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Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction

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Authors
Fuxelius, Hans-Henrik; Darby, Alistair C; Cho, Nam-Hyuk; Andersson, Siv GE
Issue Date
2008-02-28
Publisher
BioMed Central
Citation
Genome Biol. 2008;9(2):R42. Epub 2008 Feb 26.
Keywords
Base SequenceEvolution, Molecular*Genes, Bacterial*Genetic VariationInterspersed Repetitive SequencesOpen Reading Frames/geneticsPhylogenyProteobacteria/genetics*PseudogenesRickettsia/*geneticsSequence Analysis, DNA/*methods*Software
Abstract
BACKGROUND: Pseudogenes reveal ancestral gene functions. Some obligate intracellular bacteria, such as Mycobacterium leprae and Rickettsia spp., carry substantial fractions of pseudogenes. Until recently, horizontal gene transfers were considered to be rare events in obligate host-associated bacteria. RESULTS: We present a visualization tool that displays the relationships and positions of degraded and partially overlapping gene sequences in multiple genomes. With this tool we explore the origin and deterioration patterns of the Rickettsia pseudogenes and find that variably present genes and pseudogenes tend to have been acquired more recently, are more divergent in sequence, and exhibit a different functional profile compared with genes conserved across all species. Overall, the origin of only one-quarter of the variable genes and pseudogenes can be traced back to the common ancestor of Rickettsia and the outgroup genera Orientia and Wolbachia. These sequences contain only a few disruptive mutations and show a broad functional distribution profile, much like the core genes. The remaining genes and pseudogenes are extensively degraded or solely present in a single species. Their functional profile was heavily biased toward the mobile gene pool and genes for components of the cell wall and the lipopolysaccharide. CONCLUSION: Reductive evolution of the vertically inherited genomic core accounts for 25% of the predicted genes in the variable segments of the Rickettsia genomes, whereas 75% stems from the flux of the mobile gene pool along with genes for cell surface structures. Thus, most of the variably present genes and pseudogenes in Rickettsia have arisen from recent acquisitions.
ISSN
1465-6914 (Electronic)
Language
English
URI
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18302730

http://hdl.handle.net/10371/35603
DOI
https://doi.org/10.1186/gb-2008-9-2-r42
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College of Medicine/School of Medicine (의과대학/대학원)Microbiology (미생물학전공)Journal Papers (저널논문_미생물학전공)
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