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PubMed2006

Specific cpb copies within the Leishmania donovani complex: evolutionary interpretations and potential clinical implications in humans.

Leishmania infantum and Leishmania donovani both pertain to the L. (L.) donovani complex and are responsible for visceral leishmaniasis. To explore the L. donovani complex, we focused our study on cysteine protease B (cpb) and especially on 2 cpb copies: cpbE and cpbF. We selected cpb genes because of their phylogenetic interest and host-parasite interaction involvement. Sequencing these 2 copies revealed (i) that cpbE is specific to L. infantum and cpbF is specific to L. donovani and (ii) that these 2 copies are different in length and sequence. Phylogenetic analysis and protein predictions were carried out in order to compare these copies (i) with other trypanosomatid cpb, especially L. mexicana, and (ii) within the L. donovani complex. Our results revealed patterns specific to the L. donovani complex such as the COOH-terminal extension, potential epitopes and N-glycosylation sites. Moreover, phylogenetic analysis revealed different levels of polymorphism between L. infantum and L. donovani and confirmed the ancestral status of the latter. L. infantum has a shorter sequence and a deleted sequence responsible for modifications in protein conformation and catalytic triad. Considering the clinical aspect, L. infantum dermotropic strains appeared more polymorphic than L. infantum viscerotropic strains.

Amino Acid Sequence↗
PubMed1989

The tumor-rejection antigens of the 1591 ultraviolet fibrosarcoma. Potential origin and evolutionary implications.

Previously, we cloned and sequenced the three novel MHC class I genes expressed by the C3H UV fibrosarcoma, 1591. We have extended the analysis of the polymorphic nature of these genes relative to the C3H strain. Scattered nucleotide differences among the tumor genes as compared with the C3H H-2 and Qa sequences make it highly unlikely that the novel tumor genes were generated by recombination between endogenous C3H sequences. Given that two of the tumor clones, A149 and A166, are remarkably similar in amino acid and DNA sequence to H-2Lq and H-2Dq, respectively, we also examined the 1591 RP2 and GUS loci for evidence of polymorphism. Compared with C3H and B10.AKM, 1591 appears to be heterozygous at each of these loci, consistent with an H-2q origin for the two novel 1591 class I genes. Interestingly, the third tumor gene, designated A216, shares certain characteristics with the H-2Ks antigen, reminiscent of the naturally occurring combination of H-2Ks, H-2Dq, and H-2Lq antigens found in some Swiss mouse strains. As a result, we propose that the non-C3H/HeN characteristics displayed by the 1591 tumor point to a non-C3H origin for the novel tumor class I genes of 1591.

Amino Acid Sequence↗
PubMed2005

Evolutionary diversity and potential recombinogenic role of integration targets of Non-LTR retrotransposons.

Short interspersed elements (SINEs) make up a significant fraction of total DNA in mammalian genomes, providing a rich substrate for chromosomal rearrangements by SINE-SINE recombinations. Proliferation of mammalian SINEs is mediated primarily by long interspersed element 1 (L1) non-long terminal repeat retrotransposons that preferentially integrate at DNA sequence targets with an average length of approximately 15 bp and containing conserved endonucleolytic nicking signals at both ends. We report that sequence variations in the first of the two nicking signals, represented by a 5'-TT-AAAA consensus sequence, affect the position of the second signal thus leading to target site duplications (TSDs) of different lengths. The length distribution of TSDs appears to be affected also by L1-encoded enzyme variants because targets with the same 5' nicking site can be of different average lengths in different mammalian species. Taking this into account, we reanalyzed the second nicking site and found that it is larger and includes more conserved sites than previously appreciated, with a consensus of 5'-ANTNTN-AA. We also studied potential involvement of the nicking sites in stimulating recombinations between SINEs. We determined that SINEs retaining TSDs with perfect 5'-TT-AAAA nicking sites appear to be lost relatively rapidly from the human and rat genomes and less rapidly from dog. We speculate that the introduction of DNA breaks induced by recurring endonucleolytic attacks at these sites, combined with the ubiquitousness of SINEs, may significantly promote recombination between repetitive elements, leading to the observed losses. At the same time, new L1 subfamilies may be selected for "incompatibility" with preexisting targets. This provides a possible driving force for the continual emergence of new L1 subfamilies which, in turn, may affect selection of L1-dependent SINE subfamilies.

Animals↗
PubMed2003

An evolutionary approach for identifying potential transcription factor binding sites: the renin gene as an example.

Evolutionary pressure has resulted in the conservation of certain nucleotide sequences. These conserved regions are potentially important for certain functions. Here we give an example of a comparison between noncoding sequences combined with other independent database information to shed light onto the regulation of the renin gene, a gene that has great importance for cardiovascular and renal homeostasis. To combine the information regarding conservation and weight matrices of transcription factor (TF) binding sites, an algorithm was developed (TFprofile). Notably, a local peak in the resulting binding profile coincides with a previously experimentally identified regulatory region for the renin gene. The existence of further peaks in the binding profile in the conserved 3.9-kb-long hRENc DNA block upstream of the renin gene suggests additional regions of potential importance for gene regulation. The algorithm TFprofile may be used to integrate information on cross-species evolutionary conservation and aspects of TF binding characteristics to provide putative regulatory DNA regions for experimental verification.

Animals↗
PubMed2025

A comprehensive phylogeny of mammalian PRNP gene reveals no influence of prion misfolding propensity on the evolution of this gene.

Prion diseases are invariably fatal neurodegenerative diseases that affect some mammalian species, including humans. These diseases are caused by the misfolding of the cellular prion protein (PrPC) into a pathologic isoform (PrPSc). The prion protein is highly conserved across mammals. However, some species present lower susceptibility to prion diseases than others. This behavior is likely explained by the resistance of these animal species' prion proteins to acquire a pathological conformation. Therefore, the tertiary structure and interspecific variations encoded in the primary structure determine a PrP proneness to misfolding. For this reason, we studied the PRNP gene from a phylogenetic perspective, potentially unveiling evolutionary events related to prion diseases. We generated a database of mammalian PRNP sequences and constructed phylogenetic trees based on nucleotide sequence variations. We aligned 1146 PRNP gene sequences from 901 different mammalian species and built a PRNP gene-based phylogenetic tree. Classical phylogenetic orders tend to maintain their clustering in the PRNP gene tree. Nonetheless, the few differences found may shed some light on potential evolutionary constraints posed by prion disorders. Moreover, this phylogenetic study was combined with an in vitro misfolding study. Protein Misfolding Shaking Amplification (PMSA) was used to evaluate the tendency of many of these proteins to misfold. This comprehensive analysis spanned a wide range of mammalian prion protein sequences and included analysis of different variants with a focus on the human rs1799990 locus (c.385A > G, p.Met129Val). This variant, widely linked to prion disease susceptibility in humans, is explored in the context of its evolutionary origins. All in all, our PRNP gene-based tree, despite showing some topological differences with the reference species tree that could be in some cases related to prion disease susceptibility, is not significantly distinct. Indicating that the proneness of a PrP variant to misfold spontaneously has not shaped the evolution of this gene.

Phylogeny↗
PubMed2003

Extraction of short-latency evoked potentials using a combination of wavelets and evolutionary algorithms.

Somatosensory evoked potentials, recorded at the spine or scalp of a patient, are contaminated by noise. It is common practice to use ensemble averaging to remove the noise, which usually requires a large number of responses to produce one averaged signal. In this paper a post-processing technique is shown which uses a combination of wavelets and evolutionary algorithms to produce a representative waveform with fewer responses. The most suitable wavelets and a set of weights are selected by an evolutionary algorithm to form a filter bank, which enhances the extraction of evoked potentials from noisy recordings.

Algorithms↗
PubMed1975

Slow evolutionary loss of the potential for interspecific hybridization in birds: a manifestation of slow regulatory evolution.

Birds have lost the potential for interspecific hybridization slowly. This inference emerges from protein comparisons made on 36 pairs of bird species capable of hybridization. Micro-complement fixation tests show that hybridizable pairs of bird species differ by an average of 12 units of albumin immunological distance and 25 units of transferrin immunological distance. As these proteins evolve at a known and rather steady rate, it is inferred that the average hybridization species pair diverged from a common ancestor about 22 million years ago. The corresponding period for frog species pairs capable of hybridization is about 21 million years, while for hybridizable placental mammals it is only 2 to 3 million years. Thus birds resemble frogs in having lost the potential for interspecific hybridization about 10 times as slowly as have mammals. Birds have also been evolving very slowly at the anatomical level, particularly within the last 25 million years, according to Simpson, Romer, and many other vertebrate zoologists. In this respect they resemble frogs and differ from placental mammals, which have been undergoing unusually rapid anatomical evolution. Chromosomal evolution is also thought to have proceeded very slowly in both birds and frogs, relative to mammals. The above observations are consistent with the hypothesis that evolutionary changes in regulatory systems, that is, changes in the patterns of gene expression, provide the basis for both anatomical evolution and the evolutionary loss of hybridization potential.

Animals↗
PubMed2002

Sustaining fisheries yields over evolutionary time scales.

Fishery management plans ignore the potential for evolutionary change in harvestable biomass. We subjected populations of an exploited fish (Menidia menidia) to large, small, or random size-selective harvest of adults over four generations. Harvested biomass evolved rapidly in directions counter to the size-dependent force of fishing mortality. Large-harvested populations initially produced the highest catch but quickly evolved a lower yield than controls. Small-harvested populations did the reverse. These shifts were caused by selection of genotypes with slower or faster rates of growth. Management tools that preserve natural genetic variation are necessary for long-term sustainable yield.

Animals↗
PubMed1993

Fungal symbionts of grasses: evolutionary insights and agricultural potential.

Some filamentous fungal endophytes confer on their grass hosts important biological properties including resistance to grazing herbivores and resistance to nematodes and some fungal pathogens, as well as drought tolerance and greater field persistence. The production of alkaloids toxic to grazing animals is an undesirable aspect of the association in agronomic situations. Consequently, genetic strategies are being pursued to manipulate fungal endophytes and their hosts for agricultural benefit.

Agriculture↗
PubMed2005

Discovery of a large number of previously unrecognized mitochondrial pseudogenes in fish genomes.

Nuclear inserted copies of mitochondrial origin (numts) vary widely among eukaryotes, with human and plant genomes harboring the largest repertoires. Numts were previously thought to be absent from fish species, but the recent release of three fish nuclear genome sequences provides the resource to obtain a more comprehensive insight into the extent of mtDNA transfer in fishes. From the sequence analyses of the genomes of Fugu rubripes, Tetraodon nigroviridis, and Danio rerio, we have identified 2, 5, and 10 recent numt integrations, respectively, which integrated into those genomes less than 0.6 million years (Myr) ago. Such results contradict the hypothesis of absence or rarity of numts in fishes, as (i) the ratio of numts to the total size of the nuclear genome in T. nigroviridis was superior to the ratio observed in several higher vertebrate species (e.g., chicken, mouse, and rat), and only surpassed by humans, and (ii) the mtDNA coverage transferred to the nuclear genome of D. rerio is exceeded only by human and mouse, within the whole range of eukaryotic genomes surveyed for numts. Additionally, 335, 336, and 471 old numts (>12.5 Myr) were detected in F. rubripes, T. nigroviridis, and D. rerio, respectively. Surprisingly, old numts are inserted preferentially into known or predicted genes, as inferred for recent numts in human. However, because in fish genomes such integrations are old, they are likely to represent evolutionary successes and they may be considered a potential important evolutionary mechanism for the enhancement of genomic coding regions.

Animals↗
PubMed2003

Sex steroids in green anoles (Anolis carolinensis): uncoupled maternal plasma and yolking follicle concentrations, potential embryonic steroidogenesis, and evolutionary implications.

The sex steroids testosterone (T) and estradiol-17beta (E2) play important roles in vertebrate reproduction and development. However, little is known about the relationship between plasma steroid levels (which can influence reproductive function) and yolk steroid levels (which can influence embryonic development) in oviparous species. Therefore, we examined the extent to which T and E2 are coupled in plasma and yolking follicles in adult females and explored the dynamics of yolk and embryo steroid content during egg incubation in green anoles (Anolis carolinensis). T and E2 levels were determined for the plasma and yolking follicles of breeding females and for whole embryos and yolks at several developmental stages by radioimmunoassay. Plasma and yolk concentrations of T and E2 were not correlated. On average, plasma T was only 30% that of plasma E2, but yolking follicle T was over 600% that of yolking follicle E2. Total yolk T and E2 content generally declined over the course of incubation. However, yolk T was an order of magnitude higher than yolk E2, and it showed a secondary peak in magnitude after approximately 75% of incubation was completed. Similarly, total embryonic T content rose by over 400% in the latter half of incubation whereas E2 did not change. These results demonstrate that plasma and yolking follicle steroid levels produced by breeding females can be uncoupled. Furthermore, embryos themselves may begin producing T, but likely not E2, during the latter stages of incubation. Thus, steroid exposure may be independently shaped by selection to serve both reproductive and developmental functions.

Animals↗
PubMed1998

[The nature of adaptive evolutionary changes: fitness and potential].

Ecological potential of an individual can be defined as its viability in the broad sense including the ability to reproduce in various environments. From the biological viewpoint, ecological potential as a fundamental property of an organism is more important than fitness in the genetic sense, which is estimated as the relative rate of reproduction. In essence, fitness reflects the level of implementation of the biological potential. In the process of evolution, regulatory selection results in an increase of fitness: selected forms reproduce more successfully as the population size increases. By contrast, individuals with high ecological potential are more advantageous when the population size decreases, because the probability of their survival in adverse environments is high. Thus, high levels of fitness and ecological potential are achieved via operation of different types of selection.

Adaptation, Physiological↗
PubMed1998

Biological principles of heredity of and resistance to disease.

Understanding the biological principles of disease heredity and resistance to disease is a prerequisite for the incorporation of these factors into multi-trait breeding programmes. Mutations represent an evolutionary aspect of disease. The author reviews patterns of Mendelian inheritance and possible causes of non-Mendelian inheritance, such as multifactorial inheritance, expansion of trinucleotide repeats, mitochondiral inheritance and genomic imprinting, in relation to diseases of domestic animals. Host-pathogen interactions underlie genetic variability in resistance to disease. Infectious pathogens endowed with a high potential for evolutionary change use this potential to evade various host defence mechanisms. This interaction may have a competitive or co-evolutionary character. The host immune system copes with the variability of pathogens by using the potential of genetic diversity of lymphocytes in immunoglobulin, T-cell receptor and major histocompatibility complex genes. Possible mechanisms for maintenance of this diversity are discussed in the context of selection for disease resistance.

Animals↗
PubMed2002

Growth following malignancy.

Disturbed growth in the child surviving cancer is multifactorial. This chapter examines the evidence for, and the difficulties in determining, individual drug treatment or disease effects at multiple endocrine levels influencing growth and against a changing baseline of adjuvant cancer therapies with potentially additive toxicity. The evolutionary pattern and potential aetiology of the neuro-endocrine deficit and growth-plate disturbance, the (unrandomized) effects of hormone replacement therapy and areas which require further study are also addressed. The reasons why growth hormone (GH) secretion is so exquisitely sensitive to disturbance, even though deficiencies soon after lesser cranial insults can be difficult to detect, are explored with evidence cited from the few existing prospective and interventional studies. The extent and nature of the hypothalamo-pituitary disturbance needs further prospective interventional study and disease-site- and treatment-specific comparisons. Practical treatment and surveillance strategies to optimize growth potential, age-appropriate development, peak bone mineral accretion, hair re-growth and future health and well-being are also suggested. Health-related outcomes resulting from today's newer therapies and enhanced surveillance need documenting in future (inter)national cancer trials, where randomized studies of hormonal intervention may also become possible.

Adrenal Glands↗
PubMed2000

The duplication of an eight-residue helical stretch in Staphylococcal nuclease is not helical: a model for evolutionary change.

A common method of evolutionary change is gene duplication, followed by other events that lead to new function, decoration of folds, oligomerization, or other changes. As part of a study on the potential for evolutionary change created by duplicated sequences, we have carried out a crystallographic study on a mutant of Staphylococcal nuclease in which residues 55-62 have been duplicated in a wild-type variant termed PHS. In the parental protein (PHS) these residues form the first two turns of a helix running from residue 54 to 68 (hereafter designated as helix I). The crystal structure of the mutant is very similar to that of the parental, with helix I being unaltered. The duplicated residues are accommodated by expanding an existing loop N-terminal to helix I. In addition, circular dichroism (CD) studies have been carried out on a parental peptide containing helix I with six flanking residues at each terminus (residues 48-74) and on the same peptide expanded by the duplication, as a function of 2,2,2-trifluoroethanol (TFE) concentration. Each peptide possesses only modest helical propensity in solution. Our data, which is different from what was observed in T4 lysozyme, show that the conformation of the duplicated sequence is determined by a balance of sequential and longer-range effects. Thus duplicating sequence need not mean duplicating structure. Proteins 2000;40:465-472.

Algorithms↗
PubMed2001

Genetics and the fitness of hybrids.

Over the years, the evolutionary importance of natural hybridization has been a contentious issue. At one extreme is the relatively common view of hybridization as an evolutionarily unimportant process. A less common perspective, but one that has gained support over the past decade, is that of hybridization as a relatively widespread and potentially creative evolutionary process. Indeed, studies documenting the production of hybrid genotypes exhibiting a wide range of fitnesses have become increasingly common. In this review, we examine the genetic basis of such variation in hybrid fitness. In particular, we assess the genetic architecture of hybrid inferiority (both sterility and inviability). We then extend our discussion to the genetic basis of increased fitness in certain hybrid genotypes. The available evidence argues that hybrid inferiority is the result of widespread negative epistasis in a hybrid genetic background. In contrast, increased hybrid fitness can be most readily explained through the segregation of additive genetic factors, with epistasis playing a more limited role.

Animals↗
PubMed1996

Comparison of low oxidoreduction potential cytochrome c553 from Desulfovibrio vulgaris with the class I cytochrome c family.

The cytochrome c553 from Desulfovibrio vulgaris (DvH c553) is of importance in the understanding of the relationship of structure and function of cytochrome c due to its lack of sequence homology with other cytochromes, and its abnormally low oxido-reduction potential. In evolutionary terms, this protein also represents an important reference point for the understanding of both bacterial and mitochondrial cytochromes c. Using the recently determined nuclear magnetic resonance (NMR) structure of the reduced protein we compare the structural, dynamic, and functional characteristics of DvH c553 with members of both the mitochondrial and bacterial cytochromes c to characterize the protein in the context of the cytochrome c family, and to understand better the control of oxide-reduction potential in electron transfer proteins. Despite the low sequence homology, striking structural similarities between this protein and representatives of both eukaryotic [cytochrome c from tuna (tuna c)] and prokaryotic [Pseudomonas aeruginosa c551 (Psa c551)] cytochromes c have been recognized. The previously observed helical core is also found in the DvH c553. The structural framework and hydrogen bonding network of the DvH c553 is most similar to that of the tuna c, with the exception of an insertion loop of 24 residues closing the heme pocket and protecting the propionates, which is absent in the DvH c553. In contrast, the Psa c551 protects the propionates from the solvent principally by extending the methionine ligand arm. The electrostatic distribution at the recognized encounter surface around the heme in the mitochondrial cytochrome is reproduced in the DvH c553, and corresponding hydrogen bonding networks, particularly in the vicinity of the heme cleft, exist in both molecules. Thus, although the cytochrome DvH c553 exhibits higher primary sequence homology to other bacterial cytochromes c, the structural and physical homology is significantly greater with respect to the mitochondrial cytochrome c. The major structural and functional difference is the absence of solvent protection for the heme, differentiating this cytochrome from both reference cytochromes, which have evolved different mechanisms to cover the propionates. This suggests that the abnormal redox potential of the DvH c553 is linked to the raised accessibility of the heme and supports the theory that redox potential in cytochromes is controlled by heme propionate solvent accessibility.

Amino Acid Sequence↗