The genome of Paenibacillus sabinae T27 provides insight into evolution, organization and functional elucidation of nif and nif-like genes

Abstract

BackgroundMost biological nitrogen fixation is catalyzed by the molybdenum nitrogenase. This enzyme is a complex which contains the MoFe protein encoded by nifDK and the Fe protein encoded by nifH. In addition to nifHDK, nifHDK-like genes were found in some Archaea and Firmicutes, but their function is unclear.ResultsWe sequenced the genome of Paenibacillus sabinae T27. A total of 4,793 open reading frames were predicted from its 5.27 Mb genome. The genome of P. sabinae T27 contains fifteen nitrogen fixation (nif) genes, including three nifH, one nifD, one nifK, four nifB, two nifE, two nifN, one nifX and one nifV. Of the 15 nif genes, eight nif genes (nifB, nifH, nifD, nifK, nifE, nifN, nifX and nifV) and two non-nif genes (orf1 and hesA) form a complete nif gene cluster. In addition to the nif genes, there are nitrogenase-like genes, including two nifH-like genes and five pairs of nifDK-like genes. IS elements on the flanking regions of nif and nif-like genes imply that these genes might have been obtained by horizontal gene transfer. Phylogenies of the concatenated 8 nif gene (nifB, nifH, nifD, nifK, nifE, nifN, nifX and nifV) products suggest that P. sabinae T27 is closely related to Frankia. RT-PCR analysis showed that the complete nif gene cluster is organized as an operon. We demonstrated that the complete nif gene cluster under the control of σ70-dependent promoter enabled Escherichia coli JM109 to fix nitrogen. Also, here for the first time we demonstrated that unlike nif genes, the transcriptions of nifHDK-like genes were not regulated by ammonium and oxygen, and nifH-like or nifD-like gene could not restore the nitrogenase activity of Klebsiella pneumonia nifH− and nifD− mutant strains, respectively, suggesting that nifHDK-like genes were not involved in nitrogen fixation.ConclusionsOur data and analysis reveal the contents and distribution of nif and nif-like genes and contribute to the study of evolutionary history of nitrogen fixation in Paenibacillus. For the first time we demonstrated that the transcriptions of nifHDK-like genes were not regulated by ammonium and oxygen and nifHDK-like genes were not involved in nitrogen fixation.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-723) contains supplementary material, which is available to authorized users.

Evolution and Functional Analysis of orf1 Within nif Gene Cluster from Paenibacillus graminis RSA19

“…In this study, sequence analysis and RT-PCR demonstrated that the 10 genes nifB nifH nifD nifK nifE nifN nifX orf1 hesA nifV in P. graminis RSA19 were organized as an operon under the control of a -35/-10 type σ 70 -dependent promoter located upstream of nifB ( Figure 4 ). Similar results that the 10 genes nifB nifH nifD nifK nifE nifN nifX orf1 hesA nifV in P. sabinae T27 are organized as an operon were reported in [ 10 ]. In this study, qRT-PCR results showed that these 10 genes within the nif gene operon under N 2 -fixing condition (without NH 4 + and O 2 ) exhibited a significant transcript ranging from 60- to 1300-fold compared to non-N 2 -fixing condition (100 mM NH 4 + and 21% O 2 ) ( Figure 5 ), suggesting that nif gene expression in P. graminis RSA19 was strongly regulated by ammonium and oxygen.…”

“…The orf1 located between nifX and hesA is the major pronounced difference in the nif cluster between Sub-group I and Sub-group II [8]. Each of the two nif gene clusters is organized as a single operon and transcribed under the σ 70 promoter located in front of nifB [9,10]. Recently, our studies have revealed that GlnR simultaneously acts as an activator and a repressor for nif gene transcription by binding to two different loci of the single nif promoter region according to nitrogen availability [11].…”

Whole-Genome Sequencing of Bradyrhizobium diazoefficiens 113-2 and Comparative Genomic Analysis Provide Molecular Insights Into Species Specificity and Host Specificity

“…In most rhizobia, expression of genes related to secretion system, surface polysaccharides biosynthesis and RNS is needed for inducing nodule organogenesis and nodule development ( Putnoky et al, 1988 ; Lorkiewicz, 1997 ; Fauvart and Michiels, 2008 ; Li et al, 2014 ), and the type and/or number of these nodule-related genes are often play important roles in host specificity ( Horvath et al, 1986 ; Philip-Hollingsworth et al, 1989 ; Wang et al, 2014 ). Among our six tested strains, S. fredii USDA205 nodulated the same legume host (soybean) with B. diazoefficiens 113-2 and B. diazoefficiens USDA110 ( Table 1 ), while there were no genes related to secretion system, surface polysaccharides biosynthesis and RNS that were both specific and common to these three strains ( Figures 6 , 7 and Tables 4 , 5 ), suggesting that there was no gene specifically shared by rhizobia of different species to establish symbiosis with soybean, which was consistent with a previous study ( Tian et al, 2012 ).…”

Comparative genomic and functional analysis reveal conservation of plant growth promoting traits in Paenibacillus polymyxa and its closely related species

“…Recently, our lab has completed genome sequencing of 13 nitrogen-fixing Paenibacillus spp., including P. polymyxa strains WLY78, TD94 and 1–43 and other nitrogen fixers of this genus 17 18 19 . We compared these strains to each other and to 18 other strains (2 N 2 -fixing strains and 16 non-N 2 -fixing strains) and revealed the heterogeneity, organization and evolution of the nitrogen fixation genes within the 31 genomes.…”