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PubMed2006

The essential vertebrate ABCE1 protein interacts with eukaryotic initiation factors.

The ABCE1 gene is a member of the ATP-binding cassette (ABC) multigene family and is composed of two nucleotide binding domains and an N-terminal Fe-S binding domain. The ABCE1 gene encodes a protein originally identified for its inhibition of ribonuclease L, a nuclease induced by interferon in mammalian cells. The protein is also required for the assembly of the HIV and SIV gag polypeptides. However, ABCE1 is one of the most highly conserved proteins and is found in one or two copies in all characterized eukaryotes and archaea. Yeast ABCE1/RLI1 is essential to cell division and interacts with translation initiation factors in the assembly of the pre-initiation complex. We show here that the human ABCE1 protein is essential for in vitro and in vivo translation of mRNA and that it binds to eIF2alpha and eIF5. Inhibition of the Xenopus ABCE1 arrests growth at the gastrula stage of development, consistent with a block in translation. The human ABCE1 gene contains 16 introns, and the extremely high degree of amino acid identity allows the evolution of its introns to be examined throughout eukaryotes. The demonstration that ABCE1 plays a role in vertebrate translation initiation extends the known functions of this highly conserved protein. Translation is a highly regulated process important to development and pathologies such as cancer, making ABCE1 a potential target for therapeutics. The evolutionary analysis supports a model in which an ancestral eukaryote had large number of introns and that many of these introns were lost in non-vertebrate lineages.

ATP-Binding Cassette Transporters↗
PubMed2003

Parent-offspring conflict theory, signaling of need, and weight gain in early life.

Human growth in early life has major implications for fitness. During this period, the mother regulates the growth of her offspring through placental nutrition and lactation. However, parent-offspring conflict theory predicts that offspring are selected to demand more resources than the mother is selected to provide. This general issue has prompted the development of begging theory, which attempts to find the optimal levels of offspring demand and parental provisioning. Several models have been proposed to account for begging behavior, whether by biochemical or behavioral pathways, including: (1) blackmail of parents; (2) scramble competition between multiple offspring; (3) honest signaling of nutritional need; and (4) honest signaling of offspring worth. These models are all supported by data from nonhuman animals, with species varying according to which model is relevant. This paper examines the evidence that human suckling and crying signal nutritional demand, need, and worth to the mother. While suckling provides hormonal stimulation of breast milk production and signals hunger, crying fulfills a different role, with evidence suggesting that it signals both worth and need for resources (nutrition and thermoregulation). The role of signaling in nutritional demand is examined in the context of three common health problems that have traditionally been assumed to have physiological rather than behavioral causes: excess weight gain, failure to thrive, and colic. The value of such an evolutionary approach lies in its potential to enhance behavioral management of these conditions.

Colic↗
PubMed2005

Acquired immunity and stochasticity in epidemic intervals impede the evolution of host disease resistance.

Disease can generate intense selection pressure on host populations, but here we show that acquired immunity in a population subject to repeated disease outbreaks can impede the evolution of genetic disease resistance by maintaining susceptible genotypes in the population. Interference between the life-history schedule of a species and periodicity of the disease has unintuitive effects on selection intensity, and stochasticity in outbreak period further reduces the rate of spread of disease-resistance alleles. A general age-structured population genetic model was developed and parameterized using empirical data for phocine distemper virus (PDV) epizootics in harbor seals. Scenarios with acquired immunity had lower levels of epizootic mortality compared with scenarios without acquired immunity for the first PDV outbreaks, but this pattern was reversed after about five disease cycles. Without acquired immunity, evolution of disease resistance was more rapid, and long-term population size variation is efficiently dampened. Acquired immunity has the potential to significantly influence rapid evolutionary dynamics of a host population in response to age-structured disease selection and to alter predicted selection intensities compared with epidemiological models that do not consider such feedback. This may have important implications for evolutionary population dynamics in a range of human, agricultural, and wildlife disease settings.

Aging↗
PubMed2001

A plastid segregation defect in the protozoan parasite Toxoplasma gondii.

Apicomplexan parasites--including the causative agents of malaria (Plasmodium sp.) and toxoplasmosis (Toxoplasma gondii)--harbor a secondary endosymbiotic plastid, acquired by lateral genetic transfer from a eukaryotic alga. The apicoplast has attracted considerable attention, both as an evolutionary novelty and as a potential target for chemotherapy. We report a recombinant fusion (between a nuclear-encoded apicoplast protein, the green fluorescent protein and a rhoptry protein) that targets to the apicoplast but grossly alters its morphology, preventing organellar segregation during parasite division. Apicoplast-deficient parasites replicate normally in the first infectious cycle and can be isolated by fluorescence-activated cell sorting, but die in the subsequent host cell, confirming the 'delayed death' phenotype previously described pharmacologically, and validating the apicoplast as essential for parasite viability.

Animals↗
PubMed2025

Golgi_traff phylogeny reveals ancient eukaryotic genes with recent surprises: replication and diversification of HID1 domain-containing protein unique to Schizosaccharomyces.

Golgi_traff is a Pfam clan containing two members, Dymeclin (DYM) and HID1 domain-containing protein (HID). Interrogation of over 900 eukaryotic genomes with sequence models showed that both are ancient eukaryotic genes, which have exhibited different paths of gene loss, including from major taxonomic groups. For example, the Metazoa have both genes, whereas the Viridiplantae and Dikarya have lost HID and DYM, respectively. A unique replication event occurred within the genus Schizosaccharomyces in that all sequenced species possess three HID-encoding paralogs, whereas its nearest fungal relatives and other eukaryotes are almost exclusively monogenic. A phylogenetic analysis of yeasts revealed that the Golgi-resident paralog Human ortholog 3 (SPAC17A5.16) is more similar to the HID of other yeasts than to its paralogs. Transmission electron microscopy revealed that the SPAC17A5.16 mutant lacks a stacked Golgi apparatus (GA) form, suggesting a role in maintaining GA structure. Altered proliferation of the SPAC17A5.16 mutant in response to GA disrupting chemical agents indicated a perturbation of GA-related functions. Structural models suggest SPAC17A5.16 has a long, disordered N-terminal region that may facilitate anchoring to GA membranes. A modification to Schizosaccharomyces HID nomenclature is proposed to reflect their evolutionary and functional characteristics. The potential of the Golgi_traff clan to serve as a model for the diversification of protein function according to the concepts of sub/neofunctionalization is discussed.

Schizosaccharomyces↗
PubMed1998

Comparison of murine Supt4h and a nearly identical expressed, processed gene: evidence of sequence conservation through gene conversion extending into the untranslated regions.

We show herein the transcription of a processed gene that originated from a spliced transcript. Recently, we isolated the human and murine homologues of the yeast chromatin protein, SPT4. The Supt4h gene is spliced normally from five exons encoded by chromosome 11. Here we show that a related sequence on chromosome 10 encodes Supt4h2, a processed intronless gene (with a polyA tail and a tandemly-duplicated 13 bp insertion site in the genome) with a different 5' control region. Both the spliced gene, Supt4h , and the processed gene, Supt4h2 , are expressed in each of four tissues we examined. Supt4h2 encodes a 117 amino acid protein nearly identical to the Supt4h gene product with only one amino acid difference, indicating extreme conservation of this expressed processed gene with the spliced gene over evolutionary time. This illustrates another potential complexity of the mammalian genome, i.e. the use of a processed gene under the control of a different promoter region than the spliced gene.

Animals↗
PubMed2004

The NMR solution structure of the 30S ribosomal protein S27e encoded in gene RS27_ARCFU of Archaeoglobus fulgidis reveals a novel protein fold.

The Archaeoglobus fulgidis gene RS27_ARCFU encodes the 30S ribosomal protein S27e. Here, we present the high-quality NMR solution structure of this archaeal protein, which comprises a C4 zinc finger motif of the CX(2)CX(14-16)CX(2)C class. S27e was selected as a target of the Northeast Structural Genomics Consortium (target ID: GR2), and its three-dimensional structure is the first representative of a family of more than 116 homologous proteins occurring in eukaryotic and archaeal cells. As a salient feature of its molecular architecture, S27e exhibits a beta-sandwich consisting of two three-stranded sheets with topology B(decreasing), A(increasing), F(decreasing), and C(increasing), D(decreasing), E(increasing). Due to the uniqueness of the arrangement of the strands, the resulting fold was found to be novel. Residues that are highly conserved among the S27 proteins allowed identification of a structural motif of putative functional importance; a conserved hydrophobic patch may well play a pivotal role for functioning of S27 proteins, be it in archaeal or eukaryotic cells. The structure of human S27, which possesses a 26-residue amino-terminal extension when compared with the archaeal S27e, was modeled on the basis of two structural templates, S27e for the carboxy-terminal core and the amino-terminal segment of the archaeal ribosomal protein L37Ae for the extension. Remarkably, the electrostatic surface properties of archaeal and human proteins are predicted to be entirely different, pointing at either functional variations among archaeal and eukaryotic S27 proteins, or, assuming that the function remained invariant, to a concerted evolutionary change of the surface potential of proteins interacting with S27.

Amino Acid Sequence↗
PubMed2007

Host-plant effects the expression of resistance to Bacillus thuringiensis kurstaki in Trichoplusia ni (Hubner): an important factor in resistance evolution.

Pathogens are thought to exert strong selection on their hosts leading to increased host resistance. Bacillus thuringiensis kurstaki (Bkt) is a ubiquitous entomopathogen that has become the mainstay of nonchemical control of Lepidopteran pests and thus, the potential exists for the evolution of resistance in targeted host insects. We have studied the expression of Btk resistance in the cabbage looper, Trichoplusia ni (Hubner). For this generalist insect herbivore, three common host plants, tomato, pepper and cucumber, vary in suitability for larval growth and development. Here we show that the host plant also affects the overall toxicity of Btk, the relative expression of resistance between a resistant and a susceptible line and their F(1) reciprocal crosses, and importantly, the dominance of the resistance trait. This study demonstrates that tri-trophic interactions involving an insect, host plants and a pathogen have the potential to strongly influence the evolutionary response of an insect host to a pathogen.

Animals↗
PubMed2004

An evolutionarily conserved mechanism for sensitization of soluble guanylyl cyclase reveals extensive nitric oxide-mediated upregulation of cyclic GMP in insect brain.

Soluble guanylyl cyclase (SGC) is the main receptor for the gaseous signalling molecule nitric oxide (NO) in vertebrates and invertebrates. Recently, a novel class of drugs that regulate mammalian SGC by NO-independent allosteric mechanisms has been identified [e.g. 3-(5'-hydroxymethyl-2'-furyl)-1-benzyl indazole, YC-1]. To assess the evolutionary conservation and hence the potential physiological relevance of these mechanisms, we have tested YC-1 on the brains of two model insects, the cockroach Periplaneta americana and the locust Schistocerca gregaria. YC-1 strongly potentiated the NO-induced elevation of total cyclic 3',5'-guanosine monophosphate (cGMP) and amplified the intensity and consistency of NO-induced cGMP-immunoreactivity in the brain. Our data indicate that the effect of YC-1 was independent of phosphodiesterase inhibition and thus mediated by direct sensitization of SGC. Immunohistopharmacology and co-labelling with antibodies against the SGC alpha-subunit confirmed that cGMP induced by co-application of NO and YC-1 is predominantly attributable to SGC. The staggering number of NO-responsive neurons revealed by YC-1 suggests that previous studies may have considerably underestimated the number of cellular targets for NO in the insect brain. Moreover, a subset of these targets exhibited cGMP-immunoreactivity without application of exogenous NO, demonstrating that YC-1 can be exploited for visualization of physiological cGMP signals in response to endogenous NO production. In conclusion, our discovery that YC-1 is a potent sensitizer of insect SGC indicates that a NO-independent regulatory site is an evolutionarily conserved feature of SGC. Our findings add considerable momentum to the concept of an as yet unidentified endogenous ligand that regulates the gain of the NO-cGMP signalling pathway.

Amino Acid Sequence↗
PubMed2005

How obesity causes diabetes: not a tall tale.

The epidemic of obesity-associated diabetes is a major crisis in modern societies, in which food is plentiful and exercise is optional. The biological basis of this problem has been explored from evolutionary and mechanistic perspectives. Evolutionary theories, focusing on the potential survival advantages of "thrifty" genes that are now maladaptive, are of great interest but are inherently speculative and difficult to prove. Mechanistic studies have revealed numerous fat-derived molecules and a link to inflammation that, together, are hypothesized to underlie the obesity-diabetes connection and thereby represent prospective targets for therapeutic intervention.

Adipocytes↗
PubMed2004

Selection, transmission, and reversion of an antigen-processing cytotoxic T-lymphocyte escape mutation in human immunodeficiency virus type 1 infection.

Numerous studies now support that human immunodeficiency virus type 1 (HIV-1) evolution is influenced by immune selection pressure, with population studies showing an association between specific HLA alleles and mutations within defined cytotoxic T-lymphocyte epitopes. Here we combine sequence data and functional studies of CD8 T-cell responses to demonstrate that allele-specific immune pressures also select for mutations flanking CD8 epitopes that impair antigen processing. In persons expressing HLA-A3, we demonstrate consistent selection for a mutation in a C-terminal flanking residue of the normally immunodominant Gag KK9 epitope that prevents its processing and presentation, resulting in a rapid decline in the CD8 T-cell response. This single amino acid substitution also lies within a second HLA-A3-restricted epitope, with the mutation directly impairing recognition by CD8 T cells. Transmission of the mutation to subjects expressing HLA-A3 was shown to prevent the induction of normally immunodominant acute-phase responses to both epitopes. However, subsequent in vivo reversion of the mutation was coincident with delayed induction of new CD8 T-cell responses to both epitopes. These data demonstrate that mutations within the flanking region of an HIV-1 epitope can impair recognition by an established CD8 T-cell response and that transmission of these mutations alters the acute-phase CD8(+) T-cell response. Moreover, reversion of these mutations in the absence of the original immune pressure reveals the potential plasticity of immunologically selected evolutionary changes.

Amino Acid Sequence↗
PubMed2026

Tree Killer, Qu'est-ce Que C'est? Insights From Forest Pathogen Genomes.

Forests are central to planetary health but are increasingly challenged by emerging diseases driven by climate change, global trade, and anthropogenic disturbance. Despite the apparent resilience of long-lived, genetically diverse tree hosts, forest ecosystems have repeatedly experienced landscape-level pathogen-driven transformations. Advances in genomics, transcriptomics, and functional biology have transformed our understanding of how fungal and oomycete pathogens interact with their hosts across a continuum of lifestyles, from saprotrophy and necrotrophy to biotrophy. Here, we synthesize insights from comparative and population genomics and functional studies across diverse forest pathosystems to examine the traits that characterize successful tree pathogens. We highlight how lifestyle plasticity, adaptations to woody tissues, vector-mediated transmission, and biotrophic stealth enable pathogens to colonize perennial hosts and persist over long temporal scales. We further examine how genome plasticity, hybridization, and horizontal gene transfer generate adaptive potential that often outpaces host evolutionary responses under current environmental change. Finally, we discuss emerging genomic tools, including biosurveillance, machine learning-based classification, and genome editing, that are beginning to link genotype to phenotype and inform assessments of disease risk. By integrating genomic, ecological, and evolutionary perspectives, this review outlines general principles governing forest pathogen success and identifies priorities for future research aimed at improving understanding, early detection, and management of forest diseases in a changing world.

Trees↗
PubMed2002

Subtractive cloning: new genes for studying inflammatory disorders.

Understanding of the biology of interaction between pathogens and host is the central question in studying inflammatory disorders. Subtractive DNA cloning is one of the most efficient and comprehensive methods available for identifying eukaryotic genes regulated under specific physiological conditions, including inflammation and host response. Here we explore the utility of subtractive DNA cloning and describe suppression subtractive hybridization (SSH), a polymerase chain reaction (PCR)-based DNA subtraction method that has been developed and evolved in our labs over several years. The SSH method possesses a number of advantages as compared to other subtractive cloning techniques, making it one of the most adventitious methods for cloning differentially expressed genes. Besides isolation of differentially expressed eukaryotic mRNAs, subtractive DNA cloning can be used to identify genes that are differentially expressed between diverse bacterial species. These genes can be of great interest, as some may encode strain-specific traits such as drug resistance, or bacterial surface proteins involved in determining the virulence of a particular strain. Other genes may be useful as markers for epidemiological or evolutionary studies. To demonstrate the potential of the SSH technique, we describe here the comprehensive characterization of 2 SSH subtracted libraries constructed in our laboratories. One library was created using eukaryotic cDNA subtraction and is specific for mRNAs up-regulated in CD25 positive cells from mouse lymph nodes as compared to CD25 negative cells. The second subtracted library is specific for a methicillin-resistant Staphylococcus aureus bacterial strain, but not in a methicillin-sensitive strain. The bacterial genomes of these 2 strains have been completely sequenced and this second library provides an excellent reference for testing the ability of SSH to recover all strain-specific gene content. The analysis of these 2 subtracted libraries serves as the basis for a discussion of the strength and limitations of the SSH technique. We will also compare and contrast subtractive DNA cloning to other current technologies used to isolate differentially expressed genes.

Animals↗
PubMed2002

SERMs: evolutionary chemistry, revolutionary biology.

Estrogens are known as important modulators of development, growth and maintenance of primary sexual physiology. The medical field has also grown increasingly appreciative of the effects of estrogens on non-traditional target tissues such as bone, cardiovascular tissue and the CNS. Postmenopausal women have been the beneficiaries of estrogen supplementation regimes, but the proliferative actions of estrogens on uterine and breast tissue have raised concerns. Combining estrogens with progestins (HRT) has succeeded in blunting the uterine effects of estrogen but not the effects of estrogens on breast tissue, and breakthrough bleeding induced by HRT regimes continues to present compliance issues. The discovery by Jordan and coworkers in 1987 that the "antiestrogens" tamoxifen and raloxifene showed estrogenic effects in preventing bone loss in ovariectomized rats revolutionized the way we have come to the think of nuclear receptor functioning. Since that time, broad insights have been garnered into both the mechanisms involved in the primary, ligand activated nuclear transcription pathway as well as other, non-traditional pathways via which estrogens may exert their effects. The recent discovery of a second estrogen receptor ERbeta has provided additional possibilities for investigation and therapeutic intervention. Even though raloxifene (Evista) has been approved for the treatment and prevention of osteoporosis in postmenopausal women, there is room for improvement. For example, normal HRT alleviates hot flush and urogenital complaints; raloxifene does neither. In addition raloxifene does not raise overall HDL (while HRT does) but does increase venous thromboembolisms. The ideal SERM will maximize all of the positive estrogen attributes while minimizing the negatives, and to that end, there has been considerable activity in the medicinal chemistry community dedicated towards the modification of the SERM structure to achieve compounds with preferable profiles. What we have witnessed, so far, is an evolutionary march of compounds with potential clinical benefit over raloxifene, although the ideal SERM remains to be realized.

Animals↗
PubMed1999

cDNA cloning of the CEPUS, a secreted type of neural glycoprotein belonging to the immunoglobulin-like opioid binding cell adhesion molecule (OBCAM) subfamily.

GP55 is a family of glycoproteins distributed predominantly in the nervous system, and its previously characterized members, including the GP55A (EMBL Y08170) and E19S (EMBL Y08171) reveal a typical glycosyl phosphatidyl inositol (GPI)-anchored pattern for membrane proteins. CEPUS identified in this study appeared to represent the third member of GP55. This 3.2 kb long complete cDNA clone from the chicken brain exhibited 3 Ig-like domains. The open reading frame of CEPUS contains 313 amino acids, which can encode a 31.7 kDa core protein (pI 5.75) for the mature form. The signal peptide cleavage site was predicted at Gln25. The structural features of the CEPUS cDNA sequence represented a soluble counterpart to the recently identified cerebellar Purkinje cell specific antigen, CEPU-1. The sequence difference between CEPU-1 and CEPUS was only found in the C-terminus in which the CEPUS lacked the GPI-anchored binding site. It displays significant sequence homology to GP55-related molecules, including OBCAM, GP55A, E19S/LAMP, neurotrimin, and CEPU-1, which are all membrane attached types. The absence of the hydrophobic tail sequence in CEPUS may, therefore, suggest that CEPUS would represent the first identified secreted member in this group of genes. We defined that this molecule forms the opioid-binding cell adhesion molecule (OBCAM) subfamily in the molecular phylogeny. Structurally, these molecules represent acidic proteins (pI 5.47-6.09). Six cysteins, as well as 5 Asn-linked potential glycosylation sites were evolutionary-conserved, suggesting that this OBCAM subfamily resembles immunoglobulin-like and highly glycosylated molecules. The presence of CEPUS would probably suggest to us that the spatial/local expression of the CEPU gene may provide a favorable route for migrating CEPU-positive population of neurons to generate a neuron-specific guidance in developing neurons in vivo.

Amino Acid Sequence↗
PubMed2001

Mediating between nursing intervention terminology systems.

The purpose of this study is to explore the use of formal systems as a way of mediating between diverse nursing intervention terminology systems. Existing approaches to mediation, such as the UMLS Metathesaurus, make heavy use of surface language. This compromises their capacity for managing similarities and differences between terminology systems. Within this study an initial ontology, derived from three existing terminology systems, was built using the GALEN approach. The ontology overcomes many of the barriers to effective mediation; it represents a rich integrated hierarchy that may be used to identify both direct and indirect mappings between concepts from diverse terminology systems. The approach used forms part of a formative, evolutionary development methodology in which potential mappings are validated and the results fed back into the next round of development.

Nursing↗
PubMed2002

[Catheter-related central venous thrombosis in the course of an uncomplicated acute myocardial infarction: diagnostic usefulness of echocardiography].

In certain cases such as cancer patients or patients with coagulopathies, the venous thrombosis is a frequent complication that is associated with the implantation of central venous catheters. However, it is uncommon in other contexts, such as acute myocardial infarction without complications in its fifth day of evolution, after being treated with platelet inhibitors in addition to the initial anticoagulant and fibrinolytic therapy. We present a case of thrombosis in the superior vena cava and in the right atrium related to a peripherally inserted central catheter in this clinical context. The utility of transesophageal and transthoracic echocardiography in the differential diagnosis with other cardiac structures and in the evolutionary control is commented. Likewise, potential complications and the treatment of

Catheterization, Central Venous↗
PubMed1988

Comparative evolution: latent potentials for anagenetic advance.

One of the principles that has emerged from experimental evolutionary studies of microorganisms is that polymorphic alleles or new mutations can sometimes possess a latent potential to respond to selection in different environments, although the alleles may be functionally equivalent or disfavored under typical conditions. We suggest that such responses to selection in microorganisms serve as experimental models of evolutionary advances that occur over much longer periods of time in higher organisms. We propose as a general evolutionary principle that anagenic advances often come from capitalizing on preexisting latent selection potentials in the presence of novel ecological opportunity.

Animals↗