Proteomic comparison of human and great ape blood plasma reveals conserved glycosylation and differences in thyroid hormone metabolism

A general and accessible approach to enrichment and characterisation of natural anti-Neu5Gc antibodies from human samples

N-Glycolylneuraminic acid (Neu5Gc) is a non-human sialic acid which is presented on the surface of human cells following uptake from dietary sources. Antibodies against Neu5Gc have implications for many aspects of human health such as inflammation, xenograft rejection and cancer. However, current methods to detect and study anti-Neu5Gc antibodies require complex synthesis of glycan structures, animal handling expertise, or access to expensive reagents and equipment. Here, we outline a simple workflow to enrich and detect anti-Neu5Gc antibodies from small volume human serological samples. This strategy involves a micro-scale affinity purification step, followed by an indirect ELISA detection step which uses CMAH-transfected human cells as a source of Neu5Gc-containing human glycans in their native context. Parental wild type cells are also used as a paired Neu5Gc-negative control. Using this workflow, Neu5Gc-specific antibodies could be enriched from intravenous immunoglobulin (IVIG) and individual plasma specimens from ten healthy donors. Anti-Neu5Gc antibodies were detected in all donors, regardless of age or sex. The lysate ELISA assay was also sufficiently sensitive to observe reproducible individual differences in the anti-Neu5Gc reactivity of each donor specimen. Importantly, despite this individual variation, enriched antibodies from all donor specimens bound effectively to Neu5Gc-containing glycans presented on the surface of whole human cells, highlighting the potential physiological relevance of these antibodies.

Hierarchies in the energy budget: Thyroid hormones and the evolution of human life history patterns

The evolution of human life history characteristics required dramatic shifts in energy allocation mechanisms compared with our primate ancestors. Thyroid hormones, such as thyroxine (T4) and triiodothyronine (T3), are sensitive to energy balance, and are significant determinants for both tissue-specific and whole-body metabolic rate. Thus, thyroid hormones are in part responsible for setting the body's overall energy budget and likely played an important role in the evolution of human life history patterns. We propose that the dynamics of mammalian T3 production, uptake, and action have evolved so that energy allocation prioritizes the high demands of brain development and functioning, often at the expense of growth and reproduction. This paper explores the role of thyroid hormone dynamics in the evolution of human encephalization, prolonged childhood and adolescence, long lifespans, reproduction, and human aging.

Developmental and environmental modulation of fecal thyroid hormone levels in wild Assamese macaques (Macaca assamensis)

Thyroid hormones are key modulators of development, as well as mediators of environmental conditions, by regulating developmental processes and metabolism in primates. Hormone measurement in noninvasively collected samples, that is, feces and urine, is a valuable tool for studying the endocrine function of wildlife, and recent studies have demonstrated the feasibility of measuring thyroid hormones in fecal samples of zoo-housed and wild nonhuman primates. Our study aimed to (i) validate the measurement of immunoreactive fecal total triiodothyronine (IF-T3) in wild Assamese macaques (Macaca assamensis) and (ii) to investigate its developmental changes and its response to environmental changes, including stress responses, in immature individuals. Fecal samples and environmental parameters were collected from individuals of three social groups of wild Assamese macaques living at Phu Khieo Wildlife Sanctuary, Northeastern Thailand. Our study confirmed the methodological feasibility and biological validity of measuring IF-T3 in this population. Specifically, the biological validation demonstrated higher IF-T3 levels in immatures compared to adults, and higher levels in females during late gestation compared to the preconception stage. Our analysis of IF-T3 levels in developing immature macaques revealed a significant increase with age. Furthermore, we found a positive association between IF-T3 and immunoreactive fecal glucocorticoid levels, an indicator of the physiological stress response. Neither minimum temperature nor fruit abundance predicted variation in IF-T3 levels in the immatures. Our findings indicate the possibility for differing effects of climatic factors and food availability on thyroid hormone level changes in immature versus adult animals and in wild compared to experimental conditions. Overall, our study provides the basis for further investigations into the role of thyroid hormones in shaping species-specific traits, growth, and overall primate development.

Comparative physiological anthropogeny: exploring molecular underpinnings of distinctly human phenotypes

Anthropogeny is a classic term encompassing transdisciplinary investigations of the origins of the human species. Comparative anthropogeny is a systematic comparison of humans and other living nonhuman hominids (so-called "great apes"), aiming to identify distinctly human features in health and disease, with the overall goal of explaining human origins. We begin with a historical perspective, briefly describing how the field progressed from the earliest evolutionary insights to the current emphasis on in-depth molecular and genomic investigations of "human-specific" biology and an increased appreciation for cultural impacts on human biology. While many such genetic differences between humans and other hominids have been revealed over the last two decades, this information remains insufficient to explain the most distinctive phenotypic traits distinguishing humans from other living hominids. Here we undertake a complementary approach of "comparative physiological anthropogeny," along the lines of the preclinical medical curriculum, i.e., beginning with anatomy and considering each physiological system and in each case considering genetic and molecular components that are relevant. What is ultimately needed is a systematic comparative approach at all levels from molecular to physiological to sociocultural, building networks of related information, drawing inferences, and generating testable hypotheses. The concluding section will touch on distinctive considerations in the study of human evolution, including the importance of gene-culture interactions.

The aorta in humans and African great apes, and cardiac output and metabolic levels in human evolution

Humans have a larger energy budget than great apes, allowing the combination of the metabolically expensive traits that define our life history. This budget is ultimately related to the cardiac output, the product of the blood pumped from the ventricle and the number of heart beats per minute, a measure of the blood available for the whole organism physiological activity. To show the relationship between cardiac output and energy expenditure in hominid evolution, we study a surrogate measure of cardiac output, the aortic root diameter, in humans and great apes. When compared to gorillas and chimpanzees, humans present an increased body mass adjusted aortic root diameter. We also use data from the literature to show that over the human lifespan, cardiac output and total energy expenditure follow almost identical trajectories, with a marked increase during the period of brain growth, and a plateau during most of the adult life. The limited variation of adjusted cardiac output with sex, age and physical activity supports the compensation model of energy expenditure in humans. Finally, we present a first study of cardiac output in the skeleton through the study of the aortic impression in the vertebral bodies of the spine. It is absent in great apes, and present in humans and Neanderthals, large-brained hominins with an extended life cycle. An increased adjusted cardiac output, underlying higher total energy expenditure, would have been a key process in human evolution.

Leveraging homologies for cross-species plasma proteomics in ungulates using data-independent acquisition

The collection of blood plasma is minimally invasive, and the fluid is a rich source of proteins for biomarker studies in both humans and animals. Plasma protein analysis by mass spectrometry (MS) can be challenging, though modern data acquisition strategies, such as sequential window acquisition of all theoretical fragment ion spectra (SWATH), enable reproducible quantitation of hundreds of proteins in non-depleted plasma from humans and laboratory model animals. Although there is strong potential to enhance veterinary and translational research, SWATH-based plasma proteomics in non-laboratory animals is virtually non-existent. One limitation to date is the lack of comprehensively annotated genomes to aid protein identification. The current study established plasma peptide spectral repositories for sheep and cattle that enabled quantification of over 200 proteins in non-depleted plasma using SWATH approach. Moreover, bioinformatics pipeline was developed to leverage inter-species homologies to enhance the depth of baseline libraries and plasma protein quantification in bovids. Finally, the practical utility of using bovid libraries for SWATH data extraction in taxonomically related non-domestic ungulate species (giraffe) has been demonstrated. SIGNIFICANCE: Ability to quickly generate comprehensive spectral libraries is limiting the applicability of data-independent acquisition, such as SWATH, to study proteomes of non-laboratory animals. We describe an approach to obtain relatively shallow foundational plasma repositories from domestic ruminants and employ homology searches to increase the depth of data, which we subsequently extend to unsequenced ungulates using SWATH method. When applied to cross-species proteomics, the number of proteins quantified by our approach far exceeds what is traditionally used in plasma protein tests.

Thyroid Hormone Signalling in Human Evolution and Disease: A Novel Hypothesis

Thyroid hormone (TH) signalling is a universally conserved pathway with pleiotropic actions that is able to control the development, metabolism, and homeostasis of organisms. Using evidence from paleoecology/palaeoanthropology and data from the physiology of modern humans, we try to assess the natural history of TH signalling and its role in human evolution. Our net thesis is that TH signalling has likely played a critical role in human evolution by facilitating the adaptive responses of early hominids to unprecedently challenging and continuously changing environments. These ancient roles have been conserved in modern humans, in whom TH signalling still responds to and regulates adaptations to present-day environmental and pathophysiological stresses, thus making it a promising therapeutic target.

Thyroid hormone regulation of adult neural stem cell fate: A comparative analysis between rodents and primates

Thyroid hormone (TH) signaling, a highly conserved pathway across vertebrates, is crucial for brain development and function throughout life. In the adult mammalian brain, including that of humans, multipotent neural stem cells (NSCs) proliferate and generate neuronal and glial progenitors. The role of TH has been intensively investigated in the two main neurogenic niches of the adult mouse brain, the subventricular and the subgranular zone. A key finding is that T3, the biologically active form of THs, promotes NSC commitment toward a neuronal fate. In this review, we first discuss the roles of THs in the regulation of adult rodent neurogenesis, as well as how it relates to functional behavior, notably olfaction and cognition. Most research uncovering these roles of TH in adult neurogenesis was conducted in rodents, whose genetic background, brain structure and rate of neurogenesis are considerably different from that of humans. To bridge the phylogenetic gap, we also explore the similarities and divergences of TH-dependent adult neurogenesis in non-human primate models. Lastly, we examine how photoperiodic length changes TH homeostasis, and how that might affect adult neurogenesis in seasonal species to increase fitness. Several aspects by which TH acts on adult NSCs seem to be conserved among mammals, while we only start to uncover the molecular pathways, as well as how other in- and extrinsic factors are intertwined. A multispecies approach delivering more insights in the matter will pave the way for novel NSC-based therapies to combat neurological disorders.

Comparative analyses of the Pan lineage reveal selection on gene pathways associated with diet and sociality in bonobos

Chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) diverged into distinct species approximately 1.7 million years ago when the ancestors of modern-day bonobo populations were separated by the Congo River. This geographic boundary separates the two species today and the associated ecological factors, including resource distribution and feeding competition, have likely shaped the divergent social behavior of both species. The most striking behavioral differences pertain to between group interactions in which chimpanzees behave aggressively towards unfamiliar conspecifics, while bonobos display remarkable tolerance. Several hypotheses attempt to explain how different patterns of social behavior have come to exist in the two species, some with specific genetic predictions, likening the evolution of bonobos to a process of domestication. Here, we utilize 73 ape genomes and apply linkage haplotype homozygosity and structure informed allele frequency differentiation methods to identify positively selected regions in bonobos since their split from a common pan ancestor to better understand the environment and processes that resulted in the behavioral differences observed today. We find novel evidence of selection in genetic regions that aid in starch digestion (AMY2) along with support for two genetic predictions related to self-domestication processes hypothesized to have occurred in the bonobo. We also find evidence for selection on neuroendocrine pathways associated with social behavior including the oxytocin, serotonin, and gonadotropin releasing hormone pathways.

Reinterpreting patterns of variation in human thyroid function: An evolutionary ecology perspective

Two hundred million people worldwide experience some form of thyroid disorder, with women being especially at risk. However, why human thyroid function varies between populations, individuals, and across the lifespan has attracted little research to date. This limits our ability to evaluate the conditions under which patterns of variation in thyroid function are best understood as 'normal' or 'pathological'. In this review, we aim to spark interest in research aimed at understanding the causes of variation in thyroid phenotypes. We start by assessing the biomedical literature on thyroid imbalance to discuss the validity of existing reference intervals for diagnosis and treatment across individuals and populations. We then propose an evolutionary ecological framework for understanding the phylogenetic, genetic, ecological, developmental, and physiological causes of normal variation in thyroid function. We build on this approach to suggest testable predictions for how environmental challenges interact with individual circumstances to influence the onset of thyroid disorders. We propose that dietary changes, ecological disruptions of co-evolutionary processes during pregnancy and with pathogens, emerging infections, and exacerbated stress responses can contribute to explaining the onset of thyroid diseases. For patients to receive the best personalized care, research into the causes of thyroid variation at multiple levels is needed.

Lineage-Specific Changes in Biomarkers in Great Apes and Humans

Although human biomedical and physiological information is readily available, such information for great apes is limited. We analyzed clinical chemical biomarkers in serum samples from 277 wild- and captive-born great apes and from 312 healthy human volunteers as well as from 20 rhesus macaques. For each individual, we determined a maximum of 33 markers of heart, liver, kidney, thyroid and pancreas function, hemoglobin and lipid metabolism and one marker of inflammation. We identified biomarkers that show differences between humans and the great apes in their average level or activity. Using the rhesus macaques as an outgroup, we identified human-specific differences in the levels of bilirubin, cholinesterase and lactate dehydrogenase, and bonobo-specific differences in the level of apolipoprotein A-I. For the remaining twenty-nine biomarkers there was no evidence for lineage-specific differences. In fact, we find that many biomarkers show differences between individuals of the same species in different environments. Of the four lineage-specific biomarkers, only bilirubin showed no differences between wild- and captive-born great apes. We show that the major factor explaining the human-specific difference in bilirubin levels may be genetic. There are human-specific changes in the sequence of the promoter and the protein-coding sequence of uridine diphosphoglucuronosyltransferase 1 (UGT1A1), the enzyme that transforms bilirubin and toxic plant compounds into water-soluble, excretable metabolites. Experimental evidence that UGT1A1 is down-regulated in the human liver suggests that changes in the promoter may be responsible for the human-specific increase in bilirubin. We speculate that since cooking reduces toxic plant compounds, consumption of cooked foods, which is specific to humans, may have resulted in relaxed constraint on UGT1A1 which has in turn led to higher serum levels of bilirubin in humans.

Targeted methods for quantitative analysis of protein glycosylation

Quantification of proteins by LC-MS/MS-MRM has become a standard method with broad projected clinical applicability. MRM quantification of protein modifications is, however, far less utilized, especially in the case of glycoproteins. This review summarizes current methods for quantitative analysis of protein glycosylation with a focus on MRM methods. We describe advantages of this quantitative approach, analytical parameters that need to be optimized to achieve reliable measurements, and point out the limitations. Differences between major classes of N- and O-glycopeptides are described and class-specific glycopeptide assays are demonstrated.

The acquisition of novel N-glycosylation sites in conserved proteins during human evolution

Background

N-linked protein glycosylation plays an important role in various biological processes, including protein folding and trafficking, and cell adhesion and signaling. The acquisition of a novel N-glycosylation site may have significant effect on protein structure and function, and therefore, on the phenotype.

Results

We analyzed the human glycoproteome data set (2,534 N-glycosylation sites in 1,027 proteins) and identified 112 novel N-glycosylation sites in 91 proteins that arose in the human lineage since the last common ancestor of Euarchonta (primates and treeshrews). Three of them, Asn-196 in adipocyte plasma membrane-associated protein (APMAP), Asn-91 in cluster of differentiation 166 (CD166/ALCAM), and Asn-76 in thyroglobulin, are human-specific. Molecular evolutionary analysis suggested that these sites were under positive selection during human evolution. Notably, the Asn-76 of thyroglobulin might be involved in the increased production of thyroid hormones in humans, especially thyroxine (T4), because the removal of the glycan moiety from this site was reported to result in a significant decrease in T4 production.

Conclusions

We propose that the novel N-glycosylation sites described in this study may be useful candidates for functional analyses to identify innovative genetic modifications for beneficial phenotypes acquired in the human lineage.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0468-5) contains supplementary material, which is available to authorized users.

Thyroid autoantibodies are rare in nonhuman great apes and hypothyroidism cannot be attributed to thyroid autoimmunity

The great apes include, in addition to Homo, the genera Pongo (orangutans), Gorilla (gorillas), and Pan, the latter comprising two species, P. troglodytes (chimpanzees) and P. paniscus (bonobos). Adult-onset hypothyroidism was previously reported in 4 individual nonhuman great apes. However, there is scarce information on normal serum thyroid hormone levels and virtually no data for thyroid autoantibodies in these animals. Therefore, we examined thyroid hormone levels and TSH in all nonhuman great ape genera including adults, adolescents, and infants. Because hypothyroidism in humans is commonly the end result of thyroid autoimmunity, we also tested healthy and hypothyroid nonhuman great apes for antibodies to thyroglobulin (Tg), thyroid peroxidase (TPO), and the TSH receptor (TSHR). We established a thyroid hormone and TSH database in orangutans, gorillas, chimpanzees, and bonobos (447 individuals). The most striking differences are the greatly reduced free-T4 and free-T3 levels in orangutans and gorillas vs chimpanzees and bonobos, and conversely, elevated TSH levels in gorillas vs Pan species. Antibodies to Tg and TPO were detected in only 2.6% of adult animals vs approximately 10% in humans. No animals with Tg, TPO, or TSHR antibodies exhibited thyroid dysfunction. Conversely, hypothyroid nonhuman great apes lacked thyroid autoantibodies. Moreover, thyroid histology in necropsy tissues was similar in euthyroid and hypothyroid individuals, and lymphocytic infiltration was absent in 2 hypothyroid animals. In conclusion, free T4 and free T3 are lower in orangutans and gorillas vs chimpanzees and bonobos, the closest living human relatives. Moreover, thyroid autoantibodies are rare and hypothyroidism is unrelated to thyroid autoimmunity in nonhuman great apes.

Role of maternal thyroid hormones in the developing neocortex and during human evolution

The importance of thyroid hormones during brain development has been appreciated for many decades. In humans, low levels of circulating maternal thyroid hormones, e.g., caused by maternal hypothyroidism or lack of iodine in diet, results in a wide spectrum of severe neurological defects, including neurological cretinism characterized by profound neurologic impairment and mental retardation, underlining the importance of the maternal thyroid hormone contribution. In fact, iodine intake, which is essential for thyroid hormone production in the thyroid gland, has been related to the expansion of the brain, associated with the increased cognitive capacities during human evolution. Because thyroid hormones regulate transcriptional activity of target genes via their nuclear thyroid hormone receptors (THRs), even mild and transient changes in maternal thyroid hormone levels can directly affect and alter the gene expression profile, and thus disturb fetal brain development. Here we summarize how thyroid hormones may have influenced human brain evolution through the adaptation to new habitats, concomitant with changes in diet and, therefore, iodine intake. Further, we review the current picture we gained from experimental studies in rodents on the function of maternal thyroid hormones during developmental neurogenesis. We aim to evaluate the effects of maternal thyroid hormone deficiency as well as lack of THRs and transporters on brain development and function, shedding light on the cellular behavior conducted by thyroid hormones.

An evolutionary perspective on food and human taste

The sense of taste is stimulated when nutrients or other chemical compounds activate specialized receptor cells within the oral cavity. Taste helps us decide what to eat and influences how efficiently we digest these foods. Human taste abilities have been shaped, in large part, by the ecological niches our evolutionary ancestors occupied and by the nutrients they sought. Early hominoids sought nutrition within a closed tropical forest environment, probably eating mostly fruit and leaves, and early hominids left this environment for the savannah and greatly expanded their dietary repertoire. They would have used their sense of taste to identify nutritious food items. The risks of making poor food selections when foraging not only entail wasted energy and metabolic harm from eating foods of low nutrient and energy content, but also the harmful and potentially lethal ingestion of toxins. The learned consequences of ingested foods may subsequently guide our future food choices. The evolved taste abilities of humans are still useful for the one billion humans living with very low food security by helping them identify nutrients. But for those who have easy access to tasty, energy-dense foods our sensitivities for sugary, salty and fatty foods have also helped cause over nutrition-related diseases, such as obesity and diabetes.

Review and hypothesis: does Graves' disease develop in non-human great apes?

BACKGROUND

Graves' disease, caused by stimulatory thyrotropin receptor (TSHR) autoantibodies, has not been observed in animals. In contrast, Hashimoto's thyroiditis develops in chickens, rats, mice, dogs, and marmosets. Attempts to induce an immune response in mice to the luteinizing-hormone receptor suggested that autoantigen glycosylation was one parameter involved in breaking self-tolerance. Over evolution, TSHR glycosylation increased from three asparagine-linked-glycans (N-glycans) in fish to six N-glycans in humans and great apes. All other placental mammals lack one N-glycan in the shed TSHR A-subunit, the primary Graves' disease autoantigen. We hypothesized that (a) lesser TSHR A-subunit glycosylation reduces immunogenicity, accounting for the absence of Graves' disease in most placental mammals; (b) due to human-like A-subunit glycosylation, Graves' disease might arise in great apes. Here, we review and analyze the literature on this subject and report the results of a survey of veterinarians at primate centers and zoos in North America.

SUMMARY

Previous experimental data from induced TSHR antibodies in mice support a role for A-subunit glycosylation in breaking self-tolerance. An extensive search of the great-ape literature revealed five reports of noncongenital thyroid dysfunction, four with hypothyroidism and one with hyperthyroidism. The latter was a gorilla who was treated with anti-thyroid drugs but is now deceased. Neither serum nor thyroid tissue from this gorilla were available for analysis. The survey of veterinarians revealed that none of the 979 chimpanzees in primate research centers had a diagnosis of noncongenital thyroid dysfunction and among ∼1100 great apes (gorillas, orangutans, and chimpanzees) in U.S. zoos, only three were hypothyroid, and none were hyperthyroid.

CONCLUSIONS

Graves' disease appears to be either very rare or does not occur in great apes based on the literature and a survey of veterinarians. Although the available data do not advance our hypothesis, there is a paucity of information regarding thyroid function tests and thyroid autoantibodies in the great apes In addition, these primates may be protected against TSHR autoimmunity by the absence of genetic polymorphisms and putative environmental triggers. Finally, larger numbers of great apes need to be followed, and tests of thyroid function and thyroid autoantibodies be performed, to confirm that spontaneous Graves' disease is restricted to humans.

Thyroid status of female rhesus monkeys and preliminary information on impact of perchlorate administration

Thyroid status was assessed in adult female rhesus monkey breeders at the California National Primate Research Center at the beginning of the breeding season. The 95% confidence intervals for thyrotropin (TSH), thyroxine (T4) and triiodothyronine (T3) ( n = 66–80) were similar to those previously reported in smaller samples of macaque monkeys. Based on human criteria, 10 of 80 monkeys (12%) were hypothyroid (TSH > 2.0 µIU/mL). Because hypothyroxinaemia can be a risk factor in pregnancy, T4 status was compared with past breeding history, breeding outcome for that season and general health records in a subset of 42 breeders. Age, weight and parity did not differ between monkeys in the lowest T4 quartile as compared with those in the upper three quartiles. However, T4 concentrations were significantly associated with the number of missed menstrual cycles during the previous breeding season. In additional work, three healthy lactating rhesus monkeys were given three different doses of environmental contaminant and thyroid iodine uptake inhibitor, ammonium perchlorate (0.006, 0.34, 12.8 mg/kg/day, respectively) in food for two weeks. Thyroid status variables (TSH, T4, T3, thyroid radioactive iodine uptake) were then measured. In the monkey receiving the highest perchlorate dose, iodine uptake was suppressed relative to baseline. The study shows the availability of tools to study thyroid status in rhesus monkeys, the variability of thyroid status in the breeder colony and the potential ability of environmental factors to influence thyroid status.

Implications of the presence of N-glycolylneuraminic acid in recombinant therapeutic glycoproteins

Recombinant glycoprotein therapeutics produced in nonhuman mammalian cell lines and/or with animal serum are often modified with the nonhuman sialic acid N-glycolylneuraminic acid (Neu5Gc; refs. 1,2). This documented contamination has generally been ignored in drug development because healthy individuals were not thought to react to Neu5Gc (ref. 2). However, recent findings indicate that all humans have Neu5Gc-specific antibodies, sometimes at high levels. Working with two monoclonal antibodies in clinical use, we demonstrate the presence of covalently bound Neu5Gc in cetuximab (Erbitux) but not panitumumab (Vectibix). Anti-Neu5Gc antibodies from healthy humans interact with cetuximab in a Neu5Gc-specific manner and generate immune complexes in vitro. Mice with a human-like defect in Neu5Gc synthesis generate antibodies to Neu5Gc after injection with cetuximab, and circulating anti-Neu5Gc antibodies can promote drug clearance. Finally, we show that the Neu5Gc content of cultured human and nonhuman cell lines and their secreted glycoproteins can be reduced by adding a human sialic acid to the culture medium. Our findings may be relevant to improving the half-life, efficacy and immunogenicity of glycoprotein therapeutics.

Incorporation of a non-human glycan mediates human susceptibility to a bacterial toxin

AB(5) toxins comprise an A subunit that corrupts essential eukaryotic cell functions, and pentameric B subunits that direct target-cell uptake after binding surface glycans. Subtilase cytotoxin (SubAB) is an AB(5) toxin secreted by Shiga toxigenic Escherichia coli (STEC), which causes serious gastrointestinal disease in humans. SubAB causes haemolytic uraemic syndrome-like pathology in mice through SubA-mediated cleavage of BiP/GRP78, an essential endoplasmic reticulum chaperone. Here we show that SubB has a strong preference for glycans terminating in the sialic acid N-glycolylneuraminic acid (Neu5Gc), a monosaccharide not synthesized in humans. Structures of SubB-Neu5Gc complexes revealed the basis for this specificity, and mutagenesis of key SubB residues abrogated in vitro glycan recognition, cell binding and cytotoxicity. SubAB specificity for Neu5Gc was confirmed using mouse tissues with a human-like deficiency of Neu5Gc and human cell lines fed with Neu5Gc. Despite lack of Neu5Gc biosynthesis in humans, assimilation of dietary Neu5Gc creates high-affinity receptors on human gut epithelia and kidney vasculature. This, and the lack of Neu5Gc-containing body fluid competitors in humans, confers susceptibility to the gastrointestinal and systemic toxicities of SubAB. Ironically, foods rich in Neu5Gc are the most common source of STEC contamination. Thus a bacterial toxin's receptor is generated by metabolic incorporation of an exogenous factor derived from food.

Molecular evolution of the cytochrome c oxidase subunit 5A gene in primates

BACKGROUND

Many electron transport chain (ETC) genes show accelerated rates of nonsynonymous nucleotide substitutions in anthropoid primate lineages, yet in non-anthropoid lineages the ETC proteins are typically highly conserved. Here, we test the hypothesis that COX5A, the ETC gene that encodes cytochrome c oxidase subunit 5A, shows a pattern of anthropoid-specific adaptive evolution, and investigate the distribution of this protein in catarrhine brains.

RESULTS

In a dataset comprising 29 vertebrate taxa, including representatives from all major groups of primates, there is nearly 100% conservation of the COX5A amino acid sequence among extant, non-anthropoid placental mammals. The most recent common ancestor of these species lived about 100 million years (MY) ago. In contrast, anthropoid primates show markedly elevated rates of nonsynonymous evolution. In particular, branch site tests identify five positively selected codons in anthropoids, and ancestral reconstructions infer that substitutions in these codons occurred predominantly on stem lineages (anthropoid, ape and New World monkey) and on the human terminal branch. Examination of catarrhine brain samples by immunohistochemistry characterizes for the first time COX5A protein distribution in the primate neocortex, and suggests that the protein is most abundant in the mitochondria of large-size projection neurons. Real time quantitative PCR supports previous microarray results showing COX5A is expressed in cerebral cortical tissue at a higher level in human than in chimpanzee or gorilla.

CONCLUSION

Taken together, these results suggest that both protein structural and gene regulatory changes contributed to COX5A evolution during humankind's ancestry. Furthermore, these findings are consistent with the hypothesis that adaptations in ETC genes contributed to the emergence of the energetically expensive anthropoid neocortex.

Great apes show highly selective plasma carotenoids and have physiologically high plasma retinyl esters compared to humans

Great apes are the closest living relatives of humans. Physiological similarities between great apes and humans provide clues to identify which biological features in humans are primitive or derived from great apes. Vitamin A (VA) and carotenoid metabolism have been only partially studied in great apes, and comparisons between great apes and humans are not available. We aimed to investigate VA and carotenoid intake and plasma concentrations in great apes living in captivity, and to compare them to healthy humans. Dietary intakes of humans (n = 20) and, among the great apes, chimpanzees (n = 15) and orangutans (n = 5) were calculated. Plasma retinol (ROH), retinol-binding protein (RBP), retinyl esters, and major carotenoids were analyzed. The great ape diet was higher in VA than in humans, due to high intake of provitamin A carotenoids. Plasma ROH concentrations in great apes were similar to those in humans, but retinyl esters were higher in great apes than in humans. Differences in plasma carotenoid concentrations were observed between great apes and humans. Lutein was the main carotenoid in great apes, while beta-carotene was the main carotenoid for humans. RBP concentrations did not differ between great apes and humans. The molar ratio of ROH to RBP was close to 1.0 in both great apes and humans. In conclusion, great apes show homeostatic ROH regulation, with high but physiological retinyl esters circulating in plasma. Furthermore, great apes show great selectivity in their plasmatic carotenoid concentration, which is not explained by dietary intake.

Comparing the human and chimpanzee genomes: searching for needles in a haystack

The chimpanzee genome sequence is a long-awaited milestone, providing opportunities to explore primate evolution and genetic contributions to human physiology and disease. Humans and chimpanzees shared a common ancestor approximately 5-7 million years ago (Mya). The difference between the two genomes is actually not approximately 1%, but approximately 4%--comprising approximately 35 million single nucleotide differences and approximately 90 Mb of insertions and deletions. The challenge is to identify the many evolutionarily, physiologically, and biomedically important differences scattered throughout these genomes while integrating these data with emerging knowledge about the corresponding "phenomes" and the relevant environmental influences. It is logical to tackle the genetic aspects via both genome-wide analyses and candidate gene studies. Genome-wide surveys could eliminate the majority of genomic sequence differences from consideration, while simultaneously identifying potential targets of opportunity. Meanwhile, candidate gene approaches can be based on such genomic surveys, on genes that may contribute to known differences in phenotypes or disease incidence/severity, or on mutations in the human population that impact unique aspects of the human condition. These two approaches will intersect at many levels and should be considered complementary. We also cite some known genetic differences between humans and great apes, realizing that these likely represent only the tip of the iceberg.

Evolutionary neuropathology & congenital mental retardation: Environmental cues predictive of maternal deprivation influence the fetus to minimize cerebral metabolism in order to express bioenergetic thrift

This article will propose that humans have an adaptive vulnerability to certain forms of mental retardation, specifically, neuropathological disorders that cause decreased energy expenditure in the hippocampus and the cerebral cortex. This hypothesis will be analyzed in terms of the thrifty phenotype paradigm according to which adverse prenatal events can cause differential gene expression resulting in a phenotype that is better suited, metabolically, for a deprived environment. For example, a malnourished mother has an increased propensity to give birth to offspring that feature a "thrifty phenotype" which permits highly efficient calorie utilization, increased fat deposition and a sedentary nature. This article interprets several prenatal occurrences, including maternal malnourishment, low birth weight, multiparity, short birth interval, advanced maternal age and maternal stress--which are currently identified by the epidemiological literature as risk factors for neuropathology--to be environmental cues that communicate to the fetus that, because it will be neglected of maternal investment, developing a metabolically conservative brain will be the most effective ecological strategy. Success in hunting and foraging in mammals, primates and especially humans is known to be dependent on prolonged maternal investment. Low levels of maternal care are known to result in low survivorship of offspring, largely because the offspring are forced to subsist using simple, low-yield foraging strategies. A predictive, adaptive response, marked by cerebral hypometabolism, may produce a level of metabolic conservancy that mitigates the risks associated with low levels of maternal care. This article will suggest that certain, human neuropathological phenotypes would have been well suited for an ecological niche that closely resembled the less skill-intensive niche of our less encephalized, primate ancestors. The forms of congenital neuropathology discussed in this article do not cause damage to vital homeostatic systems; most simply decrease the size and energy expenditure of the cerebral cortex and the hippocampus, the two structures known to show plasticity during changes in ecological rigor in vertebrates. Also, many disorders that present comorbidly with neuropathology, such as tendency toward obesity, decrement in anabolic hormones, hypotonic musculature, up-regulation of the hypothalamic-pituitary-adrenal axis, and decreased thyroid output are associated with energy conservancy and the thrifty phenotype, further implicating neuropathology in an ecological strategy. Determining the relative impact of evolutionary causation on neuropathological disease should prove informative for medical and gene therapeutic treatment modalities. Furthermore, use of the maternal deprivation paradigm presented here may help researchers more precisely identify the risk factors that determine cognitive trajectory.

Comparative primate genomics

With the completion of the human genome sequence and the advent of technologies to study functional aspects of genomes, molecular comparisons between humans and other primates have gained momentum. The comparison of the human genome to the genomes of species closely related to humans allows the identification of genomic features that set primates apart from other mammals and of features that set certain primates notably humans apart from other primates. In this article, we review recent progress in these areas with an emphasis on how comparative approaches may be used to identify functionally relevant features unique to the human genome.

Meat‐Adaptive Genes and the Evolution of Slower Aging in Humans

The chimpanzee life span is shorter than that of humans, which is consistent with a faster schedule of aging. We consider aspects of diet that may have selected for genes that allowed the evolution of longer human life spans with slower aging. Diet has changed remarkably during human evolution. All direct human ancestors are believed to have been largely herbivorous. Chimpanzees eat more meat than other great apes, but in captivity are sensitive to hypercholesterolemia and vascular disease. We argue that this dietary shift to increased regular consumption of fatty animal tissues in the course of hominid evolution was mediated by selection for "meat-adaptive" genes. This selection conferred resistance to disease risks associated with meat eating also increased life expectancy. One candidate gene is apolipoprotein E (apoE), with the E3 allele evolved in the genus Homo that reduces the risks for Alzheimer's and vascular disease, as well as influencing inflammation, infection, and neuronal growth. Other evolved genes mediate lipid metabolism and host defense. The timing of the evolution of apoE and other candidates for meat-adaptive genes is discussed in relation to key events in human evolution.

Comparative analysis of gene-expression patterns in human and African great ape cultured fibroblasts

Although much is known about genetic variation in human and African great ape (chimpanzee, bonobo, and gorilla) genomes, substantially less is known about variation in gene-expression profiles within and among these species. This information is necessary for defining transcriptional regulatory networks that contribute to complex phenotypes unique to humans or the African great apes. We took a systematic approach to this problem by investigating gene-expression profiles in well-defined cell populations from humans, bonobos, and gorillas. By comparing these profiles from 18 human and 21 African great ape primary fibroblast cell lines, we found that gene-expression patterns could predict the species, but not the age, of the fibroblast donor. Several differentially expressed genes among human and African great ape fibroblasts involved the extracellular matrix, metabolic pathways, signal transduction, stress responses, as well as inherited overgrowth and neurological disorders. These gene-expression patterns could represent molecular adaptations that influenced the development of species-specific traits in humans and the African great apes.

Thyroid rhythm phenotypes and hominid evolution: a new paradigm implicates pulsatile hormone secretion in speciation and adaptation changes

Thyroid hormones (THs, T(3)/T(4)) are essential central regulators that link many biological tasks, including embryonic and post-natal growth, reproductive function, and the behavioral and physiological responses to stress. Recently I proposed a novel theory to explain the role of THs in vertebrate evolution. Here I review the concept and discuss its ability to explain changes over time in hominid morphology, behavior and life history. THs are produced in a distinctly pulsatile manner and appear to generate species-specific TH rhythms with distinct ontogenic shifts. Individual variations in genetically controlled TH rhythms (TR phenotypes) must generate coordinated individual variation in morphology, reproduction and behavior within populations. Selection for any manifestation of a particular TR phenotype in an ancestral population selects all traits under thyroid control, resulting in rapid and well-coordinated changes in descendants. The concept provides the first really plausible explanation for a number of phenomena, including the convergent evolution of bipedalism in early hominids, species-specific sexual dimorphism, coordinated changes in morphology, brain function and gut length over time in hominids, cold adaptation in Homo neanderthalensis, the possible independent evolution of H. sapiens in Asia, and regional adaptation of hominid populations. This new paradigm provides a unique theoretical framework for explaining human origins that has important implications for human health.

Sequencing the chimpanzee genome: insights into human evolution and disease

Large-scale sequencing of the chimpanzee genome is now imminent. Beyond the inherent fascination of comparing the sequence of the human genome with that of our closest living relative, this project is likely to yield tangible scientific benefits in two areas. First, the discovery of functionally important mutations that are specific to the human lineage offers a new path towards medical benefits. Second, chimpanzee-human comparisons are likely to yield molecular insights into how new biological characteristics evolve--findings that might be relevant throughout the tree of life.

Intra- and interspecific variation in primate gene expression patterns

Although humans and their closest evolutionary relatives, the chimpanzees, are 98.7% identical in their genomic DNA sequences, they differ in many morphological, behavioral, and cognitive aspects. The underlying genetic basis of many of these differences may be altered gene expression. We have compared the transcriptome in blood leukocytes, liver, and brain of humans, chimpanzees, orangutans, and macaques using microarrays, as well as protein expression patterns of humans and chimpanzees using two-dimensional gel electrophoresis. We also studied three mouse species that are approximately as related to each other as are humans, chimpanzees, and orangutans. We identified species-specific gene expression patterns indicating that changes in protein and gene expression have been particularly pronounced in the human brain.