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

Mizue Anda (), Shun Yamanouchi, Salvatore Cosentino, Mitsuo Sakamoto, Moriya Ohkuma, Masako Takashima, Atsushi Toyoda and Wataru Iwasaki ()
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Mizue Anda: the University of Tokyo, Kashiwa
Shun Yamanouchi: the University of Tokyo, Bunkyo-ku
Salvatore Cosentino: the University of Tokyo, Kashiwa
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

Nature Communications, 2023, vol. 14, issue 1, 1-12

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-42681-w

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