TY - JOUR
T1 - Bacterial Origin and Reductive Evolution of the CPR Group
AU - Bokhari, Rijja Hussain
AU - Amirjan, Nooreen
AU - Jeong, Hyeonsoo
AU - Kim, Kyung Mo
AU - Caetano-Anollés, Gustavo
AU - Nasir, Arshan
AU - Bapteste, Eric
N1 - Funding Information:
We thank Patrick Forterre for critical reading of the manuscript. AN is recipient of the Los Alamos National Laboratory Oppenheimer Fellowship (20180751PRD3). Research was supported by a grant from the Collaborative Genome Program (20140428) funded by the Ministry of Oceans and Fisheries, Korea to K.M.K., and grants from the National Science Foundation (OISE-1132791) and the National Institute of Food and Agriculture of the United States Department of Agriculture (ILLU-802-909 and ILLU-483-625) to G.C.-A.
Publisher Copyright:
© 2020 Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2020. This work is written by US Government employees and is in the public domain in the US.
PY - 2020/3/17
Y1 - 2020/3/17
N2 - The candidate phyla radiation (CPR) is a proposed subdivision within the bacterial domain comprising several candidate phyla. CPR organisms are united by small genome and physical sizes, lack several metabolic enzymes, and populate deep branches within the bacterial subtree of life. These features raise intriguing questions regarding their origin and mode of evolution. In this study, we performed a comparative and phylogenomic analysis to investigate CPR origin and evolution. Unlike previous gene/protein sequence-based reports of CPR evolution, we used protein domain superfamilies classified by protein structure databases to resolve the evolutionary relationships of CPR with non-CPR bacteria, Archaea, Eukarya, and viruses. Across all supergroups, CPR shared maximum superfamilies with non-CPR bacteria and were placed as deep branching bacteria in most phylogenomic trees. CPR contributed 1.22% of new superfamilies to bacteria including the ribosomal protein L19e and encoded four core superfamilies that are likely involved in cell-to-cell interaction and establishing episymbiotic lifestyles. Although CPR and non-CPR bacterial proteomes gained common superfamilies over the course of evolution, CPR and Archaea had more common losses. These losses mostly involved metabolic superfamilies. In fact, phylogenies built from only metabolic protein superfamilies separated CPR and non-CPR bacteria. These findings indicate that CPR are bacterial organisms that have probably evolved in an Archaea-like manner via the early loss of metabolic functions. We also discovered that phylogenies built from metabolic and informational superfamilies gave contrasting views of the groupings among Archaea, Bacteria, and Eukarya, which add to the current debate on the evolutionary relationships among superkingdoms.
AB - The candidate phyla radiation (CPR) is a proposed subdivision within the bacterial domain comprising several candidate phyla. CPR organisms are united by small genome and physical sizes, lack several metabolic enzymes, and populate deep branches within the bacterial subtree of life. These features raise intriguing questions regarding their origin and mode of evolution. In this study, we performed a comparative and phylogenomic analysis to investigate CPR origin and evolution. Unlike previous gene/protein sequence-based reports of CPR evolution, we used protein domain superfamilies classified by protein structure databases to resolve the evolutionary relationships of CPR with non-CPR bacteria, Archaea, Eukarya, and viruses. Across all supergroups, CPR shared maximum superfamilies with non-CPR bacteria and were placed as deep branching bacteria in most phylogenomic trees. CPR contributed 1.22% of new superfamilies to bacteria including the ribosomal protein L19e and encoded four core superfamilies that are likely involved in cell-to-cell interaction and establishing episymbiotic lifestyles. Although CPR and non-CPR bacterial proteomes gained common superfamilies over the course of evolution, CPR and Archaea had more common losses. These losses mostly involved metabolic superfamilies. In fact, phylogenies built from only metabolic protein superfamilies separated CPR and non-CPR bacteria. These findings indicate that CPR are bacterial organisms that have probably evolved in an Archaea-like manner via the early loss of metabolic functions. We also discovered that phylogenies built from metabolic and informational superfamilies gave contrasting views of the groupings among Archaea, Bacteria, and Eukarya, which add to the current debate on the evolutionary relationships among superkingdoms.
KW - candidate phyla radiation
KW - phylogenetics
KW - protein structure
KW - reductive evolution
KW - tree of life
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U2 - 10.1093/gbe/evaa024
DO - 10.1093/gbe/evaa024
M3 - Article
C2 - 32031619
AN - SCOPUS:85082399920
SN - 1759-6653
VL - 12
SP - 103
EP - 121
JO - Genome Biology and Evolution
JF - Genome Biology and Evolution
IS - 3
ER -