In Rhizobium species, nodulation genes together with other symbiotic genes, are located on large-plasmids (Sym plasmids). Sym plasmids vary from 50 to over 600 kb in R. leguminosarum bv. Trofoli to 1200 to 1500 kb in R. meliloti. Nodulation genes, nod and nol genes, are classified as regulatory, common and host specific. Regulation of nod genes is controlled by the nod gene, of which all rhizobia tested so far contain one or more copies. In conjunction with plant flavonoids or other phenolic compounds, nod proteins act as transcriptional activators of inducible nod genes. Different nod proteins respond to specific plant signal molecules and, therefore, contribute to host specificity of nodulation. Most nod genes are constitutively expressed, others are autoregulated.
The common nodABC genes are structurally and functionally conserved among Rhizobium, Bradyrhizobium and Azorhizobium strains. The inactivation of these genes completely abolishes root-hair infection and nodule formation.
Nif Genes and their regulation
K. pneumoniae: The N2 fixation (Nif) genes are organized into a regulon of 17 genes, consisting of seven or eight operons each of which is transcribed into a single, usually polycistronic mRNA. Although only five of the gene products have been purified and properly characterized, functions have been assigned to all of the gens except for nifX and nifY.
Regulation of nif gene expression has two elements, an external system designated ntr and an internal system mediated by nif A and nif L. The ntr system responds to conditions of nitrogen starvation by activating genes that enable the organism to utilize 'unusal' nitrogen sources such as arginine, proline, and histidines as well as N2 itself, in the last case by switching on the nif genes.
Actually the ntrA gene product (NtrA) is a factor of RNA polymerase which recognizes the nif and, other ntr- regulated genes, these promoters have a structure different from that of typical bacterial promoters. Ntr allows RNA polymerase to bind at the nif promoters and to initiate transcription there. The ntrB gene product (NtrB) is an enzyme that functions both as protein kinase and as a phophatase, the substrate of which NtrC (the ntrC gene product). Whether kinase or phosphatase activity predominates depends upon the nitrogen status of the bacterium, and the consequence of this is that, under condition of starvation, NtrC-P acts as an activator of, among other operons, nif LA. The nifA product is an activator of transcription of other nif genes, whilst the nif L product, in the presence of either intermediate concentrations of fixed nitrogen or O2, inactivate the nifA product, thereby preventing transcription of other nif genes.
In heterocystous cyanobacteria, the acquisition of nitrogenase activity in response to nitrogen deficiency is accompanied by the differentiation of vegetative cells into a specialized structure called 'heterocysts'.
All non-heterocystous cyanobavteria possess the genes nif H, nif D, nif K as a cluster which is similar to K. pneumoniae. In the DNA of vegetative cells of hetreocystous cyanobacteria the gene nif K is separated from the genes nif D and nif H . During the differentiation the intervening DNA of about 11000 base pairs (ii kb) is excised as a circle resulting in a clustered nif HDK operon. This excision is catalysed by the product of a gene, xisA, located within the excised 11 kb region.
A second rearrangement occurs in the region of nif S, a gene involved in K. pneumoniae. In this arrangement, a segment of DNA of approximately 50 kb is excised, again as a circle, and after this rearrangement an operon with the structure nifB: ORF-1: nifS:ORF-2 is formed. The excision occurs between ORF-1 and nifS, which is not catalysed by the xisA product.
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