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

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.

Genomic Insights into the Symbiotic and Plant Growth-Promoting Traits of “Candidatus Phyllobacterium onerii” sp. nov. Isolated from Endemic Astragalus flavescens

“…The mechanisms underlying Fe-S cluster biosynthesis in various bacterial species involved in nitrogenase are still not well understood. In IY22, a fully functional nif operon was not observed; thus, it is likely that the NifS and SufCDB proteins play the role of a specific sulfur donor and molecular scaffold, sequentially, in the assembly of nitrogenase Fe-S clusters, as observed in P. polymyxa WLY78 [ 64 ]. In contrast, the fixABCX operon in IY22 may be associated with nitrogen fixation, as in Azospirillum [ 65 ].…”

Complete genome sequence of Nguyenibacter sp. L1, a phosphate solubilizing bacterium isolated from Lespedeza bicolor rhizosphere

“…When inoculated into growth medium, Nguyenibacter sp. L1 secretes significantly higher quantities of gluconic acid relative to other organic acids, thereby aiding the solubilization of Al-P ( Li et al, 2021 ). Gluconic acid, a type of organic acid, assists in transforming the immobilized mineral phosphates (which contain phosphorus) into a form that is readily available for biological uptake.…”

“…Within our laboratory, strain L1 has been identified as exhibiting high AlPO4 solubilizing capability and was initially classified as Nguyenibacter based on its 16S rRNA gene sequence ( Li Q. et al, 2021 ). However, given the paucity of genomic information available for this species, a more comprehensive molecular examination of strain L1 is warranted.…”

Assembly of nitrogenase biosynthetic pathway in Saccharomyces cerevisiae by using polyprotein strategy

“…Also, the nitrogenase activity in the mixture of K. oxytoca Fe and MoFe protein is much higher than that in the mixture of P. sabinae Fe and MoFe (Li et al, 2021a). Recently, we have revealed that the sufCDSUB operon, nifS-like and yutI genes were involved in the Fe-S cluster biosynthesis of nitrogenase in P. polymyxa WLY78 (Li et al, 2021b). In the future, we can co-express nifH and these genes involved in Fe-S cluster biosynthesis of P. polymyxa WLY78 in yeast to investigate whether the Fe activity can be enhanced.…”