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

Nature Communications

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[1] 0000 0001 2181 7878, grid.47840.3f, Department of Earth and Planetary Science, University of California, Berkeley, 94720, Berkeley, CA, USA;0000 0001 2181 7878, grid.47840.3f, California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, 94720, Berkeley, CA, USA;0000 0004 1937 0546, grid.12136.37, School of Molecular and Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel;0000 0001 2181 7878, grid.47840.3f, Department of Earth and Planetary Science, University of California, Berkeley, 94720, Berkeley, CA, USA;Innovative Genomics Institute, 94704, Berkeley, CA, USA;0000 0001 2181 7878, grid.47840.3f, Department of Earth and Planetary Science, University of California, Berkeley, 94720, Berkeley, CA, USA;Innovative Genomics Institute, 94704, Berkeley, CA, USA;Chan Zuckerberg Biohub, 94158, San Francisco, CA, USA;0000 0001 2181 7878, grid.47840.3f, Department of Earth and Planetary Science, University of California, Berkeley, 94720, Berkeley, CA, USA;Innovative Genomics Institute, 94704, Berkeley, CA, USA;Chan Zuckerberg Biohub, 94158, San Francisco, CA, USA;0000 0001 2179 088X, grid.1008.9, University of Melbourne, 3010, Melbourne, VIC, Australia;0000 0001 2231 4551, grid.184769.5, Lawrence Berkeley National Laboratory, 94720, Berkeley, CA, USA;0000 0001 2181 7878, grid.47840.3f, Department of Environmental Science, Policy and Management, University of California, Berkeley, 94720, Berkeley, CA, USA;

DOI  :  10.1038/s41467-019-12171-z

来源: publisher

【 摘 要 】

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.

【 授权许可】

CC BY