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Coevolution of DNA uptake sequences and bacterial proteomes
1Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ontario, Canada.
Genome Biology and Evolution
|March 25, 2010
Summary
Bacterial genomes contain DNA uptake signal sequences that alter protein sequences. These sequences accumulate in genes after transfer, showing minimal impact on protein function but potentially incurring a high evolutionary cost.
Area of Science:
- Genomics
- Evolutionary Biology
- Microbial Genetics
Background:
- Naturally competent bacteria possess numerous short DNA motifs known as DNA uptake signal sequences (USS) within their genomes.
- These USS are found in hundreds or thousands of copies, particularly in species like Haemophilus influenzae, Actinobacillus pleuropneumoniae, and Neisseria meningitidis.
Purpose of the Study:
- To investigate the evolutionary interplay between coding-region USS and the proteomes of three bacterial species.
- To determine the impact of USS accumulation on protein sequence evolution and gene transfer dynamics.
Main Methods:
- Comparative genomic analysis of USS distribution in coding sequences across H. influenzae, A. pleuropneumoniae, and N. meningitidis.
- Analysis of correlations between USS presence, codon usage, gene conservation, and protein functional categories.
- Comparison of USS-encoded peptides with homologs in related bacteria lacking USS.
Main Results:
- USS accumulation in coding sequences approximately doubled the frequency of specified tripeptides in the studied genomes.
- USS presence correlated with preferred codon usage at degenerate positions but showed poor correlation with protein functional categories.
- Genes lacking homologs also lacked USS, indicating USS accumulation occurs post-gene transfer, not as a driver of distant horizontal gene transfer.
- USS-encoded amino acids showed similar conservation to other amino acids, suggesting minimal constraint on protein function.
- USS were preferentially located in poorly conserved genes and amino acid positions.
Conclusions:
- USS accumulation significantly impacts bacterial proteomes by altering tripeptide frequencies without imposing substantial constraints on protein function.
- The presence of USS in coding sequences is likely a consequence of gene transfer rather than a driver of it.
- Maintaining USS in coding sequences may incur a significant evolutionary cost due to the selective pressure needed to mitigate maladaptive mutations.
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