The so-called common nodulation (nod) gene cluster of Bradyrhizobium japonicum is characterized by a unique composition of genes that are arranged in the following order: nodY, nodA, nodB, nodC, nodS, nodU, nodI, nodJ. As reported here, the identification of the two new genes nodS and nodU resulted from the DNA sequencing of a 4.5-kilobase nodC-downstream region covering nodS, nodU, nodI, and nodJ. The predicted NodS, NodU, NodI, and NodJ proteins had the following respective amino acid (aa) lengths and molecular weights (Mr): 209 aa, Mr 23,405; 569 aa, Mr 62,068; 306 aa, Mr 34,127; and 262 aa, Mr 28,194. The 3' end of nodC overlapped the 5' end of nodS by 71 nucleotides. Using translational fusions of lacZ to nodC, nodS, and nodU, the expression of these genes was shown to be inducible by the isoflavone daidzein and depended on transcription from a DNA region farther upstream. These data and the adjacent location of all genes suggested the existence of a nodYABCSUIJ operon. The nodI and nodJ gene products shared about 70% sequence similarity with the corresponding Rhizobium leguminosarum bv. viciae proteins; NodI belongs to the family of ATP-binding proteins that are constituents of bacterial binding protein-dependent transport systems. By interspecies hybridization, DNA regions homologous to nodSU were detected in other strains of Bradyrhizobium. Likewise, nodS- and nodU-like genes were identified in Rhizobium sp. strain NGR234 (A. Lewin, E. Cervantes, W. Chee-Hoong, and W. J. Broughton, Molecular Plant-Microbe Interactions 3:317-326, 1990) in which nodS confers host specificity for Leucaena leucocephala.(ABSTRACT TRUNCATED AT 250 WORDS)