期刊
GENOME BIOLOGY AND EVOLUTION
卷 4, 期 12, 页码 1375-1390出版社
OXFORD UNIV PRESS
DOI: 10.1093/gbe/evs113
关键词
genome evolution in PVC super-phylum; cellular compartmentalization; DUF1501 and Planctomycetes-specific cytochromes; mucin-degradation by Akkermansia muciniphila
资金
- National Institutes of Health [P20 RR016474]
- National Science Foundation [DBI-0743374, MCB-0920667, EPS-0447681]
- Div Of Biological Infrastructure
- Direct For Biological Sciences [0743374] Funding Source: National Science Foundation
- Div Of Molecular and Cellular Bioscience
- Direct For Biological Sciences [0920667] Funding Source: National Science Foundation
The Planctomycetes, Verrucomicrobia, Chlamydiae (PVC) super-phylum contains bacteria with either complex cellular organization or simple cell structure; it also includes organisms of different lifestyles (pathogens, mutualists, commensal, and free-living). Genome content evolution of this group has not been studied in a systematic fashion, which would reveal genes underlying the emergence of PVC-specific phenotypes. Here, we analyzed the evolutionary dynamics of 26 PVC genomes and several outgroup species. We inferred HGT, duplications, and losses by reconciliation of 27,123 gene trees with the species phylogeny. We showed that genome expansion and contraction have driven evolution within Planctomycetes and Chlamydiae, respectively, and balanced each other in Verrucomicrobia and Lentisphaerae. We also found that for a large number of genes in PVC genomes the most similar sequences are present in Acidobacteria, suggesting past and/or current ecological interaction between organisms from these groups. We also found evidence of shared ancestry between carbohydrate degradation genes in the mucin-degrading human intestinal commensal Akkermansia muciniphila and sequences from Acidobacteria and Bacteroidetes, suggesting that glycoside hydrolases are transferred laterally between gut microbes and that the process of carbohydrate degradation is crucial for microbial survival within the human digestive system. Further, we identified a highly conserved genetic module preferentially present in compartmentalized PVC species and possibly associated with the complex cell plan in these organisms. This conserved machinery is likely to be membrane targeted and involved in electron transport, although its exact function is unknown. These genes represent good candidates for future functional studies.
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