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At least 847 records · Page 47Linked to original sources
PubMed2003

Structural mechanism of specific ligand recognition by a lipocalin tailored for the complexation of digoxigenin.

DigA16 is an artificial digoxigenin-binding protein, which was derived from the bilin-binding protein, a lipocalin of Pieris brassicae, via reshaping of its natural ligand pocket. Here we report the crystal structures of DigA16 in the presence of either digoxigenin or digitoxigenin and for the apo-protein at resolutions below 1.9A. As a consequence of the altogether 17 amino acid substitutions within the binding site significant structural changes have occurred in the four loops that form the entrance to the ligand pocket on top of the structurally conserved beta-barrel framework. For example, one loop adopts a new alpha-helical backbone structure, which seems to be induced by few critical side-chain contacts. Digoxigenin becomes almost fully buried (by 95%) upon complexation, whereby specificity for the hydrophilic steroid is maintained through hydrogen-bonding networks and shape complementarity. The differential binding of the related steroid digitoxigenin is mainly governed by an internal histidine residue, whose side-chain undergoes significant induced fit. Among those amino acids that line the ligand pocket two tyrosine and one tryptophan residue provide the largest contacts. Interestingly, corresponding three side-chains are found with the same mutual orientation in the anti-digoxigenin antibody 26-10, even though the hapten orientation is quite different there and only 66% of the steroid surface is buried in the combining site. Hence, in the case of the engineered lipocalin DigA16 an example of convergent in vitro evolution is observed. Generally, the remarkable structural plasticity of the loop region and the role of polar residues in the binding site illustrate the potential of the lipocalin scaffold for the generation of specific receptor proteins towards a variety of ligands.

Animals↗
PubMed2001

Bistability in the JNK cascade.

BACKGROUND: Important signaling properties, like adaptation, oscillations, and bistability, can emerge at the level of relatively simple systems of signaling proteins. Here, we have examined the quantitative properties of one well-studied signaling system, the JNK cascade. We experimentally assessed the response of JNK to a physiological stimulus (progesterone) and a pathological stress (hyperosmolar sorbitol) in Xenopus laevis oocytes, a cell type that is well-suited to the quantitative analysis of cell signaling. Our aim was to determine whether JNK responses are graded (Michaelian) in character; ultrasensitive in character, resembling the responses of cooperative enzymes; or bistable and all-or-none in character. RESULTS: The responses of JNK to both progesterone and sorbitol were found to be essentially all-or-none. Individual oocytes had either very high or very low JNK activities, with few oocytes possessing intermediate levels of JNK activity. Moreover, JNK activation was autocatalytic, indicating that the JNK cascade is either embedded in or downstream of a positive feedback loop. JNK also exhibited hysteresis, a form of biochemical memory, in its response to sorbitol. These findings indicate that the JNK cascade is part of a bistable signaling system in oocytes. CONCLUSIONS: In Xenopus oocytes, JNK responds to physiological and pathological stimuli in an all-or-none manner. The JNK response shows all the hallmarks of a bistable response, including strong positive feedback and hysteresis. Bistability is a recurring theme in the biochemistry of oocyte maturation and early embryogenesis; the Mos/MEK/p42 MAPK cascade also exhibits bistable responses, and the Cdc2/cyclin B system is hypothesized to be bistable as well. However, the mechanisms underpinning the positive feedback and bistability in the three cases are different, suggesting that evolution has repeatedly converged upon bistability as a way of producing digital responses.

Animals↗
PubMed1997

Making a fitting choice: common aspects of sugar-binding sites in plant and animal lectins.

Comparing sequences of plant and animal lectins reveals that the ability to bind any one type of sugar has evolved several times independently in diverse protein frameworks. Conversely, families of lectins that share common structural features often contain members that recognize different groups of sugars. In the context of this combination of convergent and divergent evolution, our knowledge of the structures of lectin-sugar complexes provides valuable insights into the principles that underlie specific sugar binding.

Amino Acid Sequence↗
PubMed2002

Seismic evidence for catastrophic slab loss beneath Kamchatka.

In the northwest Pacific Ocean, a sharp corner in the boundary between the Pacific plate and the North American plate joins a subduction zone running along the southern half of the Kamchatka peninsula with a region of transcurrent motion along the western Aleutian arc. Here we present images of the seismic structure beneath the Aleutian-Kamchatka junction and the surrounding region, indicating that: the subducting Pacific lithosphere terminates at the Aleutian-Kamchatka junction; no relict slab underlies the extinct northern Kamchatka volcanic arc; and the upper mantle beneath northern Kamchatka has unusually slow shear wavespeeds. From the tectonic and volcanic evolution of Kamchatka over the past 10 Myr (refs 3-5) we infer that at least two episodes of catastrophic slab loss have occurred. About 5 to 10 Myr ago, catastrophic slab loss shut down island-arc volcanic activity north of the Aleutian-Kamchatka junction. A later episode of slab loss, since about 2 Myr ago, seems to be related to the activity of the world's most productive island-arc volcano, Klyuchevskoy. Removal of lithospheric mantle is commonly discussed in the context of a continental collision, but our findings imply that episodes of slab detachment and loss are also important agents in the evolution of oceanic convergent margins.

Journal Article↗
PubMed1990

Speculating about pyrazines.

Of the various types of alerting signals found in nature, odours are the least well understood. The worldwide distribution of pyrazines in plants, insects, terrestrial vertebrates, marine organisms, fungi and bacteria suggests that they are of special significance. We speculate that these molecules served as natural points of convergence in the evolution of widespread alerting signals, which are used for differing but related intraspecific purposes by various species. In aposematic, self-advertising toxic insects and their mimics, for example, pyrazines function as additional warning signals; preliminary data indicates that their odour can potentiate taste aversion learning in rats and the associative learning of immune suppression in mice. The latter suggests that in addition to their alerting properties, pyrazine odours may act as ectohormones which interact with predator physiology.

Animals↗
PubMed2000

The possible role of reaction-diffusion in leaf shape.

We consider mechanisms that may determine certain simple leaf shapes. Compared with other aspects of plant morphogenesis, such as phyllotaxis or spiral leaf arrangement, rather little is known about leaf-shape-determining mechanisms. We develop mathematical models for the gross pattern of leaf shape based on reaction diffusion systems. These models are consistent with what is known about factors that might determine leaf shape. They show that diverse leaf shapes may be obtained from a single reaction diffusion system. This has implications in terms of both convergent and divergent evolution. The models make predictions that can be tested experimentally. We predict the form of pre-patterns of growth promoters in leaf primordia of different sizes when the morphogens either diffuse into the primordia or are produced locally. We also predict the effects on leaf shape of removing parts of primordia at different times. The models can also predict the effects on leaf shape of the topical application of activators and inhibitors to leaf primordia.

Biological Evolution↗
PubMed1984

25S ribosomal RNA homologies of basidiomycetous yeasts: taxonomic and phylogenetic implications.

Genera, families, and possibly orders of basidiomycetous yeasts can be defined by 25S rRNA homology and correlated phenotypic characters. The teleomorphic genera Filobasidium, Leucosporidium, and Rhodosporidium have greater than 96 relative binding percent (rb%) intrageneric 25S rRNA homology and significant intergeneric separation from each other and from Filobasidiella. The anamorphic genus Cryptococcus can be defined by morphology (monopolar budding), colony color, and greater than 75 rb% intrageneric homology; Vanrija is heterogeneous. Agaricostilbum (Phragmobasidiomycetes, Auriculariales), Hansenula (Ascomycotera, Endomycota), Tremella (Phragmobasidiomycetes, Tremellales), and Ustilago (Ustomycota, Ustilaginales) appear equally unrelated to the Cryptococcus, Filobasidiella, and Rhodosporidium spp. used as probes. The Filobasidiaceae and Sporidiaceae, Filobasidiales and Sporidiales, form coherent homology groups which appear to have undergone convergent 25S rRNA evolution, since their relatedness is much greater than that indicated by 5S rRNA homology. Ribosomal RNA homologies do not appear to measure evolutionary distance.

Biological Evolution↗
PubMed1989

Quantitative aspects of the estimation of evolutionary trees.

Various approaches to the estimation of evolutionary trees are reviewed, with emphasis on recent developments. It is argued that no approach is 'model-free', that is, without some assumptions about the processes of evolutionary change. A statistical approach provides a general framework and it is accepted that cladistic methodology represents a special case within this framework. The idea of evolutionary convergence is examined in the light of recent discussion of the existence of convergence in molecular evolution. It is concluded that attempts to estimate evolutionary trees are justifiable at least on the grounds that, despite present shortcomings, they are the most appropriate way to analyse comparative data. There are good prospects for further progress.

Animals↗
PubMed2004

Platelet aggregation and exogenous factors from animal sources.

Platelet aggregation plays a crucial role in thrombosis. This review describes exogenous factors isolated from various animal sources, including venoms and the salivary glands that interfere in platelet aggregation. Some of these factors induce platelet aggregation or agglutination, whereas others inhibit platelet aggregation. These proteins range from small molecular weight peptides to large proteins. Some of these proteins exhibit various enzymatic activities, while others are nonenzymatic. These exogenous factors affect platelet aggregation by various mechanisms and thus they have been classified based on their mechanism of action. Many of these proteins have evolved through both convergent and divergent evolution. For example, platelet aggregation inhibitors, which interfere in the interactions between fibrinogen and its receptor, the glycoprotein IIb/IIIa complex, show extreme structural diversity but they share the common functional site of Arg-Gly-Asp (RGD) tripeptide segment. On the other hand, C-type lectin related proteins exhibit diverse biological effects by interacting with different proteins, but share common structural scaffold. Thus the mechanistic and structure-function studies of these exogenous proteins have contributed significantly to the understanding of molecular mechanisms of platelet aggregation and to the development of potent antiplatelet agents, respectively. A number of new exogenous factors have been identified recently and the search is still on for novel factors that interfere with platelet aggregation. Further studies in this area will help in the development of novel strategies for treating cardiovascular and hematological disorders.

Animals↗
PubMed1998

Genetic control of murine limb morphogenesis: relationships with human syndromes and evolutionary relevance.

Over the past ten years, the discovery and functional characterisation of murine Hox genes has led to a better understanding of some of the molecular mechanisms underlying limb development. It has also shed some light on the potential genetic events which have accompanied the fin-to-limb transition, an evolutionary step of critical importance which opened the way to the evolution of higher vertebrates. This convergence between developmental biology and the sciences of evolution is one of the synergistic interface that has been established recently thanks to the use of genetic engineering and transgenic animals. The increasing number of human genetic syndromes which are derived from mutations in developmental control genes remind us that many human genetic diseases are nothing else but alterations in our developmental programme. Here, we illustrate these various issues by discussing the function of Hox genes during limb development.

Animals↗
PubMed2004

Designing the future: NBIC technologies and human performance enhancement.

Never before has any civilization had the unique opportunity to enhance human performance on the scale that we will face in the near future. The convergence of nanotechnology, biotechnology, information technology, and cognitive science (NBIC) is creating a set of powerful tools that have the potential to significantly enhance human performance as well as transform society, science, economics, and human evolution. As the NBIC convergence becomes more understood, the possibility that we may be able to enhance human performance in the three domains of therapy, augmentation, and designed evolution will become anticipated and even expected. In addition, NBIC convergence represents entirely new challenges for scientists, policymakers, and business leaders who will have, for the first time, vast new and powerful tools to shape markets, societies, and lifestyles. The emergence of NBIC convergence will challenge us in new ways to balance risk and return, threat and opportunity, and social responsibility and competitive advantage as we step into the 21st century.

Biological Evolution↗
PubMed2001

Phylogenetic evidence for colour pattern convergence in toxic pitohuis: Müllerian mimicry in birds?

Bird species in the genus Pitohui are chemically defended by a potent neurotoxic alkaloid in their skin and feathers. The two most toxic pitohui species, the hooded pitohui (Pitohui dichrous) and the variable pitohui (Pitohui kirhocephalus), are sometimes strikingly patterned and, in certain portions of their geographical ranges, both species share a nearly identical colour pattern, whereas in other areas they do not. Müllerian mimicry (the mutual resemblance of two chemically defended prey species) is common in some other animal groups and Pitohui birds have been suggested as one of the most likely cases in birds. Here, we examine pitohui plumage evolution in the context of a well-supported molecular phylogeny and use a maximum likelihood approach to test for convergent evolution in coloration. We show that the 'mimetic' phenotype is ancestral to both species and that the resemblance in most races is better explained by a shared ancestry. One large clade of P. kirhocephalus lost this mimetic phenotype early in their evolution and one race nested deep within this clade appears to have re-evolved this phenotype. These latter findings are consistent with the hypothesis that Müllerian mimicry is driving the evolution for a similar colour pattern between P. dichrous, but only in this one clade of P. kirhocephalus

Animals↗
PubMed1987

Crystal structure of muconate lactonizing enzyme at 3 A resolution.

The crystal structure of muconate lactonizing enzyme has been solved at 3 A resolution, and an unambiguous alpha-carbon backbone chain trace made. The enzyme contains three domains; the central domain is a parallel-stranded alpha-beta barrel, which has previously been reported in six other enzymes, including triose phosphate isomerase and pyruvate kinase. One novel feature of this enzyme is that its alpha-beta barrel has only seven parallel alpha-helices around the central core of eight parallel beta-strands; all other known alpha-beta barrels contain eight such helices. The N-terminal (alpha + beta) and C-terminal domains cover the cleft where the eighth helix would be. The active site of muconate lactonizing enzyme has been found by locating the manganese ion that is essential for catalytic activity, and by binding and locating an inhibitor, alpha-ketoglutarate. The active site lies in a cleft between the N-terminal and barrel domains; when the active sites of muconate lactonizing enzyme and triose phosphate isomerase are superimposed, barrel-strand 1 of triose phosphate isomerase is aligned with barrel-strand 3 of muconate lactonizing enzyme. This implies that structurally homologous active-site residues in the two enzymes are carried on different parts of the primary sequence; the ancestral gene would had to have been transposed during its evolution to the modern proteins, which seems unlikely. Therefore, these two enzymes may be related by convergent, rather than divergent, evolution.

Binding Sites↗
PubMed2003

Convergence and coevolution in a mutualism: evidence from a molecular phylogeny of Ficus.

The interaction between Ficus (Moraceae) and their pollinating wasps (Chalcidoidea: Agaonidae; more than 700 species-specific couples) is one of the most specialized mutualisms found in nature. Both partners of this interaction show extensive variation in their respective biology. Here we investigate Ficus life-history trait evolution and fig/fig wasp coadaptation in the context of a well-resolved molecular phylogeny. Mapping out variations in Ficus life-history traits on an independently derived phylogeny constructed from ribosomal DNA sequences (external and internal transcribed spacer) reveals several parallel transitions in Ficus growth habit and breeding system. Convergent trait evolution might explain the discrepancies between morphological analyses and our molecular reconstruction of the genus. Morphological characters probably correlate with growth habit and breeding system and could therefore be subject to convergent evolution. Furthermore, we reconstruct the evolution of Ficus inflorescence characters that are considered adaptations to the pollinators. Our phylogeny reveals convergences in ostiole shape, stigma morphology, and stamen:ovule ratio. Statistical tests taking into account the phylogenetic relationship of the species show that transitions in ostiole shape are correlated with variation in wasp pollinator head shape, and evolutionary changes in stigma morphology and stamen:ovule ratio correlate with changes in the pollination behavior of the associated wasp. These correlations provide evidence for reciprocal adaptations of morphological characters between these mutualistic partners that have interacted over a long evolutionary time. In light of previous ecological studies on mutualism, we discuss the adaptive significance of these correlations and what they can tell us about the coevolutionary process occurring between figs and their pollinators.

Adaptation, Biological↗
PubMed2006

Evolution of Afrotropical freshwater crab lineages obscured by morphological convergence.

We use sequence data derived from six DNA gene loci to examine evolutionary and biogeographic affinities among all freshwater crab families. With an emphasis on the Afrotropical fauna that includes Africa, Madagascar, and the Seychelles, we test the proposed Gondwanan cladogenesis of the group. Phylogenetic results demonstrate that contemporary distribution patterns of freshwater crab lineages are incongruent with the expected area cladogram of continental fragmentation. Instead, our phylogenetic estimate and divergence time estimation indicate a post-Gondwanan, early Cretaceous cladogenesis for freshwater crabs implying that the acquisition of a freshwater lifestyle was achieved more recently. A dispersal hypothesis as opposed to vicariance appears to best explain the contemporary distribution pattern of this group. However, our results do not explicitly disprove a Gondwanan origin for the Afrotropical freshwater crabs. Alarmingly, these results suggest that most of the currently recognized freshwater crab families are unreliable taxonomic groupings since virtually no Afrotropical freshwater crab families formed monophyletic units thus obscuring inferred biogeographic relationships. Convergence in characters associated with the terminal segment of the mandibular palp is clearly a pervasive obstacle in the taxonomy of this group.

Animals↗
PubMed2003

Dynamics in the evolution of sexual traits: losses and gains, radiation and convergence in yellow wagtails (Motacilla flava).

We analyse patterns of genetic diversity and song complexity in the Palaearctic yellow wagtail (Motacilla flava), a highly polytypic species complex. Mitochondrial and nuclear DNA show that the complex is polyphyletic, despite parallel plumage variation in western and eastern clades. In the western clade there is genetic structure among southern subspecies, haplotype diversity decreases with latitude, and northern subspecies show evidence of bottlenecking and rapid expansions, as expected from isolation in glacial refugia followed by postglacial colonization. However, northern subspecies, which have more divergent male plumages, lack genetic structure and sing simpler songs. Loss of song complexity and evolution of plumage in founder populations are consistent with the Kaneshiro model, which posits that variation among species is a consequence of founder-induced shifts in female preference leading to loss of ancestral male sexual traits. Our results suggest possible postglacial founder-effect mechanisms for the morhological diversification of the yellow wagtail complex.

Animals↗
PubMed2001

Theoretical analysis of mutation-adaptive evolutionary algorithms.

Adaptive evolutionary algorithms require a more sophisticated modeling than their static-parameter counterparts. Taking into account the current population is not enough when implementing parameter-adaptation rules based on success rates (evolution strategies) or on premature convergence (genetic algorithms). Instead of Markov chains, we use random systems with complete connections - accounting for a complete, rather than recent, history of the algorithm's evolution. Under the new paradigm, we analyze the convergence of several mutation-adaptive algorithms: a binary genetic algorithm, the 1/5 success rule evolution strategy, a continuous, respectively a dynamic (1+1) evolutionary algorithm.

Algorithms↗
PubMed2004

Proteomic traces of speciation.

Recent work has shown that the network of structural similarity between protein domains exhibits a power-law distribution of edges per node. The scale-free nature of this graph, termed the protein domain universe graph or PDUG, may be reproduced via a divergent model of structural evolution. The performance of this model, however, does not preclude the existence of a successful convergent model. To further resolve the issue of protein structural evolution, we explore the predictions of both convergent and divergent models directly. We show that when nodes from the PDUG are partitioned into subgraphs on the basis of their occurrence in the proteomes of particular organisms, these subgraphs exhibit a scale-free nature as well. We explore a simple convergent model of structural evolution and find that the implications of this model are inconsistent with features of these organismal subgraphs. Importantly, we find that biased convergent models are inconsistent with our data. We find that when speciation mechanisms are added to a simple divergent model, subgraphs similar to the organismal subgraphs are produced, demonstrating that dynamic models can easily explain the distributions of structural similarity that exist within proteomes. We show that speciation events must be included in a divergent model of structural evolution to account for the non-random overlap of structural proteomes. These findings have implications for the long-standing debate over convergent and divergent models of protein structural evolution, and for the study of the evolution of organisms as a whole.

Bacterial Proteins↗