Abstract
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 N2-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.
Highlights
Iron–sulfur (Fe–S) clusters are contained in a diverse group of proteins called Fe– S proteins, which participate in a wide variety of cellular processes, such as nitrogen fixation, respiration, DNA repair, and gene regulation [1,2,3,4]
We searched the genome of P. polymyxa WLY78 by using MetalPredator and identified 118 genes encoding putative Fe–S cluster-containing proteins and Fe–S cluster biosynthetic genes (Table S1)
We report that nifS-like, nifU-like, and sufCDB genes are involved in the Fe–S cluster assembly of nitrogenase in P. polymyxa WLY78
Summary
Iron–sulfur (Fe–S) clusters are contained in a diverse group of proteins called Fe– S proteins, which participate in a wide variety of cellular processes, such as nitrogen fixation, respiration, DNA repair, and gene regulation [1,2,3,4]. Three pathways for Fe–S cluster assembly identified in bacteria are the nitrogen f ixation (Nif) system, the iron sulfur cluster (Isc) system, and the sulfur f ormation (Suf) system [5]. Nitrogenase that catalyzes biological nitrogen fixation comprises two components, the Fe protein and the MoFe protein, and both of these are Fe–S proteins. Genetic and biochemical analysis has revealed that the products of nifU and nifS are required for activation of both Fe and MoFe proteins [7,8]. Subsequent studies have suggested that NifS is a cysteine desulfurase that catalyzes the production of sulfur from L-cysteine, while NifU provides a molecular scaffold for the assembly and transfer of the Fe–S cluster to the components of nitrogenase [9,10,11]
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