Potential Symbiosis-Specific Genes Uncovered by Sequencing a 410-Kilobase DNA Region of the Bradyrhizobium japonicum Chromosome

Abstract

The physical and genetic map of the Bradyrhizobium japonicum chromosome revealed that nitrogen fixation and nodulation genes are clustered. Because of the complex interactions between the bacterium and the plant, we expected this chromosomal sector to contain additional genes that are involved in the maintenance of an efficient symbiosis. Therefore, we determined the nucleotide sequence of a 410-kb region. The overall G؉C nucleotide content was 59.1%. Using a minimum gene length of 150 nucleotides, 388 open reading frames (ORFs) were selected as coding regions. Thirty-five percent of the predicted proteins showed similarity to proteins of rhizobia. Sixteen percent were similar only to proteins of other bacteria. No database match was found for 29%. Repetitive DNA sequence-derived ORFs accounted for the rest. The sequenced region contained all nitrogen fixation genes and, apart from nodM, all nodulation genes that were known to exist in B. japonicum. We found several genes that seem to encode transport systems for ferric citrate, molybdate, or carbon sources. Some of them are preceded by ؊24/؊12 promoter elements. A number of putative outer membrane proteins and cell wall-modifying enzymes as well as a type III secretion system might be involved in the interaction with the host.Nodulation (nod) genes and nitrogen fixation (nif) genes are the key determinants in the interaction between rhizobia and their host plants (14, 47). However, other loci influence the efficiency of the interaction or change the host range. Sequencing of the symbiotic plasmid of Rhizobium sp. strain NGR234 revealed a gene cluster that encodes a type III secretion system (22). Secreted proteins are encoded within the same cluster (95). The closely related Sinorhizobium fredii carries a type III secretion system as well (51, 61). Mutations within the secretion systems of the two strains influence symbiosis in a hostdependent manner. Plant and animal pathogens use related systems to target proteins to host cells (35), but such proteins have not been identified in rhizobia.During symbiosis, rhizobia exclusively rely on the carbon supply from the plant. Although bacteroids can utilize a wide range of carbon compounds, dicarboxylic acids are most likely the main carbon and energy source for bacteroids (45,83). The main argument is that several strains that have a defect in the dicarboxylic acid transport system show a Fix Ϫ phenotype (7,17,19,79,94) or are at least strongly impaired in nitrogen fixation (37).In our earlier work, we established a correlated physical and genetic map of the Bradyrhizobium japonicum genome (28,53) and discovered that all known nod and nif genes were clustered within a chromosomal region of about 400 kb. Furthermore, we found that the GϩC content of these genes was 58 mol% (76), considerably lower than the 61 to 65 mol% reported for the whole genome (43). Therefore, we concluded that the symbiotic genes have integrated into the chromosome after horizontal gene transfer from a different strain. In the absence of genomi...

Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid

“…NGR234a sym plasmid (31) and the complete genome of Mesorhizobium loti (4) are presented in the aforementioned overview paper, we will comment only on specific examples here. The sequence of a 410-kb region of the B. japonicum chromosome was recently reported (32), but except for the symbiotic genes (nod, nif, and fix), most genes in the region are not conserved in pSymA. More detailed analyses are available at http:͞͞sequence.toulouse.inra.fr͞meliloti.…”

Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California

“…Bradyrhizobium can nodulate diverse wild legumes as well as staple crops such as soybeans (Glycine), peanuts (Arachis), and cowpea (Vigna) [38,39]. In the model genome, Bradyrhizobium diazoefficiens strain USDA110 (previously B. japonicum), symbiosis-specific genes are clustered within a 410-kb symbiosis island in which the G+C content differs from the rest of the genome [40]. Some divergent Bradyrhizobium spp.…”

Potential for alternative intron–exon pairings in group II intron RmInt1 from Sinorhizobium meliloti and its relatives

“…For the Bacteroides thetaiotaomicron intron, two possible registers of EBS2-IBS2 are shown. Published group II intron sequences that were found to be part of subgroup IIB3 (Toro 2003) with 100% bootstrap support based on phylogenetic analysis (see Ferat et al 2003) of group II intron-encoded proteins using the PROTDIST program in PHYLIP (Phylogeny Inference Package v.3.6a2, University of Washington, Seattle) (accession numbers are followed by intron coordinates, when necessary, and reference[s]): E. coli IntA (AF512502, Dai and Zimmerly 2002b;Ferat et al 1993); E. coli IntB (X77508, Ferat et al 1994); Sinorhizobium meliloti RmInt1 (Y11597, Martínez-Abarca et al 1998); Ensifer adhaerens (AY248839 and AY248840, Fernandez-Lopez et al 2005); Sinorhizobium terangae (AY60890, Fernandez-Lopez et al 2005); uncultured archaeon clone GZfos32G12 (AY714856, 10054-11891, Hallam et al 2004); Methanosarcina acetivorans (NC_003552, 3708831-3706957, Galagan et al 2002); Ralstonia eutropha (AY305378, 23468-25305, Schwartz et al 2003); Photorhabdus luminescens (BX571862, 232816-234697, Duchaud et al 2003); Bradyrhizobium japonicum (AF322013, 154084-155888, Gottfert et al 2001); Bacteroides thetaiotaomicron (NC_004663, 3256655-3254752, Xu et al 2003); uncultured marine bacterium (AY075117, Podar et al 2002); E. coli IntC (AF512503, Ferat et al 1993;Dai and Zimmerly 2002b).…”