Gene duplications in prokaryotes can be associated with environmental adaptation.
BACKGROUND
Gene duplication is a normal evolutionary process. If there is no selective advantage in keeping the duplicated gene, it is usually reduced to a pseudogene and disappears from the genome. However, some paralogs are retained. These gene products are likely to be beneficial to the organism, e.g. in adaptation to new environmental conditions. The aim of our analysis is to investigate the properties of paralog-forming genes in prokaryotes, and to analyse the role of these retained paralogs by relating gene properties to life style of the corresponding prokaryotes.


RESULTS
Paralogs were identified in a number of prokaryotes, and these paralogs were compared to singletons of persistent orthologs based on functional classification. This showed that the paralogs were associated with for example energy production, cell motility, ion transport, and defence mechanisms. A statistical overrepresentation analysis of gene and protein annotations was based on paralogs of the 200 prokaryotes with the highest fraction of paralog-forming genes. Biclustering of overrepresented gene ontology terms versus species was used to identify clusters of properties associated with clusters of species. The clusters were classified using similarity scores on properties and species to identify interesting clusters, and a subset of clusters were analysed by comparison to literature data. This analysis showed that paralogs often are associated with properties that are important for survival and proliferation of the specific organisms. This includes processes like ion transport, locomotion, chemotaxis and photosynthesis. However, the analysis also showed that the gene ontology terms sometimes were too general, imprecise or even misleading for automatic analysis.


CONCLUSIONS
Properties described by gene ontology terms identified in the overrepresentation analysis are often consistent with individual prokaryote lifestyles and are likely to give a competitive advantage to the organism. Paralogs and singletons dominate different categories of functional classification, where paralogs in particular seem to be associated with processes involving interaction with the environment.
Bratlie
Marit S
MS
Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
Johansen
Jostein
J
Sherman
Brad T
BT
Huang
Da Wei
da W
Lempicki
Richard A
RA
Drabløs
Finn
F
D000222:Adaptation, Physiological / Q000235:genetics*; D000465:Algorithms; D016000:Cluster Analysis; D004777:Environment; D020558:GTP Phosphohydrolases / Q000737:chemistry; D020440:Gene Duplication; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D017136:Ion Transport / Q000235:genetics; D009068:Movement; D010802:Phylogeny; D011387:Prokaryotic Cells / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D012689:Sequence Homology, Nucleic Acid
D020558:GTP Phosphohydrolases