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Title: The distinction of CPR bacteria from other bacteria based on protein family content

Abstract

Candidate phyla radiation (CPR) bacteria separate phylogenetically from other bacteria, but the organismal distribution of their protein families remains unclear. Here, we leveraged sequences from thousands of uncultivated organisms and identified protein families that co-occur in genomes, thus are likely foundational for lineage capacities. Protein family presence/absence patterns cluster CPR bacteria together, and away from all other bacteria and archaea, partly due to proteins without recognizable homology to proteins in other bacteria. Some are likely involved in cell-cell interactions and potentially important for episymbiotic lifestyles. The diversity of protein family combinations in CPR may exceed that of all other bacteria. Over the bacterial tree, protein family presence/absence patterns broadly recapitulate phylogenetic structure, suggesting persistence of core sets of proteins since lineage divergence. The CPR could have arisen in an episode of dramatic but heterogeneous genome reduction or from a protogenote community and co-evolved with other bacteria.

Authors:
ORCiD logo [1]; ORCiD logo [2];  [3]; ORCiD logo [4]
  1. Univ. of California, Berkeley, CA (United States)
  2. Univ. of California, Berkeley, CA (United States); Tel Aviv Univ., Ramat Aviv (Israel)
  3. Univ. of California, Berkeley, CA (United States); Univ. of California, San Francisco, CA (United States)
  4. Univ. of California, Berkeley, CA (United States); Univ. of California, San Francisco, CA (United States); Univ. of Melbourne (Australia); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1572054
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Méheust, Raphaël, Burstein, David, Castelle, Cindy J., and Banfield, Jillian F. The distinction of CPR bacteria from other bacteria based on protein family content. United States: N. p., 2019. Web. doi:10.1038/s41467-019-12171-z.
Méheust, Raphaël, Burstein, David, Castelle, Cindy J., & Banfield, Jillian F. The distinction of CPR bacteria from other bacteria based on protein family content. United States. doi:10.1038/s41467-019-12171-z.
Méheust, Raphaël, Burstein, David, Castelle, Cindy J., and Banfield, Jillian F. Fri . "The distinction of CPR bacteria from other bacteria based on protein family content". United States. doi:10.1038/s41467-019-12171-z. https://www.osti.gov/servlets/purl/1572054.
@article{osti_1572054,
title = {The distinction of CPR bacteria from other bacteria based on protein family content},
author = {Méheust, Raphaël and Burstein, David and Castelle, Cindy J. and Banfield, Jillian F.},
abstractNote = {Candidate phyla radiation (CPR) bacteria separate phylogenetically from other bacteria, but the organismal distribution of their protein families remains unclear. Here, we leveraged sequences from thousands of uncultivated organisms and identified protein families that co-occur in genomes, thus are likely foundational for lineage capacities. Protein family presence/absence patterns cluster CPR bacteria together, and away from all other bacteria and archaea, partly due to proteins without recognizable homology to proteins in other bacteria. Some are likely involved in cell-cell interactions and potentially important for episymbiotic lifestyles. The diversity of protein family combinations in CPR may exceed that of all other bacteria. Over the bacterial tree, protein family presence/absence patterns broadly recapitulate phylogenetic structure, suggesting persistence of core sets of proteins since lineage divergence. The CPR could have arisen in an episode of dramatic but heterogeneous genome reduction or from a protogenote community and co-evolved with other bacteria.},
doi = {10.1038/s41467-019-12171-z},
journal = {Nature Communications},
number = 1,
volume = 10,
place = {United States},
year = {2019},
month = {9}
}

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