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Computational inference of scenarios for alpha-proteobacterial genome evolution
Bastien Boussau1, E Olof Karlberg, A Carolin Frank
1Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University, S-752 36 Uppsala, Sweden.
Summary
Alpha-proteobacteria, the ancestors of mitochondria, show significant genome size changes. Gene expansions occurred in plant-associated bacteria, while intracellular bacteria experienced gene losses.
Area of Science:
- Microbiology
- Evolutionary Biology
- Genomics
Background:
- Mitochondria are believed to have originated from alpha-proteobacteria.
- Alpha-proteobacteria exhibit a tenfold variation in genome size, making them a model for bacterial genome evolution.
- Understanding gene flux in alpha-proteobacteria provides insights into evolutionary processes.
Purpose of the Study:
- To infer ancestral gene sets and quantify gene flux in the alpha-proteobacterial species tree.
- To investigate the evolutionary dynamics of genome size in bacteria.
- To identify potential bacterial drug targets.
Main Methods:
- Computational approaches were used to infer ancestral gene sets.
- Gene flux was quantified along the branches of the alpha-proteobacterial species tree.
- Comparative genomics was employed to analyze gene content and identify conserved genes without eukaryotic homologs.
Main Results:
- Massive gene expansions were observed in branches diversifying plant-associated bacteria.
- Extreme gene losses were identified in branches separating intracellular bacteria of animals and humans.
- Alterations in gene numbers primarily affected regulation, transport, and small-molecule metabolism, often involving paralogous gene families on auxiliary chromosomes.
Conclusions:
- The alpha-proteobacterial ancestor likely possessed 3,000-5,000 genes and was a free-living, aerobic, motile bacterium.
- About one-third of the ancestral gene set lacks homologs in eukaryotes.
- Genes conserved in alpha-proteobacteria but absent in eukaryotes, particularly those with unknown functions, are potential targets for novel antibacterial drug development.