Unlinked rRNA genes are widespread among bacteria and archaea

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Unlinked rRNA genes are widespread among bacteria and archaea. / Brewer, Tess E.; Albertsen, Mads; Edwards, Arwyn; Kirkegaard, Rasmus; Rocha, Eduardo; Fierer, Noah.

In: ISME Journal, 11.11.2019.

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Harvard

Brewer, TE, Albertsen, M, Edwards, A, Kirkegaard, R, Rocha, E & Fierer, N 2019, 'Unlinked rRNA genes are widespread among bacteria and archaea', ISME Journal. https://doi.org/10.1038/s41396-019-0552-3

APA

Brewer, T. E., Albertsen, M., Edwards, A., Kirkegaard, R., Rocha, E., & Fierer, N. (2019). Unlinked rRNA genes are widespread among bacteria and archaea. ISME Journal. https://doi.org/10.1038/s41396-019-0552-3

Vancouver

Brewer TE, Albertsen M, Edwards A, Kirkegaard R, Rocha E, Fierer N. Unlinked rRNA genes are widespread among bacteria and archaea. ISME Journal. 2019 Nov 11. https://doi.org/10.1038/s41396-019-0552-3

Author

Brewer, Tess E. ; Albertsen, Mads ; Edwards, Arwyn ; Kirkegaard, Rasmus ; Rocha, Eduardo ; Fierer, Noah. / Unlinked rRNA genes are widespread among bacteria and archaea. In: ISME Journal. 2019.

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@article{5828502bd0db4f06bd3ce302c6c67303,
title = "Unlinked rRNA genes are widespread among bacteria and archaea",
abstract = "Ribosomes are essential to cellular life and the genes for their RNA components are the most conserved and transcribed genes in bacteria and archaea. Ribosomal RNA genes are typically organized into a single operon, an arrangement thought to facilitate gene regulation. In reality, some bacteria and archaea do not share this canonical rRNA arrangement—their 16S and 23S rRNA genes are separated across the genome and referred to as “unlinked”. This rearrangement has previously been treated as an anomaly or a byproduct of genome degradation in intracellular bacteria. Here, we leverage complete genome and long-read metagenomic data to show that unlinked 16S and 23S rRNA genes are more common than previously thought. Unlinked rRNA genes occur in many phyla, most significantly within Deinococcus-Thermus, Chloroflexi, and Planctomycetes, and occur in differential frequencies across natural environments. We found that up to 41% of rRNA genes in soil were unlinked, in contrast to the human gut, where all sequenced rRNA genes were linked. The frequency of unlinked rRNA genes may reflect meaningful life history traits, as they tend to be associated with a mix of slow-growing free-living species and intracellular species. We speculate that unlinked rRNA genes may confer selective advantages in some environments, though the specific nature of these advantages remains undetermined and worthy of further investigation. More generally, the prevalence of unlinked rRNA genes in poorly-studied taxa serves as a reminder that paradigms derived from model organisms do not necessarily extend to the broader diversity of bacteria and archaea.",
author = "Brewer, {Tess E.} and Mads Albertsen and Arwyn Edwards and Rasmus Kirkegaard and Eduardo Rocha and Noah Fierer",
year = "2019",
month = nov,
day = "11",
doi = "10.1038/s41396-019-0552-3",
language = "English",
journal = "ISME Journal",
issn = "1751-7362",
publisher = "Springer Nature",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - Unlinked rRNA genes are widespread among bacteria and archaea

AU - Brewer, Tess E.

AU - Albertsen, Mads

AU - Edwards, Arwyn

AU - Kirkegaard, Rasmus

AU - Rocha, Eduardo

AU - Fierer, Noah

PY - 2019/11/11

Y1 - 2019/11/11

N2 - Ribosomes are essential to cellular life and the genes for their RNA components are the most conserved and transcribed genes in bacteria and archaea. Ribosomal RNA genes are typically organized into a single operon, an arrangement thought to facilitate gene regulation. In reality, some bacteria and archaea do not share this canonical rRNA arrangement—their 16S and 23S rRNA genes are separated across the genome and referred to as “unlinked”. This rearrangement has previously been treated as an anomaly or a byproduct of genome degradation in intracellular bacteria. Here, we leverage complete genome and long-read metagenomic data to show that unlinked 16S and 23S rRNA genes are more common than previously thought. Unlinked rRNA genes occur in many phyla, most significantly within Deinococcus-Thermus, Chloroflexi, and Planctomycetes, and occur in differential frequencies across natural environments. We found that up to 41% of rRNA genes in soil were unlinked, in contrast to the human gut, where all sequenced rRNA genes were linked. The frequency of unlinked rRNA genes may reflect meaningful life history traits, as they tend to be associated with a mix of slow-growing free-living species and intracellular species. We speculate that unlinked rRNA genes may confer selective advantages in some environments, though the specific nature of these advantages remains undetermined and worthy of further investigation. More generally, the prevalence of unlinked rRNA genes in poorly-studied taxa serves as a reminder that paradigms derived from model organisms do not necessarily extend to the broader diversity of bacteria and archaea.

AB - Ribosomes are essential to cellular life and the genes for their RNA components are the most conserved and transcribed genes in bacteria and archaea. Ribosomal RNA genes are typically organized into a single operon, an arrangement thought to facilitate gene regulation. In reality, some bacteria and archaea do not share this canonical rRNA arrangement—their 16S and 23S rRNA genes are separated across the genome and referred to as “unlinked”. This rearrangement has previously been treated as an anomaly or a byproduct of genome degradation in intracellular bacteria. Here, we leverage complete genome and long-read metagenomic data to show that unlinked 16S and 23S rRNA genes are more common than previously thought. Unlinked rRNA genes occur in many phyla, most significantly within Deinococcus-Thermus, Chloroflexi, and Planctomycetes, and occur in differential frequencies across natural environments. We found that up to 41% of rRNA genes in soil were unlinked, in contrast to the human gut, where all sequenced rRNA genes were linked. The frequency of unlinked rRNA genes may reflect meaningful life history traits, as they tend to be associated with a mix of slow-growing free-living species and intracellular species. We speculate that unlinked rRNA genes may confer selective advantages in some environments, though the specific nature of these advantages remains undetermined and worthy of further investigation. More generally, the prevalence of unlinked rRNA genes in poorly-studied taxa serves as a reminder that paradigms derived from model organisms do not necessarily extend to the broader diversity of bacteria and archaea.

U2 - 10.1038/s41396-019-0552-3

DO - 10.1038/s41396-019-0552-3

M3 - Article

C2 - 31712737

JO - ISME Journal

JF - ISME Journal

SN - 1751-7362

ER -

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