Cited by 73Bacteriophages and microbial interactionsRNA and protein synthesis mechanismsGenomics and Phylogenetic Studies

Viroid-like colonists of human microbiomes

Open access
Zheludev, Ivan N., Edgar, Robert C., Lopez-Galiano, Maria Jose, de la Peña, Marcos, Babaian, Artem, Bhatt, Ami S., Fire, Andrew Z.·2024·Cell

Published version of a preprint

Abstract

Here, we describe "obelisks," a class of heritable RNA elements sharing several properties: (1) apparently circular RNA ∼1 kb genome assemblies, (2) predicted rod-like genome-wide secondary structures, and (3) open reading frames encoding a novel "Oblin" protein superfamily. A subset of obelisks includes a variant hammerhead self-cleaving ribozyme. Obelisks form their own phylogenetic group without detectable similarity to known biological agents. Surveying globally, we identified 29,959 distinct obelisks (clustered at 90% sequence identity) from diverse ecological niches. Obelisks are prevalent in human microbiomes, with detection in ∼7% (29/440) and ∼50% (17/32) of queried stool and oral metatranscriptomes, respectively. We establish Streptococcus sanguinis as a cellular host of a specific obelisk and find that this obelisk's maintenance is not essential for bacterial growth. Our observations identify obelisks as a class of diverse RNAs of yet-to-be-determined impact that have colonized and gone unnoticed in human and global microbiomes.

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Crossref · 10.1016/j.cell.2024.09.033

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Authors
Zheludev, I. N., Edgar, R. C., Lopez-Galiano, M. J., de la Peña, M., Babaian, A., Bhatt, A. S., & Fire, A. Z.
Affiliations
  • Stanford University (US)
  • University of Toronto (CA)
  • Stanford Medicine (US)
Corresponding author
  • Zheludev, Ivan N.
  • Fire, Andrew Z.
Venue
Cell
Publisher
Elsevier BV
Published
2024-11
Volume
187
Issue
23
Pages
6521-6536.e18
ISSN
0092-8674 (ISSN-L)
OpenAlex
W4403959930
Cited by
73
References
125
Citations by year
2026: 21 · 2025: 27 · 2024: 24
FWCI
19.75
Type
journal article
Language
en
Open access
Locations
  • Cell (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • RiuNet (Universitat Politècnica de València) (publishedVersion, cc-by-nc-nd)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, other-oa)
  • PubMed Central (submittedVersion, cc-by-nc)
  • Repository of Digital Objects for Teaching Research and Culture (University of Valencia) (submittedVersion, cc-by-nc)
Funders
  • National Institute of Allergy and Infectious Diseases Division of Intramural Research (R01AI148623, R01AI143757)
  • University of Valencia
  • National Institute of General Medical Sciences (R35GM130366)
  • Allen Institute
  • Canadian Institutes of Health Research (PTJ-496709)
  • University of Toronto
  • National Institutes of Health
  • American Welding Society
  • Stanford University School of Medicine
  • Stand up to Cancer
  • Government of Valencia (PROMETEO CIPROM/2022/21)
  • The University of British Columbia
  • National Institute of Allergy and Infectious Diseases (3.1416)
Topics
  • Physical Sciences › Environmental Science › Ecology › Bacteriophages and microbial interactions
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
obelisks, human microbiome, Streptococcus sanguinis, RNA secondary structure, metatranscriptomics, oral microbiota, gut microbiota

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