Alternative nitrogenase and pseudogenes: unique features of the Paenibacillus riograndensis nitrogen fixation system

Biological nitrogen fixation (BNF) is a tightly regulated process that is carried out by diazotrophic microorganisms. The regulatory mechanisms of BNF-related genes are well characterized in Gram-negative models, but they are poorly understood in Gram-positive bacteria. Paenibacillus riograndensis SBR5T is a Gram-positive, endospore-forming facultative aerobic diazotroph. Three clusters of BNF-related genes with dissimilar phylogenetic histories were identified in the P. riograndensis genome, and no regulatory genes were recognized. P. riograndensis nifH2 was considered inactive based on transcript and promoter analyses, whereas transcripts of nifH1 and anfH were induced upon nitrogen-limited conditions. The functionality of the alternative nitrogenase system was also validated by enzymatic activity analysis. Fragments upstream of the two active clusters seem to harbor primary functional promoter sequences, producing a constitutive expression pattern in Escherichia coli. Sequences upstream of the anf genes were not recognized by this heterologous host, indicating a very distinct promoter pattern. These results shed light upon the evolutionary history of nitrogen fixation genes in this Gram-positive bacterium and highlight the presence of novel regulatory elements that are yet to be described.