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Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years

Author

Listed:
  • Mizue Anda

    (the University of Tokyo, Kashiwa
    the University of Tokyo, Bunkyo-ku)

  • Shun Yamanouchi

    (the University of Tokyo, Bunkyo-ku)

  • Salvatore Cosentino

    (the University of Tokyo, Kashiwa
    the University of Tokyo, Bunkyo-ku)

  • Mitsuo Sakamoto

    (RIKEN BioResource Research Center, Tsukuba)

  • Moriya Ohkuma

    (RIKEN BioResource Research Center, Tsukuba)

  • Masako Takashima

    (RIKEN BioResource Research Center, Tsukuba)

  • Atsushi Toyoda

    (National Institute of Genetics, Mishima)

  • Wataru Iwasaki

    (the University of Tokyo, Kashiwa
    the University of Tokyo, Bunkyo-ku
    the University of Tokyo, Kashiwa
    the University of Tokyo, Kashiwa)

Abstract

It is generally assumed that all bacteria must have at least one rRNA operon (rrn operon) on the chromosome, but some strains of the genera Aureimonas and Oecophyllibacter carry their sole rrn operon on a plasmid. However, other related strains and species have chromosomal rrn loci, suggesting that the exclusive presence of rrn operons on a plasmid is rare and unlikely to be stably maintained over long evolutionary periods. Here, we report the results of a systematic search for additional bacteria without chromosomal rrn operons. We find that at least four bacterial clades in the phyla Bacteroidota, Spirochaetota, and Pseudomonadota (Proteobacteria) lost chromosomal rrn operons independently. Remarkably, Persicobacteraceae have apparently maintained this peculiar genome organization for hundreds of millions of years. In our study, all the rrn-carrying plasmids in bacteria lacking chromosomal rrn loci possess replication initiator genes of the Rep_3 family. Furthermore, the lack of chromosomal rrn operons is associated with differences in copy numbers of rrn operons, plasmids, and chromosomal tRNA genes. Thus, our findings indicate that the absence of rrn loci in bacterial chromosomes can be stably maintained over long evolutionary periods.

Suggested Citation

  • Mizue Anda & Shun Yamanouchi & Salvatore Cosentino & Mitsuo Sakamoto & Moriya Ohkuma & Masako Takashima & Atsushi Toyoda & Wataru Iwasaki, 2023. "Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-42681-w
    DOI: 10.1038/s41467-023-42681-w
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    References listed on IDEAS

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    1. Sishuo Wang & Haiwei Luo, 2021. "Dating Alphaproteobacteria evolution with eukaryotic fossils," Nature Communications, Nature, vol. 12(1), pages 1-9, December.
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