Using evolutionary rates to investigate protein functional divergence and conservation. A case study of the carbonic anhydrases

Evolution and functional role prediction of the CYP6DE and CYP6DJ subfamilies in Dendroctonus (Curculionidae: Scolytinae) bark beetles

Dendroctonus-bark beetles are natural components and key ecological agents of coniferous forests. They spend most of their lives under the bark, where they are exposed to highly toxic terpenes present in the oleoresin. Cytochrome P450 (CYP) is a multigene family involved in the detoxification of these compounds. It has been demonstrated that CYP6DE and CYP6DJ subfamilies hydroxylate monoterpenes, whose derivatives can act as pheromone synergist compounds or be pheromones themselves in these insects. Given the diversity and functional role of CYPs, we investigated whether these cytochromes have retained their function throughout the evolution of these insects. To test this hypothesis, we performed a Bayesian phylogenetic analysis to determine phylogenetic subgroups of cytochromes in these subfamilies. Subgroups were mapped and reconciled with the Dendroctonus phylogeny. Molecular docking analyses were performed with the cytochromes of each subgroup and enantiomers of α-pinene and β-pinene, (+)-3-carene, β-myrcene and R-(+)-limonene. In addition, functional divergence analysis was performed to identify critical amino acid sites that influence changes in catalytic site conformation and/or protein folding. Three and two phylogenetic subgroups were recovered for the CYP6DE and CYP6DJ subfamilies, respectively. Mapping and reconciliation analysis showed different gain and loss patterns for cytochromes of each subgroup. Functional predictions indicated that the cytochromes analyzed are able to hydroxylate all monoterpenes; however, they showed preferential affinities to different monoterpenes. Functional divergence analyses indicated that the CYP6DE subfamily has experimented type I and II divergence, whereas the CYP6DJ subfamily has evolved under strong functional constraints. Results suggest cytochromes of the CYP6DE subfamily evolve to reinforce their detoxifying capacity hydroxylating mainly α- and β-pinene to (+) and (-)-trans-verbenol, being the negative enantiomer used as a pheromone by several Dendroctonus species; whereas cytochromes of the CYP6DJ subfamily appear to retain their original function related to the detoxification of these compounds.

Toxicological Implications of Biological Heterogeneity

From a micro to macro scale of biological organization, macromolecular diversity and biological heterogeneity are fundamental properties of biological systems. Heterogeneity may result from genetic, epigenetic, and non-genetic characteristics (e.g., tissue microenvironment). Macromolecular diversity and biological heterogeneity are tolerated as long as the sustenance and propagation of life are not disrupted. They also provide the raw materials for microevolutionary changes that may help organisms adapt to new selection pressures arising from the environment. Sequence evolution, functional divergence, and positive selection of gene and promoter dosage play a major role in the evolution of life's diversity including complex metabolic networks, which is ultimately reflected in changes in the allele frequency over time. Robustness in evolvable biological systems is conferred by functional redundancy that is often created by macromolecular diversity and biological heterogeneity. The ability to investigate biological macromolecules at an increasingly finer level has uncovered a wealth of information in this regard. Therefore, the dynamics of biological complexity should be taken into consideration in biomedical research.

Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory sequences

Gene duplication is an important evolutionary mechanism that can result in functional divergence in paralogs due to neo-functionalization or sub-functionalization. Consistent with functional divergence after gene duplication, recent studies have shown accelerated evolution in retained paralogs. However, little is known in general about the impact of this accelerated evolution on the molecular functions of retained paralogs. For example, do new functions typically involve changes in enzymatic activities, or changes in protein regulation? Here we study the evolution of posttranslational regulation by examining the evolution of important regulatory sequences (short linear motifs) in retained duplicates created by the whole-genome duplication in budding yeast. To do so, we identified short linear motifs whose evolutionary constraint has relaxed after gene duplication with a likelihood-ratio test that can account for heterogeneity in the evolutionary process by using a non-central chi-squared null distribution. We find that short linear motifs are more likely to show changes in evolutionary constraints in retained duplicates compared to single-copy genes. We examine changes in constraints on known regulatory sequences and show that for the Rck1/Rck2, Fkh1/Fkh2, Ace2/Swi5 paralogs, they are associated with previously characterized differences in posttranslational regulation. Finally, we experimentally confirm our prediction that for the Ace2/Swi5 paralogs, Cbk1 regulated localization was lost along the lineage leading to SWI5 after gene duplication. Our analysis suggests that changes in posttranslational regulation mediated by short regulatory motifs systematically contribute to functional divergence after gene duplication.

How a protein is controlled is intimately linked to its function. Therefore, evolution can drive the functional divergence of proteins by tweaking their regulation, even if enzymatic capacities are preserved. Changes in posttranslational regulation (protein phosphorylation, degradation, subcellular localization, etc.) could therefore represent key mechanisms in functional divergence and lead to different phenotypic outcomes. Since disordered protein regions contain sites of protein modification and interaction (known as short linear motifs) and evolve rapidly relative to domains encoding enzymatic functions, these regions are good candidates to harbour sequence changes that underlie changes in function. In this study, we develop a statistical framework to identify changes in rate of evolution specific to protein regulatory sequences and identify hundreds of short linear motifs in disordered regions that are likely to have diverged after the whole-genome duplication in budding yeast. We show that these divergent motifs are much more frequent in paralogs than in single-copy proteins, and that they are more frequent in duplicate pairs that have functionally diverged. Our analysis suggests that changes in short linear motifs in disordered protein regions could be important molecular mechanisms of functional divergence after gene duplication.

A phylogenetic mixture model for the identification of functionally divergent protein residues

MOTIVATION

To understand the evolution of molecular function within protein families, it is important to identify those amino acid residues responsible for functional divergence; i.e. those sites in a protein family that affect cofactor, protein or substrate binding preferences; affinity; catalysis; flexibility; or folding. Type I functional divergence (FD) results from changes in conservation (evolutionary rate) at a site between protein subfamilies, whereas type II FD occurs when there has been a shift in preferences for different amino acid chemical properties. A variety of methods have been developed for identifying both site types in protein subfamilies, both from phylogenetic and information-theoretic angles. However, evaluation of the performance of these methods has typically relied upon a handful of reasonably well-characterized biological datasets or analyses of a single biological example. While experimental validation of many truly functionally divergent sites (true positives) can be relatively straightforward, determining that particular sites do not contribute to functional divergence (i.e. false positives and true negatives) is much more difficult, resulting in noisy 'gold standard' examples.

RESULTS

We describe a novel, phylogeny-based functional divergence classifier, FunDi. Unlike previous approaches, FunDi uses a unified mixture model-based approach to detect type I and type II FD. To assess FunDi's overall classification performance relative to other methods, we introduce two methods for simulating functionally divergent datasets. We find that the FunDi method performs better than several other predictors over a wide variety of simulation conditions.

AVAILABILITY

http://rogerlab.biochem.dal.ca/Software

CONTACT

andrew.roger@dal.ca

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Cloning and functional characterization of Chondrichthyes, cloudy catshark, Scyliorhinus torazame and whale shark, Rhincodon typus estrogen receptors

Sex-steroid hormones are essential for normal reproductive activity in both sexes in all vertebrates. Estrogens are required for ovarian differentiation during a critical developmental stage and promote the growth and differentiation of the female reproductive system following puberty. Recent studies have shown that environmental estrogens influence the developing reproductive system as well as gametogenesis, especially in males. To understand the molecular mechanisms of estrogen actions and to evaluate estrogen receptor-ligand interactions in Elasmobranchii, we cloned a single estrogen receptor (ESR) from two shark species, the cloudy catshark (Scyliorhinus torazame) and whale shark (Rhincodon typus) and used an ERE-luciferase reporter assay system to characterize the interaction of these receptors with steroidal and other environmental estrogens. In the transient transfection ERE-luciferase reporter assay system, both shark ESR proteins displayed estrogen-dependent activation of transcription, and shark ESRs were more sensitive to 17beta-estradiol compared with other natural and synthetic estrogens. Further, the environmental chemicals, bisphenol A, nonylphenol, octylphenol and DDT could activate both shark ESRs. The assay system provides a tool for future studies examining the receptor-ligand interactions and estrogen disrupting mechanisms in Elasmobranchii.

Salmonid genomes have a remarkably expanded akirin family, coexpressed with genes from conserved pathways governing skeletal muscle growth and catabolism

Metazoan akirin genes regulate innate immunity, myogenesis, and carcinogenesis. Invertebrates typically have one family member, while most tetrapod and teleost vertebrates have one to three. We demonstrate an expanded repertoire of eight family members in genomes of four salmonid fishes, owing to paralog preservation after three tetraploidization events. Retention of paralogs secondarily lost in other teleosts may be related to functional diversification and posttranslational regulation. We hypothesized that salmonid akirins would be transcriptionally regulated in fast-twitch skeletal muscle during activation of conserved pathways governing catabolism and growth. The in vivo nutritional state of Arctic charr (Salvelinus alpinus L.) was experimentally manipulated, and transcript levels for akirin family members and 26 other genes were measured by quantitative real-time PCR (qPCR), allowing the establishment of a similarity network of expression profiles. In fasted muscle, a class of akirins was upregulated, with one family member showing high coexpression with catabolic genes coding the NF-kappaB p65 subunit, E2 ubiquitin-conjugating enzymes, E3 ubiquitin ligases, and IGF-I receptors. Another class of akirin was upregulated with subsequent feeding, coexpressed with 14-3-3 protein genes. There was no similarity between expression profiles of akirins with IGF hormones or binding protein genes. The level of phylogenetic relatedness of akirin family members was not a strong predictor of transcriptional responses to nutritional state, or differences in transcript abundance levels, indicating a complex pattern of regulatory evolution. The salmonid akirins epitomize the complexity linking the genome to physiological phenotypes of vertebrates with a history of tetraploidization.

Phylogeny, taxonomy, and evolution of the endothelin receptor gene family

A gene phylogeny provides the natural historical order to classify genes and to understand their functional, structural, and genomic diversity. The gene family of endothelin receptors (EDNR) is responsible for many key physiological and developmental processes of tetrapods and teleosts. This study provides a well-defined gene phylogeny for the EDNR family, which is used to classify its members and to assess their evolution. The EDNR phylogeny supports the recognition of the EDNRA, EDNRB, and EDNRC subfamilies, as well as more lineage-specific duplicates of teleosts and the African clawed frog. The duplications for these nominal genes are related to the various whole-genome amplifications of vertebrates, jawed vertebrates, fishes, and frog. The EDNR phylogeny also identifies several gene losses, including that of EDNRC from placental and marsupial (therian) mammals. When coupled with structural and biochemical information, site-specific analyses of evolutionary rate shifts reveal two distinct patterns of potential functional changes at the sequence level between therian versus non-therian EDNRA and EDNRB (i.e., between groups without and with EDNRC). An analysis of linkage maps and tetrapod synteny further suggests that the loss of therian EDNRC may be related to a chromosomal deletion in its common ancestor.

Comparative and evolutionary genomics of globin genes in fish

Sequencing genomes of model organisms is a great challenge for biological sciences. In the past decade, scientists have developed a large number of methods to align and compare sequenced genomes. The analysis of a given sequence provides much information on the genome structure but to a lesser extent on the function. Comparative genomics are a useful tool for functional and evolutionary annotation of genomes. In principle, comparison of genomic sequences may allow for identification of the evolutionary selection (negative or positive) that the functional sequences have been subjected to over time. Positively selected genome regions are the most important ones for evolution, because most changes are adaptive and often induce biological differences in organisms. The draft genomes of five fish species have recently become available. We herewith review and discuss some new insights into comparative genomics in fish globin genes. Special attention will be given to a complementary methodological approach to comparative genomics, fluorescence in situ hybridization (FISH). Internet resources for analyzing sequence alignments and annotations and new bioinformatic tools to address critical problems are thoroughly discussed.

Tracking the connection between evolutionary and functional shifts using the fungal lipase/feruloyl esterase A family

Background

There have been many claims of adaptive molecular evolution, but what role does positive selection play in functional divergence? The aim of this study was to test the relationship between evolutionary and functional shifts with special emphasis on the role of the environment. For this purpose, we studied the fungal lipase/feruloyl esterase A family, whose functional diversification makes it a very promising candidate.

Results

The results suggested functional shift following a duplication event where neofunctionalisation of feruloyl esterase A had occurred with conservation of the ancestral lipase function. Evolutionary shift was detected using the branch-site model for testing positive selection on individual codons along specific lineages. Positively selected amino acids were detected. Furthermore, biological data obtained from site-directed mutagenesis experiments clearly demonstrated that certain amino acids under positive selection were involved in the functional shift. We reassessed evolutionary history in terms of environmental response, and hypothesized that environmental changes such as colonisation by terrestrial plants might have driven adaptation by functional diversification in Euascomycetes (Aspergilli), thus conferring a selective advantage on this group.

Conclusion

The results reported here illustrate a rare example of connection between fundamental events in molecular evolution. We demonstrated an unequivocal connection between evolutionary and functional shifts, which led us to conclude that these events were probably linked to environmental change.

Evolution of the Circadian Clock Mechanism in Prokaryotes

The circadian system of prokaryotes is probably the oldest among the circadian systems of living organisms. The genes comprising the system are very different in their evolutionary histories. The reconstruction of macroevolution of the circadian genes in cyanobacteria suggests that there are probably at least two types of circadian systems, based either on the threekaigenes (kaiA, kaiB, andkaiC) or onkaiBandkaiC.When referred to the recently published results about a genomic timescale of prokaryote evolution, the origin ofkaiBandsasAcorresponds to the appearance of anoxygenic photosynthesis, while the origin of thekaiBCoperon corresponds to the time when oxygenic photosynthesis evolved.

The results of the studies performed so far suggest that major steps in macroevolution of the circadian system in cyanobacteria have been related to global changes in the environment and to keystone advances in biological evolution. This macroevolution has involved selection, multiple lateral transfers, gene duplications, and fusions as its primary driving forces. The proposed scenario of the circadian system's macroevolution is far from complete and will be updated as new genomic and sequence data are accumulated.

Responses to Nickel in the Proteome of the Hyperaccumulator Plant Alyssum lesbiacum

A proteomic analysis of the Ni hyperaccumulator plant Alyssum lesbiacum was carried out to identify proteins that may play a role in the exceptional degree of Ni tolerance and accumulation characteristic of this metallophyte. Of the 816 polypeptides detected in root tissue by 2D SDS-PAGE, eleven increased and one decreased in abundance relative to total protein after 6-week-old plants were transferred from a standard nutrient solution containing trace concentrations of Ni to a moderately high Ni treatment (0.3 mM NiSO4) for 48 h. These polypeptides were identified by tandem mass spectrometry and the majority were found to be involved in sulphur metabolism (consistent with a re-allocation of sulphur towards cysteine and glutathione), protection against reactive oxygen species, or heat-shock response. In contrast, very few polypeptides were found to change in abundance in root or shoot tissue after plants were exposed for 28 days to 0.03 mM NiSO4, a concentration representing the optimum for growth of this species but sufficient to lead to hyperaccumulation of Ni in the shoot. Under these conditions, constitutively expressed genes in this highly Ni-tolerant species may be sufficient to allow for effective chelation and sequestration of Ni without the need for additional protein synthesis.

Functional divergence of the circadian clock proteins in prokaryotes

Cyanobacteria are only prokaryotes known so far to have a circadian system. It may be based either on two (kaiB and kaiC) or three (kaiA, kaiB and kaiC) circadian genes. The homologs of two circadian proteins, KaiB and KaiC, form four major subfamilies (K1-K4) and also occur in some other prokaryotes. Using the likelihood-ratio tests, we studied a rate shift at the functional divergence of the proteins from the different subfamilies. It appears that only two of the subfamilies (K1 and K2) perform circadian functions. We identified in total 92 sites that have significantly different rates of evolution between the clades K1/K2 and K3/K4; 67 sites (15 in KaiB and 52 in KaiC) been evolving significantly slower in K1/K2 than the overall average for the entire sequence. Many critical sites are located in the identified functionally important motifs and regions, e.g. one of the Walker's motif As, DXXG motif, and two KaiA-binding domains of KaiC. There are also 36 sites (approximately 5%) with rate shift between K1 and K2. The rate shift at these sites may be related to the interaction with KaiA. Rate shift analyses have identified residues whose manipulation in the Kai proteins may lead to better understanding of their functions in the two different types of the cyanobacterial circadian system.

Evolutionary conservation and diversification of Rh family genes and proteins

Rhesus (Rh) proteins were first identified in human erythroid cells and recently in other tissues. Like ammonia transporter (Amt) proteins, their only homologues, Rh proteins have the 12 transmembrane-spanning segments characteristic of transporters. Many think Rh and Amt proteins transport the same substrate, NH(3)/NH(4)(+), whereas others think that Rh proteins transport CO(2) and Amt proteins NH(3). In the latter view, Rh and Amt are different biological gas channels. To reconstruct the phylogeny of the Rh family and study its coexistence with and relationship to Amt in depth, we analyzed 111 Rh genes and 260 Amt genes. Although Rh and Amt are found together in organisms as diverse as unicellular eukaryotes and sea squirts, Rh genes apparently arose later, because they are rare in prokaryotes. However, Rh genes are prominent in vertebrates, in which Amt genes disappear. In organisms with both types of genes, Rh had apparently diverged away from Amt rapidly and then evolved slowly over a long period. Functionally divergent amino acid sites are clustered in transmembrane segments and around the gas-conducting lumen recently identified in Escherichia coli AmtB, in agreement with Rh proteins having new substrate specificity. Despite gene duplications and mutations, the Rh paralogous groups all have apparently been subject to strong purifying selection indicating functional conservation. Genes encoding the classical Rh proteins in mammalian red cells show higher nucleotide substitution rates at nonsynonymous codon positions than other Rh genes, a finding that suggests a possible role for these proteins in red cell morphogenetic evolution.

Large-scale prediction of function shift in protein families with a focus on enzymatic function

Protein function shift can be predicted from sequence comparisons, either using positive selection signals or evolutionary rate estimation. None of the methods have been validated on large datasets, however. Here we investigate existing and novel methods for protein function shift prediction, and benchmark the accuracy against a large dataset of proteins with known enzymatic functions. Function change was predicted between subfamilies by identifying two kinds of sites in a multiple sequence alignment: Conservation-Shifting Sites (CSS), which are conserved in two subfamilies using two different amino acid types, and Rate-Shifting Sites (RSS), which have different evolutionary rates in two subfamilies. CSS were predicted by a new entropy-based method, and RSS using the Rate-Shift program. In principle, the more CSS and RSS between two subfamilies, the more likely a function shift between them. A test dataset was built by extracting subfamilies from Pfam with different EC numbers that belong to the same domain family. Subfamilies were generated automatically using a phylogenetic tree-based program, BETE. The dataset comprised 997 subfamily pairs with four or more members per subfamily. We observed a significant increase in CSS and RSS for subfamily comparisons with different EC numbers compared to cases with same EC numbers. The discrimination was better using RSS than CSS, and was more pronounced for larger families. Combining RSS and CSS by discriminant analysis improved classification accuracy to 71%. The method was applied to the Pfam database and the results are available at http://FunShift.cgb.ki.se. A closer examination of some superfamily comparisons showed that single EC numbers sometimes embody distinct functional classes. Hence, the measured accuracy of function shift is underestimated.

Molecular evolution of ldpA, a gene mediating the circadian input signal in cyanobacteria

The ldpA gene is an element of the cyanobacterial circadian system and mediates input to the clock. Using complete prokaryotic genomes from various public databases, I analyzed the structure and phylogeny of the ldpA genes. This gene belongs to the large superfamily of ferredoxins and has a HycB domain as a core element of its structure. In addition to this domain, ldpA has two conserved terminal domains that are specific to this gene and have no homologs in the databases. All three domains are under different selective constraints. The ldpA tree topology features two very distinct clades that are essentially the same as those in the previously reported trees of the sasA gene and the kaiBC operon, two other elements of the circadian system. The data on the ldpA polymorphism and evolutionary patterns give further support to the existence of two types of the system, kaiABC- and kaiBC-based, respectively. Each type has specific functional and selective constraints, which have likely been attained through highly concordant evolution of the system's components.

The evolutionary implications of knox-I gene duplications in conifers: correlated evidence from phylogeny, gene mapping, and analysis of functional divergence

Class I knox genes code for transcription factors that play an essential role in plant growth and development as central regulators of meristem cell identity. Based on the analysis of new cDNA sequences from various tissues and genomic DNA sequences, we identified a highly diversified group of class I knox genes in conifers. Phylogenetic analyses of complete amino acid sequences from various seed plants indicated that all conifer sequences formed a monophyletic group. Within conifers, four subgroups here named genes KN1 to KN4 were well delineated, each regrouping pine and spruce sequences. KN4 was sister group to KN3, which was sister group to KN1 and KN2. Genetic mapping on the genomes of two divergent Picea species indicated that KN1 and KN2 are located close to each other on the same linkage group, whereas KN3 and KN4 mapped on different linkage groups, correlating the more ancient divergence of these two genes. The proportion of synonymous and nonsynonymous substitutions suggested intense purifying selection for the four genes. However, rates of substitution per year indicated an evolution in two steps: faster rates were noted after gene duplications, followed subsequently by lower rates. Positive directional selection was detected for most of the internal branches harboring an accelerated rate of evolution. In addition, many sites with highly significant amino acid rate shift were identified between these branches. However, the tightly linked KN1 and KN2 did not diverge as much from each other. The implications of the correlation between phylogenetic, structural, and functional information are discussed in relation to the diversification of the knox-I gene family in conifers.

Genomic Background Predicts the Fate of Duplicated Genes: Evidence From the Yeast Genome

Gene duplication with subsequent divergence plays a central role in the acquisition of genes with novel function and complexity during the course of evolution. With reduced functional constraints or through positive selection, these duplicated genes may experience accelerated evolution. Under the model of subfunctionalization, loss of subfunctions leads to complementary acceleration at sites with two copies, and the difference in average rate between the sequences may not be obvious. On the other hand, the classical model of neofunctionalization predicts that the evolutionary rate in one of the two duplicates is accelerated. However, the classical model does not tell which of the duplicates experiences the acceleration in evolutionary rate. Here, we present evidence from the Saccharomyces cerevisiae genome that a duplicate located in a genomic region with a low-recombination rate is likely to evolve faster than a duplicate in an area of high recombination. This observation is consistent with population genetics theory that predicts that purifying selection is less effective in genomic regions of low recombination (Hill-Robertson effect). Together with previous studies, our results suggest the genomic background (e.g., local recombination rate) as a potential force to drive the divergence between nontandemly duplicated genes. This implies the importance of structure and complexity of genomes in the diversification of organisms via gene duplications.

Evolutionary divergence of thyrotropin receptor structure

The availability of 18 thyrotropin receptor (TSHR) sequences, including two recent entries for primates and seven from fish, have allowed us to investigate diversification of residues or domains during evolution. We used a likelihood ratio test for evolutionary rate shifts [Proc. Natl. Acad. Sci. 98 (2001) 14512] using LH/CGR sequences as an out-group. At each residue in the alignment, a statistical test was performed for a rate shift at the divergence between mammals and fish. Eighty-two rate shift sites were found, significantly more than was expected (p < 0.0001). The occurrence of rate shifts was highest in the intracellular tail, lowest in the transmembrane serpentine and intermediate in the ectodomain. In 52 mammalian sites, the rates were significantly faster than for the corresponding sites in fish. We have identified rate shift in sites important to TSHR function or in intimate proximity to such regions. The former category includes residues 53 and 55 (of LLR1 beta strand) and 253 and 255 (of LLR9 beta strand), crucial to TSH thyrotropic activity, residue 113, the site of N-linked glycosylation limited to humans, residue 310, an important switch in the hinge region for receptor binding and constitutive activity and residue 382 which centres a motif important for TSH-mediated receptor activation. The rate shifts positions close to functional region include a site proximal to a TSHR-specific motif on LLR3 beta strand, sites important in TM helix structure and homodimerization as well as, in the case of the third intracellular loop, to TSHR/G protein coupling. Rate shift analyses have identified residues whose manipulation in the human TSHR may lead to better understanding of receptor functions and help in the creation of designer analogues.