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PubMed1994

Molecular evolution and domain structure of plasminogen-related growth factors (HGF/SF and HGF1/MSP).

Plasminogen-related growth factors, a new family of polypeptide growth factors with the basic domain organization and mechanism of activation of the blood proteinase plasminogen, include hepatocyte growth factor/scatter factor (HGF/SF), a potent effector of the growth, movement, and differentiation of epithelia and endothelia, and hepatocyte growth factor-like/macrophage stimulating protein (HGF1/MSP), an effector of macrophage chemotaxis and phagocytosis. Phylogeny of the serine proteinase domains and analysis of intron-exon boundaries and kringle sequences indicate that HGF/SF, HGF1/MSP, plasminogen, and apolipoprotein (a) have evolved from a common ancestral gene that consisted of an N-terminal domain corresponding to plasminogen activation peptide (PAP), 3 copies of the kringle domain, and a serine proteinase domain. Models of the N domains of HGF/SF, HGF1/MSP, and plasminogen, characterized by the presence of 4 conserved Cys residues forming a loop in a loop, have been modeled based on disulfide-bond constraints. There is a distinct pattern of charged and hydrophobic residues in the helix-strand-helix motif proposed for the PAP domain of HGF/SF; these may be important for receptor interaction. Three-dimensional structures of the 4 kringle and the serine proteinase domains of HGF/SF were constructed by comparative modeling using the suite of programs COMPOSER and were energy minimized. Docking of a lysine analogue indicates a putative lysine-binding pocket within kringle 2 (and possibly another in kringle 4). The models suggest a mechanism for the formation of a noncovalent HGF/SF homodimer that may be responsible for the activation of the Met receptor. These data provide evidence for the divergent evolution and structural similarity of plasminogen, HGF/SF, and HGF1/MSP, and highlight a new strategy for growth factor evolution, namely the adaptation of a proteolytic enzyme to a role in receptor activation.

Amino Acid Sequence↗
PubMed2005

The quantum yield of CO2 fixation is reduced for several minutes after prior exposure to darkness. Exploration of the underlying causes.

Previous work has shown that the apparent quantum yield of CO2 fixation can be reduced for up to several minutes after prior exposure to darkness. In the work reported here, we investigated this phenomenon more fully and have deduced information about the underlying processes. This was done mainly by concurrent measurements of O2 and CO2 exchange in an oxygen-free atmosphere. Measurements of O2 evolution indicated that photochemical efficiency was not lost through dark adaptation, and that O2 evolution could proceed immediately at high rates provided that there were reducible pools of photosynthetic intermediates. Part of the delay in reaching the full quantum yield of CO2 fixation could be attributed to the need to build up pools of photosynthetic intermediates to high enough levels to support steady rates of CO2 fixation. There was no evidence that Rubisco inactivation contributed towards delayed CO2 uptake (under measurement conditions of low light). However, we obtained evidence that an enzyme in the reaction path between triose phosphates and RuBP must become completely inactivated in the dark. As a consequence, in dark-adapted leaves, a large amount of triose phosphates were exported from the chloroplast over the first minute of light rather than being converted to RuBP for CO2 fixation. That pattern was not observed if the pre-incubation light level was increased to just 3-5 micromol quanta m(-2) s(-1). The findings from this work underscore that there are fundamental differences in enzyme activation between complete darkness and even a very low light level of only 3-5 micromol quanta m(-2) s(-1) which predispose leaves to different gas exchange patterns once leaves are transferred to higher light levels.

Carbon Dioxide↗
PubMed1996

A Dryopithecus skeleton and the origins of great-ape locomotion.

The evolution of skeletal adaptations to orthograde postures, characteristic of extant hominoids, is of great interest as it provides the key to understanding the origins of apes and humans. We report here the recent discovery of an extraordinary partial skeleton of Dryopithecus laietanus from Can Llobateres (Spain). It provides evidence that orthograde postures and locomotion appeared at least 9.5 million years ago. Our results indicate that the body structure of this Miocene ape closely resembles that of extant hominoids and differs from the pronograde pattern of Miocene proconsulids in a set of important morphological characters. Dryopithecus also shows more traits reflecting structural adaptations for suspension than occurs in African apes. A similar positional behaviour is inferred for Sivapithecus indicus, thus strengthening previous hypotheses linking both Miocene forms with Pongo.

Animals↗
PubMed2026

Hidden genomic structure and widespread structural polymorphism across environmental gradients in the spiny sea star Marthasterias glacialis.

Genomic regions of reduced recombination can preserve linkage among co-adapted alleles, facilitating local adaptation despite high connectivity. Such regions-often generated by chromosomal inversions-may be especially important in highly dispersive marine taxa yet remain poorly documented in echinoderms. Here, we combined a chromosome-level reference genome with genome-wide ddRAD-seq from 296 Marthasterias glacialis individuals across 19 Atlantic-Mediterranean locations to quantify population structure and scan for recombination-suppressed haploblocks. Genome-wide neutral markers showed significant population differentiation together with evidence of high connectivity, revealed by the presence of inter-ecoregion migrants. Additionally, we identified 16 polymorphic haploblocks with patterns consistent with putative chromosomal inversions spanning 18.6% of the genome. Haploblock haplotypes were strongly environmentally and geographically structured and contained genes with key functions in stress response, osmoregulation and thermal tolerance. Haplotype distributions also paralleled previously described mitochondrial lineages despite nuclear gene flow, consistent with a model of ancient divergence followed by secondary contact. Overall, our results suggest a role for widespread structural polymorphism in adaptive differentiation in Echinodermata, providing a framework for linking echinoderm genome rearrangements to ecological divergence. Marthasterias glacialis thus emerges as a promising system to explore how structural variation contributes to adaptation and genome evolution in highly dispersive organisms.

Animals↗
PubMed2006

Molecular diversity and evolution of the large lipid transfer protein superfamily.

Circulatory lipid transport in animals is mediated to a substantial extent by members of the large lipid transfer (LLT) protein (LLTP) superfamily. These proteins, including apolipoprotein B (apoB), bind lipids and constitute the structural basis for the assembly of lipoproteins. The current analyses of sequence data indicate that LLTPs are unique to animals and that these lipid binding proteins evolved in the earliest multicellular animals. In addition, two novel LLTPs were recognized in insects. Structural and phylogenetic analyses reveal three major families of LLTPs: the apoB-like LLTPs, the vitellogenin-like LLTPs, and the microsomal triglyceride transfer protein (MTP)-like LLTPs, or MTPs. The latter are ubiquitous, whereas the two other families are distributed differentially between animal groups. Besides similarities, remarkable variations are also found among LLTPs in their major lipid-binding sites (i.e., the LLT module as well as the predicted clusters of amphipathic secondary structure): variations such as protein modification and number, size, or occurrence of the clusters. Strikingly, comparative research has also highlighted a multitude of functions for LLTPs in addition to circulatory lipid transport. The integration of LLTP structure, function, and evolution reveals multiple adaptations, which have come about in part upon neofunctionalization of duplicated genes. Moreover, the change, exchange, and expansion of functions illustrate the opportune application of lipid-binding proteins in nature. Accordingly, comparative research exposes the structural and functional adaptations in animal lipid carriers and brings up novel possibilities for the manipulation of lipid transport.

Animals↗
PubMed2001

Multichoice minority game.

The generalization of the problem of adaptive competition, known as the minority game, to the case of K possible choices for each player, is addressed, and applied to a system of interacting perceptrons with input and output units of a type of K-state Potts spins. An optimal solution of this minority game, as well as the dynamic evolution of the adaptive strategies of the players, are solved analytically for a general K and compared with numerical simulations.

Journal Article↗
PubMed2004

Ecological sources of zoonotic diseases.

Although of zoonotic origin, pathogens or infections posing a global threat to human health such as human immunodeficiency virus, severe acute respiratory syndrome or emerging influenza type A viruses may actually have little in common with known, established zoonotic agents, as these new agents merely underwent a transient zoonotic stage before adapting to humans. Evolution towards person-to-person transmission depends on the biological features of the pathogen, but may well be triggered or facilitated by external factors such as changes in human exposure. Disease emergence may thus be depicted as an evolutionary response to changes in the environment, including anthropogenic factors such as new agricultural practices, urbanisation, or globalisation, as well as climate change. Here the authors argue that in the case of zoonotic diseases emerging in livestock, change in agricultural practices has become the dominant factor determining the conditions in which zoonotic pathogens evolve, spread, and eventually enter the human population. Livestock pathogens are subjected to pressures resulting from the production, processing and retail environment which together alter host contact rate, population size and/or microbial traffic flows in the food chain. This process is illustrated by two study cases: a) livestock development in the 'Eurasian ruminant street' (the area extending from central Asia to the eastern Mediterranean basin) and the adjacent Arabian peninsula b) poultry production in Southeast Asia. In both scenarios, environmental factors relating to demography, land pressure and imbalances in production intensification have led to an unstable epidemiological situation, as evidenced by the highly pathogenic avian influenza upsurge early in 2004, when the main outbreaks were located in areas which had both large scale, peri-urban commercial holdings and a high density of smallholder poultry units.

Adaptation, Physiological↗
PubMed1991

Evolution and relatedness in two aminoacyl-tRNA synthetase families.

Sequence segments of about 140 amino acids in length, each containing a selected consensus region, were used in alignments of the aminoacyl-tRNA synthetases with the aim of discerning their evolutionary relationships. In all cases tested, enzymes specific for the same amino acid from a variety of organisms grouped together, reinforcing the supposition that the aminoacyl-tRNA synthetases are very ancient enzymes that evolved to include the full complement of 20 amino acids long before the divergence leading to prokaryotes and eukaryotes. The enzymes are divided into two mutually exclusive groups that appear to have evolved from independent roots. Group I, for which two sequence segments were analyzed, contains the enzymes specific for glutamic acid, glutamine, tryptophan, tyrosine, valine, leucine, isoleucine, methionine, and arginine. Group II enzymes include those activating threonine, proline, serine, lysine, aspartic acid, asparagine, histidine, alanine, glycine, and phenylalanine. Both groups contain a spectrum of amino acid types, suggesting the possibility that each could have once supported an independent system for protein synthesis. Within each group, enzymes specific for chemically similar amino acids tend to cluster together, indicating that a major theme of synthetase evolution involved the adaptation of binding sites to accommodate related amino acids with subsequent specialization to a single amino acid. In a few cases, however, synthetases activating dissimilar amino acids are grouped together.

Amino Acid Sequence↗
PubMed2003

Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation.

Microorganisms have been mutating and evolving on Earth for billions of years. Now, a field of research has developed around the idea of using microorganisms to study evolution in action. Controlled and replicated experiments are using viruses, bacteria and yeast to investigate how their genomes and phenotypic properties evolve over hundreds and even thousands of generations. Here, we examine the dynamics of evolutionary adaptation, the genetic bases of adaptation, tradeoffs and the environmental specificity of adaptation, the origin and evolutionary consequences of mutators, and the process of drift decay in very small populations.

Adaptation, Biological↗
PubMed2004

Re-adaptation hypothesis: explaining health benefits of caloric restriction.

For the effectiveness of under-eating or caloric restriction a simple evolution-based re-adaptation hypothesis is offered. Our ancient ancestors, whose bodies we inherited, ate and weighed a good deal less in relation to their size than we do. Over hundred thousands of years their desire for food was checked by its scarcity and the effort it took to collect it daily from all over the countryside. Thereby they set the reference standard for living and eating normally and healthily, not we. We eat as much as we like. No creature has ever been adapted to that. By practicing caloric restriction and daily exercise, we simulate to some degree the essentials of the way of life of our well adapted forbears. By such re-adaptation to our generic heritage, we re-gain their health at least approximately.

Acclimatization↗
PubMed2001

An ancient lectin-dependent complement system in an ascidian: novel lectin isolated from the plasma of the solitary ascidian, Halocynthia roretzi.

Mannose-binding lectin (MBL) is a C-type lectin involved in the first line of host defense against pathogens and it requires MBL-associated serine protease (MASP) for activation of the complement lectin pathway. To elucidate the origin and evolution of MBL, MBL-like lectin was isolated from the plasma of a urochordate, the solitary ascidian Halocynthia roretzi, using affinity chromatography on a yeast mannan-Sepharose. SDS-PAGE of the eluted proteins revealed a major band of approximately 36 kDa (p36). p36 cDNA was cloned from an ascidian hepatopancreas cDNA library. Sequence analysis revealed that the carboxy-terminal half of the ascidian lectin contains a carbohydrate recognition domain (CRD) that is homologous to C-type lectin, but it lacks a collagen-like domain that is present in mammalian MBLs. Purified p36 binds specifically to glucose but not to mannose or N-acetylglucosamine, and it was designated glucose-binding lectin (GBL). The two ascidian MASPs associated with GBL activate ascidian C3, which had been reported to act as an opsonin. The removal of GBL-MASPs complex from ascidian plasma using Ab against GBL inhibits C3-dependent phagocytosis. These observations strongly suggest that GBL acts as a recognition molecule and that the primitive complement system, consisting of the lectin-proteases complex and C3, played a major role in innate immunity before the evolution of an adaptive immune system in vertebrates.

Amino Acid Sequence↗
PubMed2006

Brave New World: the epistatic foundations of natives adapting to invaders.

Classical examples indicated rapid evolution to be both rare and largely anthropogenic. As the pace and scale of human disturbance increase, such evolution is becoming more the norm. Genetically based adaptation may underlie successful biological invasions, and may likewise characterize responses in natives to invasives. Recent published studies confirm that natives are adapting morphologically, behaviorally, physiologically and life historically to selection from invasive species. Some of the processes involved are evident in our studies of recent host shifts to invasive plants by native soapberry bugs in North America and Australia. On both continents populations have differentiated extensively in fitness traits. Genetic architecture of these adaptations involves a surprising degree of non-additive variation (epistasis, dominance), a result that in theory may reflect a history of colonization by a small number of individuals followed by population growth. Such "founder-flush" events may unleash extraordinary evolutionary potential, and their importance will be clarified as more studies take advantage of the accidental perturbation experiments that biotic invasions represent. From a conservation standpoint, rapid evolution in natives will present challenges for ecologically appropriate and sustainable management, but at the same time may enhance the capacity of the native community to act in the biological control of invasive species.

Adaptation, Physiological↗
PubMed2006

Genetic architecture of traits associated with serpentine adaptation of Silene vulgaris.

Serpentine soils provide a difficult substrate for plant colonization and growth and therefore represent an ideal system for studying the genetics of habitat adaptation and the evolution of plant-ecotypes. Using an F2 mapping population derived from an intraspecific cross between a serpentine and a nonserpentine ecotype of Silene vulgaris, the genetic architecture of seven morphological, physiological and life-history traits was explored. A quantitative trait locus (QTL) analysis identified 23 QTLs, 15 of which were classified as major QTLs. The observed genetic architecture suggests that traits potentially involved in habitat adaptation are controlled by few genes of major effect and have evolved under consistent directional selection. Several linkage groups harboured overlapping QTLs for different traits, which can be due to either pleiotropy or linkage. The potential roles of these factors and of the time available for habitat adaptation and ecological speciation on serpentine are discussed.

Adaptation, Physiological↗
PubMed2006

The life-cycle of operons.

Operons are a major feature of all prokaryotic genomes, but how and why operon structures vary is not well understood. To elucidate the life-cycle of operons, we compared gene order between Escherichia coli K12 and its relatives and identified the recently formed and destroyed operons in E. coli. This allowed us to determine how operons form, how they become closely spaced, and how they die. Our findings suggest that operon evolution may be driven by selection on gene expression patterns. First, both operon creation and operon destruction lead to large changes in gene expression patterns. For example, the removal of lysA and ruvA from ancestral operons that contained essential genes allowed their expression to respond to lysine levels and DNA damage, respectively. Second, some operons have undergone accelerated evolution, with multiple new genes being added during a brief period. Third, although genes within operons are usually closely spaced because of a neutral bias toward deletion and because of selection against large overlaps, genes in highly expressed operons tend to be widely spaced because of regulatory fine-tuning by intervening sequences. Although operon evolution may be adaptive, it need not be optimal: new operons often comprise functionally unrelated genes that were already in proximity before the operon formed.

Bacillus subtilis↗
PubMed2003

Experimental evolution in Drosophila melanogaster: interaction of temperature and food quality selection regimes.

In Drosophila, both the phenotypic and evolutionary effect of temperature on adult size involves alterations to larval resource processing and affects other life-history traits, that is, development time but most notably, larval survival. Therefore, thermal evolution of adult body size might not be independent of simultaneous adaptation of larval traits to resource availability. Using experimental evolution lines adapted to high and low temperatures at different levels of food, we show that selection pressures interact in shaping larval resource processing. Evolution on poor food invariably leads to lower resource acquisition suggesting a cost to feeding behavior. However, following low temperature selection, lower resource acquisition led to a higher adult body size, probably by more efficient allocation to growth. In contrast, following high temperature selection, low resource acquisition benefited larval survival, possibly by reducing feeding-associated costs. We show that evolved differences to larval resource processing provide a possible proximate mechanism to variation in a suite of correlated life-history traits during adaptation to different climates. The implication for natural populations is that in nature, thermal evolution drives populations to opposite ends of an adult size versus larval survival trade-off by altering resource processing, if resource availability is limited.

Analysis of Variance↗
PubMed2006

Advances in fish cytokine biology give clues to the evolution of a complex network.

Complex immune systems require complex regulatory mechanisms. Whilst the control of innate and inflammatory responses is likely to be ancient in origin, and potentially ubiquitous in the animal kingdom, clearly the evolution of an adaptive immune system in vertebrates is likely to coincide with new regulatory mechanisms and molecules. Key amongst these is the cytokine network, well characterised in mammals and becoming increasingly well characterised in fish and birds. This article will review our current understanding of which components of this network are crucial for adaptive immunity and evolved early, being present from fish to mammals. It will also consider which components of this network potentially evolved later (after the fish-tetrapod divergence) leading to unique cytokine genes in particular vertebrate groups.

Animals↗
PubMed2026

Evolution after whole-genome duplication (WGD) drives phenotypic and transcriptomic divergence more than WGD in an autopolyploid herb.

Whole-genome duplication (WGD) is a major driver of plant speciation and often hypothesized to promote rapid adaptation to new or changing environmental conditions. However, the extent to which WGD per se fosters phenotypic and transcriptional novelties, and the relative contribution of WGD-induced changes vs post-WGD evolution to trait differentiation between cytotypes remains poorly understood. Here, we investigated the phenotypic and transcriptomic consequences of WGD and subsequent evolution in the Biscutella laevigata diploid-autotetraploid complex by comparing replicated diploid, synthetic autotetraploids, and natural autotetraploids (originated some 24,000 to 7,000 generations ago) under moderate daily temperature fluctuations (stable) vs. daily heat stress (changing) conditions. WGD led to reduced specific leaf area and slower rosette growth but had no significant effect on biomass. Post-WGD evolution acted in contrasting directions on WGD-induced changes, either reverting traits to diploid-like values or maintaining them in natural autotetraploids. Overall, WGD induced a decrease in fitness that was mitigated by post-WGD evolution, resulting in natural autotetraploids with similar or higher fitness under changing conditions than diploids. While the genetic background modulates the effects of WGD, cytotype-level transcriptomic analyses revealed limited immediate effects of WGD under stable conditions, although heat stress induced different responses across cytotypes. Altogether, our results highlight a complex interplay between immediate WGD-induced and subsequent evolution at the phenotypic and transcriptomic levels, supporting a predominant role of post-WGD evolution in the differentiation of current cytotypes and the adaptive evolution of autotetraploids of B. laevigata.

Genome, Plant↗
PubMedDate not supplied

[Feeding behavior of Trichinella as a leading factor of adaptation to the body of the mammals].

Studies were carried out of the permeability of the cuticle of Trichinella spiralis (Owen, 1835) for fluorochromes and histidine, the filling of the mid-gut and the amino-acids contents in it. The quantity of glicogene in different organs was estimated. A conclusion has been grown that a larva consumes food through the integuments of its body; intestinal Trichinella use within the first 20 hours of their development the reserves of glicogene and later consume food monomeres and oxygen from the host's mucous membrane through their integuments. The mode of feeding of Trichinella was formed during their evolution as an adaptation to parasitism on the mucous membrane of the host.

Adaptation, Physiological↗