Identification of Genes Involved in Fe-S Cluster Biosynthesis of Nitrogenase in Paenibacillus polymyxa WLY78

NifS and NifU (encoded by nifS and nifU) are generally dedicated to biogenesis of the nitrogenase Fe-S cluster in diazotrophs. However, nifS and nifU are not found in N-2-fixing Paenibacillus strains, and the mechanisms involved in Fe-S cluster biosynthesis of nitrogenase is not clear. Here, we found that the genome of Paenibacillus polymyxa WLY78 contains the complete sufCDSUB operon, a partial sufC2D2B2 operon, a nifS-like gene, two nifU-like genes (nfuA-like and yutI), and two iscS genes. Deletion and complementation studies showed that the sufC, sufD, and sufB genes of the sufCDSUB operon, and nifS-like and yutI genes were involved in the Fe-S cluster biosynthesis of nitrogenase. Heterologous complementation studies demonstrated that the nifS-like gene of P. polymyxa WLY78 is interchangeable with Klebsiella oxytoca nifS, but P. polymyxa WLY78 SufCDB cannot be functionally replaced by K. oxytoca NifU. In addition, K. oxytoca nifU and Escherichia coli nfuA are able to complement the P. polymyxa WLY78 yutI mutant. Our findings thus indicate that the NifS-like and SufCDB proteins are the specific sulfur donor and the molecular scaffold, respectively, for the Fe-S cluster formation of nitrogenase in P. polymyxa WLY78. YutI can be an Fe-S cluster carrier involved in nitrogenase maturation in P. polymyxa WLY78.

Automated summary

This study identified a number of genes related to nitrogenase Fe-S cluster biosynthesis in Paenibacillus polymyxa WLY78, with nifS-like, SufC, SufD, SufB, and YutI being key genes involved in the formation of the Fe-S cluster of nitrogenase.