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Organization of nif gene cluster in Frankia sp. EuIK1 strain, a symbiont of Elaeagnus umbellata

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Abstract

The nucleotide sequence of a 20.5-kb genomic region harboring nif genes was determined and analyzed. The fragment was obtained from Frankia sp. EuIK1 strain, an indigenous symbiont of Elaeagnus umbellata. A total of 20 ORFs including 12 nif genes were identified and subjected to comparative analysis with the genome sequences of 3 Frankia strains representing diverse host plant specificities. The nucleotide and deduced amino acid sequences showed highest levels of identity with orthologous genes from an Elaeagnus-infecting strain. The gene organization patterns around the nif gene clusters were well conserved among all 4 Frankia strains. However, characteristic features appeared in the location of the nifV gene for each Frankia strain, depending on the type of host plant. Sequence analysis was performed to determine the transcription units and suggested that there could be an independent operon starting from the nifW gene in the EuIK strain. Considering the organization patterns and their total extensions on the genome, we propose that the nif gene clusters remained stable despite genetic variations occurring in the Frankia genomes.

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Acknowledgments

This research was supported in part by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (grant No. 2009-0076694) to C.S. An. In addition, C.J. Oh was supported by the BK21 Post-Doctoral Research fellowship from the Ministry of Education, Science and Technology.

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Authors and Affiliations

  1. School of Biological Sciences, Seoul National University, Seoul, 151-747, Korea

    Chang Jae Oh, Won Jin Kim & Chung Sun An

  2. Natural Science Research Institute, Myongji University, Yongin, 449-728, Korea

    Ho Bang Kim

  3. Department of Plant Biology, Cornell University, Ithaca, NY, 14853, USA

    Jitae Kim

  4. Polar BioCenter, Korea Polar Research Institute, KORDI, Incheon, 406-840, Korea

    Hyoungseok Lee

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  1. Chang Jae Oh
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  2. Ho Bang Kim
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  3. Jitae Kim
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  4. Won Jin Kim
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  5. Hyoungseok Lee
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Correspondence to Chung Sun An.

Additional information

Communicated by Erko Stackebrandt.

Chang Jae Oh and Ho Bang Kim are equally contributed to this work.

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Oh, C.J., Kim, H.B., Kim, J. et al. Organization of nif gene cluster in Frankia sp. EuIK1 strain, a symbiont of Elaeagnus umbellata . Arch Microbiol 194, 29–34 (2012). https://doi.org/10.1007/s00203-011-0732-7

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  • DOI: https://doi.org/10.1007/s00203-011-0732-7

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