Abstract
We provide here a comparative genome analysis of 31 strains within the genus Paenibacillus including 11 new genomic sequences of N2-fixing strains. The heterogeneity of the 31 genomes (15 N2-fixing and 16 non-N2-fixing Paenibacillus strains) was reflected in the large size of the shell genome, which makes up approximately 65.2% of the genes in pan genome. Large numbers of transposable elements might be related to the heterogeneity. We discovered that a minimal and compact nif cluster comprising nine genes nifB, nifH, nifD, nifK, nifE, nifN, nifX, hesA and nifV encoding Mo-nitrogenase is conserved in the 15 N2-fixing strains. The nif cluster is under control of a σ70-depedent promoter and possesses a GlnR/TnrA-binding site in the promoter. Suf system encoding [Fe–S] cluster is highly conserved in N2-fixing and non-N2-fixing strains. Furthermore, we demonstrate that the nif cluster enabled Escherichia coli JM109 to fix nitrogen. Phylogeny of the concatenated NifHDK sequences indicates that Paenibacillus and Frankia are sister groups. Phylogeny of the concatenated 275 single-copy core genes suggests that the ancestral Paenibacillus did not fix nitrogen. The N2-fixing Paenibacillus strains were generated by acquiring the nif cluster via horizontal gene transfer (HGT) from a source related to Frankia. During the history of evolution, the nif cluster was lost, producing some non-N2-fixing strains, and vnf encoding V-nitrogenase or anf encoding Fe-nitrogenase was acquired, causing further diversification of some strains. In addition, some N2-fixing strains have additional nif and nif-like genes which may result from gene duplications. The evolution of nitrogen fixation in Paenibacillus involves a mix of gain, loss, HGT and duplication of nif/anf/vnf genes. This study not only reveals the organization and distribution of nitrogen fixation genes in Paenibacillus, but also provides insight into the complex evolutionary history of nitrogen fixation.
Highlights
Biological nitrogen fixation, the conversion of atmospheric N2 to NH3, plays an important role in the global nitrogen cycle and in world agriculture [1]
The 31 genomes vary in size by approximately three megabases with the number of coding sequences (CDSs) ranging from 4460–9087, indicating substantial strain-tostrain variation
We sequenced the genomes of 11 N2-fixing Paenibacillus strains and made a comparative genomic analysis with 20 other strains (4 N2-fixing and 16 non-N2-fixing strains) that were sequenced previously
Summary
Biological nitrogen fixation, the conversion of atmospheric N2 to NH3, plays an important role in the global nitrogen cycle and in world agriculture [1]. Nitrogen fixation is mainly catalyzed by the Mo-nitrogenase. The contents and organization of nitrogen fixation (nif) genes vary significantly among the different N2-fixing organisms. In Klebsiella pneumoniae, twenty nif genes are co-located within a ,24 kb cluster [3], whereas in Azotobacter vinelandii the nif genes are more dispersed and distributed as two clusters in the genome [4]. The random distribution pattern and the difference in contents and organization of nif genes raise the question of origins and evolution of Monitrogenase. Phylogenetic inference based on the sequences of nif genes is generally used to understand the evolution of nif genes [5,6,7]. Two conflicting hypotheses for origins of Mo-nitrogenase have been proposed on the basis of phylogenetic examination of
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