Genetic Organization and Transcriptional Regulation of Rhizobial Nodulation Genes

Abstract

The ability of Rhizobium spp., Mesorhizobium spp., Sinorhizobium spp., Bradyrhizobium spp. and Azorhizobium spp., collectively called rhizobia, to nodulate plants is determined by both plant and bacterial genes. Nodulation genes are defined as those rhizobial genes which play a role in nodulation or which are coordinately regulated with such genes. In chronological order of discovery they were designated as nod, nol and noe genes followed by a subsequent letter of the alphabet. Thus, nodA, nodB and nodC were the first nodulation genes described (Rossen et al., 1984; Török et al., 1984), and noeL in Rhizobium sp. NGR234 was the one most recently identified (Freiberg et al., 1997). Homologous nodulation genes in various rhizobia have identical names. Protein products of nodulation genes commonly are represented with a capitalized abbreviation (e.g. NodA is the protein encoded by the nodA gene). The nodD-homologue syrM was identified as a symbiotic regulator involved both in enhanced exopolysaccharide synthesis and in nodulation gene regulation (Mulligan and Long, 1989) and is therefore also discussed in this chapter. Initial studies on nodulation genes were carried out mainly in Sinorhizobium meliloti and in Rhizobium leguminosarum biovars viciae and trifolii. The identification of nodulation genes was advanced enormously by the discovery that in these rhizobia many of the nodulation genes are localized extra chromosomal on a large indigenous plasmid (Johnston and Beringer, 1977). These plasmids encoding symbiotic functions are the so-called Sym plasmids whose size can be even as large as one third of the chromosome in the case of S. meliloti (Banfalvi et al., 1981). When these rhizobial strains are cured of their Sym plasmid, they are unable to nodulate, whereas re-introduction of the homologous or a heterologous Sym plasmid restored nodulation (Bánfalvi et al., 1981; Beynon et al., 1980; Djordjevic et al., 1983; Hooykaas et al., 1981; Johnston et al., 1978; Kondorosi et al., 1982; van Brussel et al., 1982). Transferring the rhizobial Sym plasmid into Agrobacterium tumefaciens and Philobacterium myrsinacearum also results in a capacity to induce root nodule formation (Hooykaas et al., 1981, 1982; Rodriquez-Quinones et al., 1989; van Veen et al., 1988). The development of genetic tools, such as the availability of broad-host range cloning and cosmid vectors (Ditta et al., 1980; Friedman et al., 1982), construction of cosmid libraries, complementation and mapping of nodulation-deficient mutants, introduction of random and directed transposon mutagenesis techniques coupled to marker exchange (Beringer et al., 1978; Buchanan-Wollaston, 1979; Meade et al., 1982) or used in combination with phage transduction methods (Pees et al., 1986; Wijffelman et al., 1985), led to the identification of regions involved in nodulation and, subsequently the first nodulation genes (Djordjevic et al., 1985; Downie et al., 1983, 1985; Fisher et al., 1985; Kondorosi et al., 1984; Rossen et al., 1984; Schofield et al., 1984; Török et al., 1984). DNA sequence analysis, as well as complementation studies, revealed that some nodulation genes are conserved in all rhizobia, whereas others are restricted to a few or a single species or strain. Thus, in early literature nodulation genes were designated as “common” or “host specific” (hsn) respectively (Horvath et al., 1986; Kondorosi et al., 1984; Putnoky and Kondorosi, 1986). The DNA sequence revealed also that promoters of many nodulation genes contain a conserved DNA sequence called the nod box that allows coordinated regulation of nod genes (Rostas et al., 1986).