovar viciae strain 3841 has been widely used in laboratory studies over the past 20 years. It is a spontaneous streptomycin-resistant mutant of strain 300. It has a circular chromosome and 6 circular plasmids, ranging in size from approximately 147 to 870 kb. One of these plasmids (pRL10JI) carries the genes for nodulation and nitrogen fixation, but the function of the great majority of the plasmid-borne genes is unknown at present. All strains of R. leguminosarum have several large plasmids, but the number and sizes of plasmids varies among strains. This large number of plasmids distinguishes R. leguminosarum from the other rhizobia for which complete genome sequences have been determined.

Genome sequences of other rhizobia

The complete genome sequences of several rhizobia and related bacteria have already been determined:

Mesorhizobium loti strain MAFF303099 has a large circular chromosome, into which the nodulation and nitrogen fixation genes are integrated as a "symbiosis island", and two circular plasmids. Its host plants are Lotus japonicus and related species.  Note that a comparison of several basic genes suggests that this strain is more similar to the type strain of M. huakuii than to that of M. loti (TURNER, S L, ZHANG, X X, LI, F D, YOUNG  J P W. 2002. What does a bacterial genome sequence represent? Mis-assignment of MAFF 303099 to the genospecies Mesorhizobium loti.  Microbiology 148: 3330-3331.)

Sinorhizobium meliloti strain 1021 has a circular chromosome and two circular megaplasmids, one of which carries the nodulation and nitrogen fixation genes. Its host plants are alfalfa, Medicago sativa, and related species.

Agrobacterium tumefaciens strain C58 has a circular chromosome, a linear megaplasmid, and two circular plasmids. The smallest plasmid carries genes for tumour induction. This species is not a rhizobium, in that it does not nodulate legumes or fix nitrogen. Instead, it is a pathogen that causes stem galls on a wide range of plants. A. tumefaciens is, however, more closely related to R. leguminosarum than is either of the other two species, and some taxonomists favour its inclusion within the genus Rhizobium as R. radiobacter.
Bradyrhizobium japonicum strain 110 has a very large chromosome (9.1 Mb) but no plasmids. As in Mesorhizobium loti, the symbiosis genes are in an "island" of lower G+C content.

 Brucella melitensis strain 16M and B. suis strain 1330 are animal pathogens, not rhizobia.  They both have two small chromosomes (2.1 and 1.2 Mb).  These strains are very similar in sequence and could be considered to belong to the same species.  The larger chromosome shows extensive synteny with the chromosomes of Sinorhizobium meliloti and Agrobacterium tumefaciens.

Rhizobium etli  is a close relative of R. leguminosarum, and the complete genome of strain CFN42 has been published.

A number of other genome projects for rhizobia have been completed or are under way, including the genomes of beta-proteobacteria that form root nodules on legumes, including Burkholderia phymatum STM815 and Cupriavidus taiwanensis LMG19424.

This page is maintained by Peter Young at the University of York, and was updated on 8 April 2008.