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Open Access Research article

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

Xinxin Li12, Zhiping Deng1, Zhanzhi Liu1, Yongliang Yan3, Tianshu Wang1, Jianbo Xie1, Min Lin3, Qi Cheng3 and Sanfeng Chen12*

Author Affiliations

1 Key Laboratory for Agrobiotechnology, Ministry of Agriculture, China Agricultural University, Beijing 100193, P. R. China

2 Key laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Yuanmingyuan west road no.2, Haidian District, Beijing 100193, P. R. China

3 Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China

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BMC Genomics 2014, 15:723  doi:10.1186/1471-2164-15-723

Published: 27 August 2014

Abstract

Background

Most 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.

Results

We 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.

Conclusions

Our 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.

Keywords:
Paenibacillus sabinae T27; nif gene cluster; nif-like gene; Genome sequence