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PubMed2000

Protein surface similarities: a survey of methods to describe and compare protein surfaces.

Many methods have been developed to analyse protein sequences and structures, although less work has been undertaken describing and comparing protein surfaces. Evolution can lead sequences to diverge or structures to change topology; nevertheless, surface determinants that are essential to protein function itself may be mantained. Moreover, different molecules could converge to similar functions by gaining specific surface determinants. In such cases, sequence or structure comparisons are likely to be inadequate in describing or identifying protein functions and evolutionary relationships among proteins. Surface analysis can identify function determinants that are independent of sequence or secondary structure and can therefore be a powerful tool to highlight cases of possible convergent or divergent evolution. This kind of approach can be useful for a better understanding of protein molecular and biochemical mechanisms of catalysis or interaction with a ligand, which are usually surface dependent. Protein surface comparison, when compared to sequence or structure comparison methods, is a hard computational challenge and evaluated methods allowing the comparison of protein surfaces are difficult to find. In this review, we will survey the current knowledge about protein surface similarity and the techniques to detect it.

Algorithms↗
PubMed2006

Neutral theory and the evolution of ecological equivalence.

Since the publication of the unified neutral theory in 2001, there has been much discussion of the theory, pro and con. The hypothesis of ecological equivalence is the fundamental yet controversial idea behind neutral theory. Assuming trophically similar species are demographically alike (symmetric) on a per capita basis is only an approximation, but it is equivalent to asking: How many of the patterns of ecological communities are the result of species similarities, rather than of species differences? The strategy behind neutral theory is to see how far one can get with the simplification of assuming ecological equivalence before introducing more complexity. In another paper, I review the empirical evidence that led me to hypothesize ecological equivalence among many of the tree species in the species-rich tropical forest on Barro Colorado Island (BCI). In this paper, I develop a simple model for the evolution of ecological equivalence or niche convergence, using as an example evolution of the suite of life history traits characteristic of shade tolerant tropical tree species. Although the model is simple, the conclusions from it seem likely to be robust. I conclude that ecological equivalence for resource use are likely to evolve easily and often, especially in species-rich communities that are dispersal and recruitment limited. In the case of the BCI forest, tree species are strongly dispersal- and recruitment-limited, not only because of restricted seed dispersal, but also because of low recruitment success due to heavy losses of the seedling stages to predators and pathogens and other abiotic stresses such as drought. These factors and the high species richness of the community strongly reduce the potential for competitive exclusion of functionally equivalent or nearly equivalent species.

Biodiversity↗
PubMed2004

Convergence, divergence, and homogenization in the ecological structure of emydid turtle communities: the effects of phylogeny and dispersal.

Studies that have explored the origins of patterns of community structure from a phylogenetic perspective have generally found either convergence (similarity) in community structure between regions through adaptive evolution or lack of convergence (dissimilarity) due to phylogenetic conservatism in the divergent ecological characteristics of lineages inhabiting different regions. We used a phylogenetic approach to document a third pattern in the structure of emydid turtle communities. Emydid communities in southeastern North America tend to have a higher proportion of aquatic species than those in the northeast. This pattern reflects phylogenetic conservatism in the ecology and biogeography of two basal emydid clades, limiting convergence in community structure between these regions. However, differences in community structure between northeastern and southeastern North America have also been homogenized considerably by the dispersal of species with phylogenetically conserved ecological characteristics between regions. This pattern of ecologically conservative dispersal may be important in many continental and oceanic systems.

Animals↗
PubMed2005

Confrontation of morphological and molecular data: the Praomys group (Rodentia, Murinae) as a case of adaptive convergences and morphological stasis.

Phylogenetic relationships in a group of 21 African rodent species designated as the Praomys group (Murinae) were investigated using morphological characters and sequence data from the complete mitochondrial cytochrome b gene and nuclear IRBP gene fragment (840bp). The molecular results confirm the monophyly of the Praomys group, including the species Malacomys verschureni, while the other Malacomys species appear very divergent. The basal relationships within the Praomys group are poorly resolved, suggesting a rapid radiation at about 7-9 million years ago based on genetic divergence rates calibrated from the fossil record. Discrepancies between molecular and morphological results probably reflect of numerous convergences as well as variations in the rates of morphological evolution among lineages. Reconstructions of the ancestral character states suggest a savannah origin for the Praomys group, along with some morphological traits conserved by stasis in savannah taxa. At the same time, forest taxa seem to be characterized by an accelerated morphological evolution, with acquisition of convergent adaptive characters.

Adaptation, Biological↗
PubMed2005

Converging on a general model of protein evolution.

The availability of high-throughput genomic databases that establish protein dispensability, expression and interaction networks enables rigorous tests of competing models of protein evolution. Recent research utilizing these new data sets shows that protein evolution is more complex than was previously thought. Several variables, including protein dispensability, expression, functional density, and genetic modularity, appear to have independent effects on the evolutionary rate of proteins, suggesting that proteomes have evolved via an assembly of selectional regimes. These results indicate that a general model of protein evolution will emerge as more functional genomic data from a diversity of organisms accumulate.

Evolution, Molecular↗
PubMed2002

Convergent maternal provisioning and life-history evolution in echinoderms.

In marine invertebrates, the frequent evolution of lecithotrophic nonfeeding development from a planktotrophic feeding ancestral developmental mode has involved the repeated, independent acquisition of a large, lipid-rich, usually buoyant egg. To investigate the mechanistic basis of egg-size evolution and the role of maternally provisioned lipids in lecithotrophic development, we identified and quantified the egg lipids in six sea urchin species and five sea star species encompassing four independent evolutionary transformations to lecithotrophy. The small eggs of species with planktotrophic development were dominated by triglycerides with low levels of wax esters, whereas the larger eggs of lecithotrophs contain measurable triglycerides but were dominated by wax ester lipids, a relatively minor egg component of planktotrophs. Comparative analysis by independent contrasts confirmed that after removing the influence of phylogeny, the evolution of a large egg by lecithotrophs was correlated with the conspicuous deposition of wax esters. Increases in wax ester abundance exceeded expectations based solely on changes in egg volume. Wax esters may have roles in providing buoyancy to the egg and for postmetamorphic provisioning. Experimentally reducing the amount of wax esters in blastula stage embryos of the lecithotroph Heliocidaris erythrogramma resulted in a viable but nonbuoyant larvae. During normal development for H. erythrogramma, wax ester biomass remained constant during development to metamorphosis (five days postfertilization), but decreased during juvenile development before complete mouth formation (12 days postfertilization) and was further reduced at 18 days postfertilization. The function of wax esters may be specific to the lecithotrophic developmental mode because there were negligible wax esters present in competent pluteus larvae of Strongylocentrotus drobachiensis, a planktotrophic species. These data suggest that this seminal evolutionary modification, the production of a large egg, has been accomplished in part by the elaboration of a preexisting oogenic component, wax esters. The modification of preexisting oogenic processes may facilitate the observed high frequency of transformations in larval mode in marine invertebrates.

Animals↗
PubMed2006

Protein folding as posttranslational regulation: evolution of a mechanism for controlled plasma membrane expression of a G protein-coupled receptor.

Recent studies reveal that a number of G protein-coupled receptors (GPCRs) and other proteins are expressed inefficiently at the site normally associated with their biological action. In the case of some GPCRs, large amounts of receptor (perhaps more than half) may be destroyed without ever binding ligand or even arriving at the plasma membrane. For the human GnRH receptor (GnRHR), this apparent inefficiency has evolved under strong and convergent evolutionary pressure. The result is a human GnRHR molecule that is delicately balanced between either expression at the plasma membrane (PM) or retention/degradation in the endoplasmic reticulum, an effect mediated by engagement with the cellular quality control system. This balance appears to be the reason that the human receptor, but not the rat or mouse counterpart (which are more robustly routed to the PM), is highly susceptible to single-point mutations that result in disease. A single change in net charge is sufficient to tip the balance in favor of the endoplasmic reticulum and diminish GnRHR available at the PM. The apparent paradox that results from observing convergent pressure for evolution of a receptor that is both inefficiently produced and highly susceptible to mutational disease suggests that this approach must offer a strong advantage. This review focuses on the evolved mechanisms and considers that this is an underappreciated mechanism by which the cell controls functional levels of receptors and other proteins at the posttranslational level.

Animals↗
PubMed1996

Phylogenetics and evolution of the Daphnia longispina group (Crustacea) based on 12S rDNA sequence and allozyme variation.

Although members of the crustacean genus Daphnia have been the target of much research, there is little understanding of the group's evolutionary history. We addressed this gap by inferring a phylogeny for one of the major species groups (longispina) using nucleotide sequence variation of a 525-bp segment of the mitochondrial 12S rDNA and allozyme variation at 21 loci. We identified the major lineages and their relationships, assessed the phylogenetic utility of the few morphological characters in the group, and examined Daphnia phylogeography. Nuclear and mtDNA phylogenies were generally concordant in recognizing the same four species complexes. An exception was the position of Daphnia galeata mendotae. The allozyme tree paired this species with the Daphnia rosea lineage, whereas the mtDNA trees grouped D. g. mendotae with Daphnia galeata galeata. This discordance was consistent with the reticulate evolution of nuclear genes supporting the hypothesis that D. g. mendotae represents a case of homoploid hybrid speciation. Striking morphological stasis in the longispina group was evidenced by its very limited morphological divergence over an estimated 100 MY, and by the unusual transitional saturation of the conservative 12S rRNA gene within a species group. Phylogenetic inference also provided evidence that similarities in cephalic crest shape likely resulted from convergent or parallel evolution among species. Endemism at the continental level was indicated for previously cosmopolitan species, but the estimated times of these divisions were inconsistent with vicariance events suggesting recent dispersal among continents. A significant role for divergent selection in new habitats during speciation was suggested by the neighboringly sympatric distributions of four sister species pairs over broad geographic areas.

Alleles↗
PubMed2005

The current molecular phylogeny of Eutherian mammals challenges previous interpretations of placental evolution.

Based on histology, the placentae of eutherians are currently grouped in epitheliochorial, endotheliochorial and haemochorial placentae. In a haeckelian sense, the epitheliochorial contact with marked histiotrophic feeding by uterine milk is generally considered as primitive, especially since similar contacts exist in Marsupials. In contrast, the more intimate endotheliochorial and haemochorial contact, facilitating haemotrophic nutrition, is interpreted as a derived state. A cladistic analysis based on the phylogenetic relationships established by molecular analyses reveals that the basic clades are all characterized by an endotheliochorial or haemochorial placenta, and that the epitheliochorial placenta evolved at least three times in a convergent manner. This evolution may be explained by the fact that the epitheliochorial placenta in eutherians is more efficient in nutritional transfer (flow rate by exchange surface). Moreover, this arrangement may confer an advantage to the mother who can probably reduce the degree of manipulation by a genetically imprinted embryo.

Animals↗
PubMed2001

Evolution of locomotory attachment pads of hexapods.

This study shows that, in their evolution, hexapods have convergently developed two distinctly different mechanisms to attach themselves to a variety of substrates during locomotion. The first mechanism is provided by hairy surfaces and the second one by smooth flexible pads. The main similarity of both mechanisms is that the structured pad surface or particular properties of pad materials guarantee a maximum real contact with diverse substrata, regardless of their microsculpture. Ten characters of the two alternative designs were coded and analyzed together with a data matrix containing 105 additional morphological characters of different stages and body parts. The analysis demonstrates that similar structures (arolium, euplantulae, hairy tarsomeres) have evolved independently in several hexapod lineages. The evolution of flight and the associated necessity of being able to cling to vegetation or other substrates are suggested to be major triggers for the evolution of attachment structures.

Animals↗
PubMed2001

Molecular evolution of leptin.

Leptin, a hormone produced mainly by adipocytes, is involved in the regulation of food intake, metabolism, and reproduction. The objective of this study was to determine the evolutionary relationships of leptin genes. Partial nucleotide sequences of leptin were cloned and sequenced from six mammalian species: large hairy armadillo (Chaetophractus villosus), rabbit (Oryctolagus cuniculus), big brown bat (Eptesicus fuscus) [corrected], striped skunk (Mephitis mephitis), raccoon (Procyon lotor), and beluga whale (Delphinapterus leucas). The PUZZLE program was used to construct maximum-likelihood trees. Our phylogenetic analysis shows that the grouping of these new mammalian sequences with those currently available in GenBank respect the evolutionary relationships generally accepted for mammals. However, when leptin sequences for chicken and turkey are included in the analysis, these are found to group with mouse and rat leptins. Chicken and mouse leptins are 95% identical. However, when mouse is compared with closer relatives, such as rabbit or bat, identities are approximately 80%. A comparison of extant and ancestral leptin sequences suggests that convergent or parallel evolution is the most plausible hypothesis to explain the similarity between bird and rodent leptins.

Adipose Tissue↗
PubMed2006

Some introductory formalizations on the affine Hilbert spaces model of the origin of life. I. On quantum mechanical measurement and the origin of the genetic code: a general physical framework theory.

A physical (affine Hilbert spaces) frame is developed for the discussion of the interdependence of the problem of the origin (symbolic assignment) of the genetic code and a possible endophysical (a kind of "internal") quantum measurement in an explicite way, following the general considerations of Balázs (Balázs, A., 2003. BioSystems 70, 43-54; Balázs, A., 2004a. BioSystems 73, 1-11). Using the Everett (a dynamic) interpretation of quantum mechanics, both the individual code assignment and the concatenated linear symbolism is discussed. It is concluded that there arises a skewed quantal probability field, with a natural dynamic non-linearity in codon assignment within the physical model adopted (essentially corresponding to a much discussed biochemical frame of self-catalyzed binding (charging) of t RNA like proto RNAs (ribozymes) with amino acids). This dynamic specific molecular complex assumption of individual code assignment, and the divergence of the code in relation to symbol concatenation, are discussed: our frame supports the former and interpret the latter as single-type codon (triplet), also unambiguous and extended assignment, selection in molecular evolution, corresponding to converging towards the fixedpoint of the internal dynamics of measurement, either in a protein- or RNA-world. In this respect, the general physical consequence is the introduction of a fourth rank semidiagonal energy tensor (see also Part II) ruling the internal dynamics as a non-linear in principle second-order one. It is inferred, as a summary, that if the problem under discussion could be expressed by the concepts of the Copenhagen interpretation of quantum mechanics in some yet not quite specified way, the matter would be particularly interesting with respect to both the origin of life and quantum mechanics, as a dynamically supported natural measurement-theoretical split between matter ("hardware") and (internal) symbolism ("software") aspects of living matter.

Biological Evolution↗
PubMed2003

A new bioinformatic approach to detect common 3D sites in protein structures.

An innovative bioinformatic method has been designed and implemented to detect similar three-dimensional (3D) sites in proteins. This approach allows the comparison of protein structures or substructures and detects local spatial similarities: this method is completely independent from the amino acid sequence and from the backbone structure. In contrast to already existing tools, the basis for this method is a representation of the protein structure by a set of stereochemical groups that are defined independently from the notion of amino acid. An efficient heuristic for finding similarities that uses graphs of triangles of chemical groups to represent the protein structures has been developed. The implementation of this heuristic constitutes a software named SuMo (Surfing the Molecules), which allows the dynamic definition of chemical groups, the selection of sites in the proteins, and the management and screening of databases. To show the relevance of this approach, we focused on two extreme examples illustrating convergent and divergent evolution. In two unrelated serine proteases, SuMo detects one common site, which corresponds to the catalytic triad. In the legume lectins family composed of >100 structures that share similar sequences and folds but may have lost their ability to bind a carbohydrate molecule, SuMo discriminates between functional and non-functional lectins with a selectivity of 96%. The time needed for searching a given site in a protein structure is typically 0.1 s on a PIII 800MHz/Linux computer; thus, in further studies, SuMo will be used to screen the PDB.

Algorithms↗
PubMed1998

Crystal structure of a functional unit from Octopus hemocyanin.

Hemocyanins are giant oxygen transport proteins found in many arthropods and molluscs. Freely dissolved in the hemolymph, they are multisubunit proteins that contain many copies of the active site, a copper atom pair that reversibly binds oxygen. Octopus hemocyanin is composed of ten subunits, each of which contain seven oxygen-binding "functional units". The carboxyl-terminal 47 kDa functional unit, Odg, is a proteolytic isolate that binds oxygen reversibly while exhibiting slight Bohr and magnesium ion effects. In this work we present the X-ray structure determination and analysis of Odg at 2.3 A resolution. Odg has two structural domains: a largely alpha-helical copper binding domain, and a five-stranded anti-parallel beta-sandwich with the jelly roll topology found in many viruses. Six histidine residues ligate the copper atoms, one of which is involved in a thioether bridge. The results show that the hemocyanin from the mollusc and that from the arthropod have distinct tertiary folds in addition to the long recognized differences in their quaternary structures. Nonetheless, a comparison of Octopus and horseshoe crab hemocyanin reveals a similar active site, in a striking example of perhaps both convergent and divergent evolution.

Allosteric Regulation↗
PubMed1994

Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: instability of a tree based on a single gene.

The phylogenetic relationships among Primates (human), Artiodactyla (cow), Cetacea (whale), Carnivora (seal), and Rodentia (mouse and rat) were estimated from the inferred amino acid sequences of the mitochondrial genomes using Marsupialia (opossum), Aves (chicken), and Amphibia (Xenopus) as an outgroup. The overall evidence of the maximum likelihood analysis suggests that Rodentia is an outgroup to the other four eutherian orders and that Cetacea and Artiodactyla form a clade with Carnivora as a sister taxon irrespective of the assumed model for amino acid substitutions. Although there remains an uncertainty concerning the relation among Artiodactyla, Cetacea, and Carnivora, the existence of a clade formed by these three orders and the outgroup status of Rodentia to the other eutherian orders seems to be firmly established. However, analyses of individual genes do not necessarily conform to this conclusion, and some of the genes reject the putatively correct tree with nearly 5% significance. Although this discrepancy can be due to convergent or parallel evolution in the specific genes, it was pointed out that, even without a particular reason, such a discrepancy can occur in 5% of the cases if the branching among the orders in question occurred within a short period. Due to uncertainty about the assumed model underlying the phylogenetic inference, this can occur even more frequently. This demonstrates the importance of analyzing enough sequences to avoid the danger of concluding an erroneous tree.

Animals↗
PubMed1981

Transfer-RNA: the early adaptor.

Evolutionary history of tRNA is studied by comparative sequence analysis of two specified tRNA's at various phylogenetic levels and of tRNA families within four different species. Criteria are developed that allow 1) to distinguish between convergent and divergent evolution, 2) to determine the mechanism of divergence and 3) to estimate the degree of randomization of the variable parts of the sequences. The conclusion of these investigations is that tRNA's represent ancient molecules that existed in the form of a mutant distribution prior to their integration into genomes.

Bacteria↗
PubMed2006

Structural classification of small, disulfide-rich protein domains.

Disulfide-rich domains are small protein domains whose global folds are stabilized primarily by the formation of disulfide bonds and, to a much lesser extent, by secondary structure and hydrophobic interactions. Disulfide-rich domains perform a wide variety of roles functioning as growth factors, toxins, enzyme inhibitors, hormones, pheromones, allergens, etc. These domains are commonly found both as independent (single-domain) proteins and as domains within larger polypeptides. Here, we present a comprehensive structural classification of approximately 3000 small, disulfide-rich protein domains. We find that these domains can be arranged into 41 fold groups on the basis of structural similarity. Our fold groups, which describe broader structural relationships than existing groupings of these domains, bring together representatives with previously unacknowledged similarities; 18 of the 41 fold groups include domains from several SCOP folds. Within the fold groups, the domains are assembled into families of homologs. We define 98 families of disulfide-rich domains, some of which include newly detected homologs, particularly among knottin-like domains. On the basis of this classification, we have examined cases of convergent and divergent evolution of functions performed by disulfide-rich proteins. Disulfide bonding patterns in these domains are also evaluated. Reducible disulfide bonding patterns are much less frequent, while symmetric disulfide bonding patterns are more common than expected from random considerations. Examples of variations in disulfide bonding patterns found within families and fold groups are discussed.

Amino Acid Sequence↗