DIVERGE: phylogeny-based analysis for
  functional–structural divergence of a protein family

Gu, Xun; Velden, Kent Vander

doi:10.1093/bioinformatics/18.3.500

Cited by 270 publications

(269 citation statements)

References 6 publications

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“…The program DIVERGE [47] was used to estimate the coefficients of both type I ( θ I ) and type II ( θ II ) functional divergence between serine peptidase clades A and B. Because subfamilies with fewer than four sequences cannot be analyzed using this method, three other serine peptidase proteins were excluded from this analysis.…”

Section: Methodsmentioning

confidence: 99%

Evidence for acquisition of virulence effectors in pathogenic chytrids

et al. 2011

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BackgroundThe decline in amphibian populations across the world is frequently linked to the infection of the chytrid fungus Batrachochytrium dendrobatidis (Bd). This is particularly perplexing because Bd was only recently discovered in 1999 and no chytrid fungus had previously been identified as a vertebrate pathogen.ResultsIn this study, we show that two large families of known virulence effector genes, crinkler (CRN) proteins and serine peptidases, were acquired by Bd from oomycete pathogens and bacteria, respectively. These two families have been duplicated after their acquisition by Bd. Additional selection analyses indicate that both families evolved under strong positive selection, suggesting that they are involved in the adaptation of Bd to its hosts.ConclusionsWe propose that the acquisition of virulence effectors, in combination with habitat disruption and climate change, may have driven the Bd epidemics and the decline in amphibian populations. This finding provides a starting point for biochemical investigations of chytridiomycosis.

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Section: Methodsmentioning

confidence: 99%

Evidence for acquisition of virulence effectors in pathogenic chytrids

et al. 2011

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“…We analyzed the functional divergence of the protein families by using the software DIVERGE (33). We adopted the ML superfamily tree in the previous analysis, defined three clusters [sulfur carriers (ThiS and MoaD), Urm1, and Ubiquitin-like proteins (all other families)], then calculated the functional divergence branch length of each cluster by using the least squares estimation (34,35).…”

Section: Methodsmentioning

confidence: 99%

Solution structure of Urm1 and its implications for the origin of protein modifiers

Zhang

Wang

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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Protein modifiers are involved in diverse biological processes and regulate the activity or function of target proteins by covalently conjugating to them. Although ubiquitin and a number of ubiquitin-like protein modifiers (Ubls) in eukaryotes have been identified, no protein modifier has been found in prokaryotes; thus, their evolutionary origin remains a puzzle. To infer the evolutionary relationships between the protein modifiers and sulfur carrier proteins, we solved the solution NMR structure of the Urm1 (ubiquitin-related modifier-1) protein from Saccharomyces cerevisiae. Both structural comparison and phylogenetic analysis of the ubiquitin superfamily, with emphasis on the Urm1 family, indicate that Urm1 is the unique ''molecular fossil'' that has the most conserved structural and sequence features of the common ancestor of the entire superfamily. The similarities of 3D structure and hydrophobic and electrostatic surface features between Urm1 and MoaD (molybdopterin synthase small subunit) suggest that they may interact with partners in a similar manner, and similarities between Urm1-Uba4 and MoaD-MoeB establish an evolutionary link between ATP-dependent protein conjugation in eukaryotes and ATP-dependent cofactor sulfuration.evolution ͉ NMR structure

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“…To examine whether this pattern reflects the functional divergence between the two genes, we examined the site-specific difference in evolutionary rate between the two clades using DIVERGE (Gu and Velden 2002;Gu 2006). The software examines two types of functional divergence: type I functional divergence in which the site-specific evolutionary rate is different between two clades and type II functional divergence in which functionally different amino acids are conserved at the corresponding sites between two clades.…”

Section: Resultsmentioning

confidence: 99%

“…The software examines two types of functional divergence: type I functional divergence in which the site-specific evolutionary rate is different between two clades and type II functional divergence in which functionally different amino acids are conserved at the corresponding sites between two clades. In general, the type I functional divergence is observed when the functional constraint on particular sites was lost in either clade and maintained in the other clade, while the type II divergence is observed when a novel functional role was acquired at particular sites in either clade (Gu and Velden 2002;Roth et al 2007). Because the software accepts only bifurcating trees, we tested two tree shapes that approximate the actual topology between the species ( Figure 5, B and C).…”

Section: Resultsmentioning

confidence: 99%

“…An original script running on the R statistical package was used for ancestral state inference and for counting the number of amino acid substitution events for each site (see supplemental materials at http:/ /www.genetics.org/supplemental/ for the script and a detailed description). Types I and II functional divergences between Obp57d and Obp57e were examined using DIVERGE 2.0 (Gu and Velden 2002;Gu 2006).…”

Section: Methodsmentioning

confidence: 99%

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Rapid Evolution of Two Odorant-Binding Protein Genes, Obp57d and Obp57e, in the Drosophila melanogaster Species Group

Matsuo

2008

Genetics

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Genes encoding odorant-binding protein (OBP) form a large family in an insect genome. Two OBP genes, Obp57d and Obp57e, were previously identified to be involved in host-plant recognition in Drosophila sechellia. Here, by comparing the genomic sequences at the Obp57d/e locus from 27 Drosophila species, we found large differences in gene number between species. Phylogenetic analysis revealed that Obp57d and Obp57e in the D. melanogaster species group arose by gene duplication of an ancestral OBP gene that remains single in the obscura species group. Further gain and loss of OBP genes were observed in several lineages in the melanogaster group. Site-specific analysis of evolutionary rate suggests that Obp57d and Obp57e have functionally diverged from each other. Thus, there are two classes of gene number differences in the Obp57d/e region: the difference of the genes that have functionally diverged from each other and the difference of the genes that appear to be functionally identical. Our analyses demonstrate that these two classes of differences can be distinguished by comparisons of many genomic sequences from closely related species. G ENES involved in the animal chemosensory system, such as the olfactory and gustatory receptorencoding genes, tend to form large families in a genome. Size differences in these multigene families among animal species were explained by differences in selection pressure maintaining functional genes. For example, the higher proportion of olfactory receptor pseudogenes in monkeys was explained by the acquisition of full trichromatic color vision that reduced the dependence of these species on olfactory cues (Gilad et al. 2004). Also, the loss of gustatory receptor functions in primates was suggested to be the result of changes in the environment and species-specific food preference (Go et al. 2005).With the completion of many genome sequences, however, comparisons of genomic data have raised a question of whether all the differences in multigenefamily size are consequences of selection. Alternatively, they might be caused by merely a stochastic gain and loss of genes. Indeed, results from genome analyses revealed that, at least in part, the size difference in multigene families between species can be explained by neutral evolution (Karev et al. 2003(Karev et al. , 2004Reed and Hughes 2004;Hahn et al. 2005;De Bie et al. 2006;Rudnicki et al. 2006). On the basis of these observations, it was proposed that the size difference in multigene families is not a consequence, but a cause of evolutionary changes in phenotypes (Nei 2005).These two theories, however, may not look at the same phenomenon. It is known that genes generated by a duplication undergo two successive but distinct stages of evolution (Lynch and Conery 2000). At the earlier stage, the two genes are functionally identical and tend to be reduced to a single gene by degeneration of either gene. Once they have functionally diverged from each other, however, both genes independently contribute to fitness, and selection ...

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DIVERGE: phylogeny-based analysis for functional–structural divergence of a protein family

Abstract: DIVERGE is available free of charge from http://xgu1.zool.iastate.edu/. Distribution packages for both Linux and Microsoft Windows operating systems are available, including manual and example files.

Cited by 270 publications

References 6 publications

Evidence for acquisition of virulence effectors in pathogenic chytrids

Evidence for acquisition of virulence effectors in pathogenic chytrids

Solution structure of Urm1 and its implications for the origin of protein modifiers

Rapid Evolution of Two Odorant-Binding Protein Genes, Obp57d and Obp57e, in the Drosophila melanogaster Species Group

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