Characterization of species-specific genes using a flexible, web-based querying system

Charlebois, Robert L.; Clarke, G; Beiko, Robert G.; Jean, Andrew St.

doi:10.1016/s0378-1097(03)00512-3

Cited by 27 publications

(37 citation statements)

References 35 publications

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“…Similar to what has been observed for bacteria (Charlebois et al 2003;Daubin et al 2003), the ORFans in Drosophila are short, AT rich, and quickly evolving relative to ancestral genes (Domazet-Loso and Tautz 2003). Unfortunately, the sparse sampling of insect genomes raises the possibility that the ORFans identified in Drosophila include genes that originated recently as well as those lost by (or not detected in) other lineages.…”

Section: Discussionsupporting

confidence: 57%

“…Whereas the degenerative or accelerated evolution of ancestral genes can serve as a mechanism for generating ORFans both in bacteria species undergoing genome reduction (Amiri et al 2003) and in eukaryotes (Domazet-Loso and Tautz 2003), the extreme differences in base composition of ORFans and native genes indicate that this is not the case for ORFans in E. coli. Because all bacterial genomes with G+C contents >30% have intergenic regions that are relatively A+T rich, it has also been suggested that ORFans arise from errors in annotating noncoding regions (Charlebois et al 2003). But the fact that most of the intergenic regions are homologous among strains of E. coli indicates that these regions are not the source of unique, strain-specific sequences.…”

Section: Discussionmentioning

confidence: 99%

“…ORFans, particularly those that are short, have been attributed to errors in gene annotation or possibly pseudogenes (Fischer and Eisenberg 1999;Amiri et al 2003;Charlebois et al 2003). One method for determining the functional status of a sequence is by a comparative approach.…”

Section: Orfans Encode Functional Proteinsmentioning

confidence: 99%

“…Charlebois et al (2003), noting that intergenic regions are often A+T rich in bacterial genomes, interpreted the biased base composition of species-specific ORFans as indicating that they might be either annotation artifacts or fast-evolving genes. In contrast, Daubin et al (2003) viewed the existence of unique ORFans in very closely related genomes as evidence that these sequences arose by lateral gene transfer.…”

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confidence: 99%

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Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli

Daubin¹,

Ochman²

2004

Genome Res.

244

259

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Differences in gene repertoire among bacterial genomes are usually ascribed to gene loss or to lateral gene transfer from unrelated cellular organisms. However, most bacteria contain large numbers of ORFans, that is, annotated genes that are restricted to a particular genome and that possess no known homologs. The uniqueness of ORFans within a genome has precluded the use of a comparative approach to examine their function and evolution. However, by identifying sequences unique to monophyletic groups at increasing phylogenetic depths, we can make direct comparisons of the characteristics of ORFans of different ages in the Escherichia coli genome, and establish their functional status and evolutionary rates. Relative to the genes ancestral to γ-Proteobacteria and to those genes distributed sporadically in other prokaryotic species, ORFans in the E. coli lineage are short, A+T rich, and evolve quickly. Moreover, most encode functional proteins. Based on these features, ORFans are not attributable to errors in gene annotation, limitations of current databases, or to failure of methods for detecting homology. Rather, ORFans in the genomes of free-living microorganisms apparently derive from bacteriophage and occasionally become established by assuming roles in key cellular functions

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Section: Discussionsupporting

confidence: 57%

Section: Discussionmentioning

confidence: 99%

Section: Orfans Encode Functional Proteinsmentioning

confidence: 99%

mentioning

confidence: 99%

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Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli

Daubin¹,

Ochman²

2004

Genome Res.

244

259

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“…We constructed the following six trees with the 147 genomes currently available to us within our genomic analysis system, NGIBWS (7).…”

Section: Methodsmentioning

confidence: 99%

Weighted Genome Trees: Refinements and Applications

Gophna

Doolittle

Charlebois³

2005

J Bacteriol

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There are many ways to group completed genome sequences in hierarchical patterns (trees) reflecting relationships between their genes. Such groupings help us organize biological information and bear crucially on underlying processes of genome and organismal evolution. Genome trees make use of all comparable genes but can variously weight the contributions of these genes according to similarity, congruent patterns of similarity, or prevalence among genomes. Here we explore such possible weighting strategies, in an analysis of 142 prokaryotic and 5 eukaryotic genomes. We demonstrate that alternate weighting strategies have different advantages, and we propose that each may have its specific uses in systematic or evolutionary biology. Comparisons of results obtained with different methods can provide further clues to major events and processes in genome evolution.

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Structural features and the persistence of acquired proteins

2008

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ORFan genes can constitute a large fraction of a bacterial genome, but due to their lack of homologs, their functions have remained largely unexplored. To determine if particular features of ORFan-encoded proteins promote their presence in a genome, we analyzed properties of ORFans that originated over a broad evolutionary timescale. We also compared ORFan genes to another class of acquired genes (HOPs), which have homologs in other bacteria. A total of 54 ORFan and HOP genes selected from different phylogenetic depths in the Escherichia coli lineage were cloned, expressed, purified and subjected to CD spectroscopy. A majority of genes could be expressed, but only 18 yielded sufficient soluble protein for spectral analysis. Of these, half were significantly α-helical, three were predominantly β-sheet, and six were of intermediate or indeterminate structure. Although a higher proportion of HOPs yielded soluble proteins with resolvable secondary structures, ORFans resembled HOPs with regard to most of the other features tested. Overall, we found that those ORFan and HOP genes that have persisted in the E. coli lineage were more likely to encode soluble and folded proteins, more likely to display environmental modulation of their gene expression, and by extrapolation, are more likely to be functional.

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Characterization of species-specific genes using a flexible, web-based querying system

Cited by 27 publications

References 35 publications

Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli

Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli

Weighted Genome Trees: Refinements and Applications

Structural features and the persistence of acquired proteins

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