Revealing potential functions of hypothetical proteins induced by genistein in the symbiosis island of Bradyrhizobium japonicum commercial strain SEMIA 5079 (= CPAC 15)

Abstract

Background: Bradyrhizobium japonicum strain SEMIA 5079 (= CPAC 15) is a nitrogen-fixing symbiont of soybean broadly used in commercial inoculants in Brazil. Its genome has about 50% of hypothetical (HP) protein-coding genes, many in the symbiosis island, raising questions about their putative role on the biological nitrogen fixation (BNF) process. This study aimed to infer functional roles to 15 HP genes localized in the symbiosis island of SEMIA 5079, and to analyze their expression in the presence of a nod-gene inducer.

Results: A workflow of bioinformatics tools/databases was established and allowed the functional annotation of the HP genes. Most were enzymes, including transferases in the biosynthetic pathways of cobalamin, amino acids and secondary metabolites that may help in saprophytic ability and stress tolerance, and hydrolases, that may be important for competitiveness, plant infection, and stress tolerance. Putative roles for other enzymes and transporters identified are discussed. Some HP proteins were specific to the genus Bradyrhizobium, others to specific host legumes, and the analysis of orthologues helped to predict roles in BNF.

Conclusions: All 15 HP genes were induced by genistein and high induction was confirmed in five of them, suggesting major roles in the BNF process.

Keywords: Biological nitrogen fixation; Functional inference; Gene expression; Symbiosis.

Fig. 1

Genomic neighborhood of the 14 hypothetical protein-coding genes and of the aspC gene selected for this study in the symbiosis island of Bradyrhizobium japonicum strain SEMIA 5079 (= CPAC 15)

Fig. 2

Distribution of the selected hypothetical proteins and of the aspC gene of Bradyrhizobium japonicum strain SEMIA 5079 (= CPAC 15) in other genomes of Bradyrhizobium species and strains not classified at species level

Fig. 3

Phylogenetic inference of GFA proteins of Bradyrhizobium strains showing similarity with BJS_07621 of Bradyrhizobium japonicum SEMIA 5079 (= CPAC 15) and the relation with their host plants. B. sp. refers to strains not classified at the species level, only as Bradyrhizobium sp

Fig. 4

Phylogenetic inference of trypsin-like peptides of Bradyrhizobium strains showing similarity with BJS_08254 and BJS_08251 of Bradyrhizobium japonicum SEMIA 5079 (= CPAC 15) and the relation with their host plants. B. sp. refers to strains not classified at the species level, only as Bradyrhizobium sp

Fig. 5

Expression levels of the hypothetical protein-coding and of aspC (bjs_08258) genes localized in the symbiosis island of Bradyrhizobium japonicum strain SEMIA 5079 (= CPAC 15) when induced by the nod-gene inducer genistein. Expression data shown for each gene represent the average of three biological replicates, with each one with three technical replicates. Data were normalized in relation to the endogen control (16 S rRNA gene). ^*All genes obtained an expression statistically significant at the 5% level determined by REST2009 software