Is there adaptation in the human genome for taste perception and phase I biotransformation?

The Role of CYP3A in Health and Disease

CYP3A is an enzyme subfamily in the cytochrome P450 (CYP) superfamily and includes isoforms CYP3A4, CYP3A5, CYP3A7, and CYP3A43. CYP3A enzymes are indiscriminate toward substrates and are unique in that these enzymes metabolize both endogenous compounds and diverse xenobiotics (including drugs); almost the only common characteristic of these compounds is lipophilicity and a relatively large molecular weight. CYP3A enzymes are widely expressed in human organs and tissues, and consequences of these enzymes' activities play a major role both in normal regulation of physiological levels of endogenous compounds and in various pathological conditions. This review addresses these aspects of regulation of CYP3A enzymes under physiological conditions and their involvement in the initiation and progression of diseases.

Cytochrome P450 1B1: A Key Regulator of Ocular Iron Homeostasis and Oxidative Stress

Cytochrome P450 (CYP) 1B1 belongs to the superfamily of heme-containing monooxygenases. Unlike other CYP enzymes, which are highly expressed in the liver, CYP1B1 is predominantly found in extrahepatic tissues, such as the brain, and ocular tissues including retina and trabecular meshwork. CYP1B1 metabolizes exogenous chemicals such as polycyclic aromatic hydrocarbons. CYP1B1 also metabolizes endogenous bioactive compounds including estradiol and arachidonic acid. These metabolites impact various cellular and physiological processes during development and pathological processes. We previously showed that CYP1B1 deficiency mitigates ischemia-mediated retinal neovascularization and drives the trabecular meshwork dysgenesis through increased levels of oxidative stress. However, the underlying mechanisms responsible for CYP1B1-deficiency-mediated increased oxidative stress remain largely unresolved. Iron is an essential element and utilized as a cofactor in a variety of enzymes. However, excess iron promotes the production of hydroxyl radicals, lipid peroxidation, increased oxidative stress, and cell damage. The retinal endothelium is recognized as a major component of the blood-retinal barrier, which controls ocular iron levels through the modulation of proteins involved in iron regulation present in retinal endothelial cells, as well as other ocular cell types including trabecular meshwork cells. We previously showed increased levels of reactive oxygen species and lipid peroxidation in the absence of CYP1B1, and in the retinal vasculature and trabecular meshwork, which was reversed by administration of antioxidant N-acetylcysteine. Here, we review the important role CYP1B1 expression and activity play in maintaining retinal redox homeostasis through the modulation of iron levels by retinal endothelial cells. The relationship between CYP1B1 expression and activity and iron levels has not been previously delineated. We review the potential significance of CYP1B1 expression, estrogen metabolism, and hepcidin-ferroportin regulatory axis in the local regulation of ocular iron levels.

Ortholog genes from cactophilic Drosophila provide insight into human adaptation to hallucinogenic cacti

Cultural transformations of lifestyles and dietary practices have been key drivers of human evolution. However, while most of the evidence of genomic adaptations is related to the hunter-gatherer transition to agricultural societies, little is known on the influence of other major cultural manifestations. Shamanism is considered the oldest religion that predominated throughout most of human prehistory and still prevails in many indigenous populations. Several lines of evidence from ethno-archeological studies have demonstrated the continuity and importance of psychoactive plants in South American cultures. However, despite the well-known importance of secondary metabolites in human health, little is known about its role in the evolution of ethnic differences. Herein, we identified candidate genes of adaptation to hallucinogenic cactus in Native Andean populations with a long history of shamanic practices. We used genome-wide expression data from the cactophilic fly Drosophila buzzatii exposed to a hallucinogenic columnar cactus, also consumed by humans, to identify ortholog genes exhibiting adaptive footprints of alkaloid tolerance. Genomic analyses in human populations revealed a suite of ortholog genes evolving under recent positive selection in indigenous populations of the Central Andes. Our results provide evidence of selection in genetic variants related to alkaloids toxicity, xenobiotic metabolism, and neuronal plasticity in Aymara and Quechua populations, suggesting a possible process of gene-culture coevolution driven by religious practices.

Demographic history was a formative mechanism of the genetic structure for the taste receptor TAS2R16 in human populations inhabiting Africa's Sahel/Savannah Belt

OBJECTIVES

Mode of subsistence is an important factor influencing dietary habits and the genetic structure of various populations through differential intensity of gene flow and selection pressures. Previous studies suggest that in Africa Taste 2 Receptor Member 16 (TAS2R16), which encodes the 7-transmembrane receptor protein for bitterness, might also be under positive selection pressure.

METHODS

However, since sampling coverage of populations was limited, we created a new TAS2R16 population dataset from across the African Sahel/Savannah belt representing various local populations of differing subsistence modes, linguistic affiliations, and geographic provenience. We sequenced the TAS2R16 exon gene and analyzed 2250 haplotypes among 19 populations.

RESULTS

We found no evidence for selection as a driving force of genetic variation at this locus; instead, we discovered a highly significant correlation between TAS2R16 genetic and geographical distances based on provenience of the sampled populations, strongly suggesting that genetic drift most likely prevailed over positive selection at this specific locus. We also found significant correlations with other independent loci, mainly in sedentary farmers.

DISCUSSION

Our results do not support the notion that the genetic diversity of TAS2R16 in Sahelian populations was shaped by selective pressures. This could result from several alternative and not mutually exclusive mechanisms, of which the possibility that, due to the pleiotropic nature of TAS2R16, selective pressures on other traits could counterbalance those acting on bitter taste perception, or that the change of diet in the Neolithic generally relaxed selective pressure on this gene.

Contrasting Patterns of Gene Duplication, Relocation, and Selection Among Human Taste Genes

In humans, taste genes are responsible for perceiving at least 5 different taste qualities. Human taste genes’ evolutionary mechanisms need to be explored. We compiled a list of 69 human taste-related genes and divided them into 7 functional groups. We carried out comparative genomic and evolutionary analyses for these taste genes based on 8 vertebrate species. We found that relative to other groups of human taste genes, human TAS2R genes have a higher proportion of tandem duplicates, suggesting that tandem duplications have contributed significantly to the expansion of the human TAS2R gene family. Human TAS2R genes tend to have fewer collinear genes in outgroup species and evolve faster, suggesting that human TAS2R genes have experienced more gene relocations. Moreover, human TAS2R genes tend to be under more relaxed purifying selection than other genes. Our study sheds new insights into diverse and contrasting evolutionary patterns among human taste genes.

Genomic selection signatures in autism spectrum disorder identifies cognitive genomic tradeoff and its relevance in paradoxical phenotypes of deficits versus potentialities

Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder characterized by paradoxical phenotypes of deficits as well as gain in brain function. To address this a genomic tradeoff hypothesis was tested and followed up with the biological interaction and evolutionary significance of positively selected ASD risk genes. SFARI database was used to retrieve the ASD risk genes while for population datasets 1000 genome data was used. Common risk SNPs were subjected to machine learning as well as independent tests for selection, followed by Bayesian analysis to identify the cumulative effect of selection on risk SNPs. Functional implication of these positively selected risk SNPs was assessed and subjected to ontology analysis, pertaining to their interaction and enrichment of biological and cellular functions. This was followed by comparative analysis with the ancient genomes to identify their evolutionary patterns. Our results identified significant positive selection signals in 18 ASD risk SNPs. Functional and ontology analysis indicate the role of biological and cellular processes associated with various brain functions. The core of the biological interaction network constitutes genes for cognition and learning while genes in the periphery of the network had direct or indirect impact on brain function. Ancient genome analysis identified de novo and conserved evolutionary selection clusters. The de-novo evolutionary cluster represented genes involved in cognitive function. Relative enrichment of the ASD risk SNPs from the respective evolutionary cluster or biological interaction networks may help in addressing the phenotypic diversity in ASD. This cognitive genomic tradeoff signatures impacting the biological networks can explain the paradoxical phenotypes in ASD.

Evolutionary genetics and acclimatization in nephrology

Evolutionary processes, including mutation, migration and natural selection, have influenced the prevalence and distribution of various disorders in humans. However, despite a few well-known examples, such as the APOL1 variants - which have undergone positive genetic selection for their ability to confer resistance to Trypanosoma brucei infection but confer a higher risk of chronic kidney disease - little is known about the effects of evolutionary processes that have shaped genetic variation on kidney disease. An understanding of basic concepts in evolutionary genetics provides an opportunity to consider how findings from ancient and archaic genomes could inform our knowledge of evolution and provide insights into how population migration and genetic admixture have shaped the current distribution and landscape of human kidney-associated diseases. Differences in exposures to infectious agents, environmental toxins, dietary components and climate also have the potential to influence the evolutionary genetics of kidneys. Of note, selective pressure on loci associated with kidney disease is often from non-kidney diseases, and thus it is important to understand how the link between genome-wide selected loci and kidney disease occurs in relation to secondary nephropathies.

Adaptive selection drives TRPP3 loss-of-function in an Ethiopian population

TRPP3 (also called PKD2L1) is a nonselective, cation-permeable channel activated by multiple stimuli, including extracellular pH changes. TRPP3 had been considered a candidate for sour sensor in humans, due to its high expression in a subset of tongue receptor cells detecting sour, along with its membership to the TRP channel family known to function as sensory receptors. Here, we describe the functional consequences of two non-synonymous genetic variants (R278Q and R378W) found to be under strong positive selection in an Ethiopian population, the Gumuz. Electrophysiological studies and 3D modelling reveal TRPP3 loss-of-functions produced by both substitutions. R278Q impairs TRPP3 activation after alkalinisation by mislocation of H⁺ binding residues at the extracellular polycystin mucolipin domain. R378W dramatically reduces channel activity by altering conformation of the voltage sensor domain and hampering channel transition from closed to open state. Sour sensitivity tests in R278Q/R378W carriers argue against both any involvement of TRPP3 in sour detection and the role of such physiological process in the reported evolutionary positive selection past event.

Ecological Sensing Through Taste and Chemosensation Mediates Inflammation: A Biological Anthropological Approach

Ecological sensing and inflammation have evolved to ensure optima between organism survival and reproductive success in different and changing environments. At the molecular level, ecological sensing consists of many types of receptors located in different tissues that orchestrate integrated responses (immune, neuroendocrine systems) to external and internal stimuli. This review describes emerging data on taste and chemosensory receptors, proposing them as broad ecological sensors and providing evidence that taste perception is shaped not only according to sense epitopes from nutrients but also in response to highly diverse external and internal stimuli. We apply a biological anthropological approach to examine how ecological sensing has been shaped by these stimuli through human evolution for complex interkingdom communication between a host and pathological and symbiotic bacteria, focusing on population-specific genetic diversity. We then focus on how these sensory receptors play a major role in inflammatory processes that form the basis of many modern common metabolic diseases such as obesity, type 2 diabetes, and aging. The impacts of human niche construction and cultural evolution in shaping environments are described with emphasis on consequent biological responsiveness.

The roles of genes in the bitter taste

The aims of this review were to understand the roles of bitter taste genes in humans. Some of the peoples have the capacity to taste some chemical substance such as phenylthiocarbamide (PTC) while others cant not based on the dietary hazards and food preferences. There are two alleles responsible to express these phenotypes which are homozygous recessive. In human TAS2R38 genes located on the chromosome number 7 and consist of different nucleotide polymorphism that related to detection of the phenotype of different chemical compounds such as 6-n-propylthiouracil (PROP) and phenylthiocarbamide bitterness and this Gene is the member of the TAS2R genes which are eleven pseudogenes and twenty that has roles in many biological processes.

There are many factors that affect the bitter taste such as food, age, sex, and different diseases. The mechanism of food bitter taste and genotype of TAS2R38 until know not well understood due to that the proof of relation between bitter taste sensitivity and food is harmful. there are many different diseases can impact the influence of taste such as neoplasm and lifestyle such as consumption of alcohol along with the use of medication, head trauma, upper tract infections. On the other hand, A relation between TAS2R38 genotype and meal preferences has been observed among children, however, no associations have been mentioned among older adults. Some previous research proved some vital points that show an association between type 1 of diabetes and phenylthiocarbamide (PTC) but other studies cannot demonstrate that. However, of other disease such as obesity is controversial but other studies reported to the relationship between them.